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Langham F, Tsai D, Forde BM, Camilleri S, Harris PNA, Roberts JA, Chiong F. Demographic, clinical and molecular epidemiology of extended-spectrum beta-lactamase-producing Escherichia coli bloodstream infections in Central Australia. Pathology 2024:S0031-3025(24)00172-7. [PMID: 39060195 DOI: 10.1016/j.pathol.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/06/2024] [Accepted: 04/28/2024] [Indexed: 07/28/2024]
Abstract
We describe the demographics, clinical and molecular epidemiology of extended-spectrum β-lactamase (ESBL) Escherichia coli bloodstream infections (BSI) in Central Australia. All ESBL-producing E. coli bloodstream isolates from January 2018 to December 2020 were retrospectively identified. Demographic and clinical information was extracted by chart review. Whole-genome sequencing was performed for multi-locus sequence typing, antibiotic-resistance genes, and phylogenetic relationships. We identified 41 non-duplicate episodes of ESBL E. coli BSI. Median age was 55 years (IQR 47-63), 78% were female, 93% were Aboriginal, and half came from a remote community. Infections were predominantly urinary (68%, 28/41). In the 12 months prior, 70% (26/37) of identified patients had been hospitalised and 81% (30/37) prescribed antibiotics. Meropenem and piperacillin-tazobactam susceptibility was maintained in 100% and 95% of isolates, respectively. Co-resistance to non-β-lactam antibiotics was 32% to gentamicin, 61% to trimethoprim/sulfamethoxazole, and 68% to ciprofloxacin. For sequenced isolates, 41% (16/35) were sequence type 131 (ST131). Mean acquired antibiotic-resistance genes for each isolate was 12.3 (SD 3.1). Four isolates carried an OXA-1 gene. Only non-ST131 isolates carried AmpC and acquired quinolone-resistance genes. There was some evidence of clustering of closely related strains, but no evidence of community or healthcare admission overlap. ESBL rates are rapidly rising in Central Australia, which is a conducive environment for antibiotic resistance development (e.g., overcrowding, socioeconomic disadvantages, high healthcare exposure and high antibiotic use). Future research is required to explore resistance-transmission dynamics in this unique setting.
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Affiliation(s)
- Freya Langham
- Department of Infectious Diseases, Monash Health, Melbourne, Vic, Australia; Alice Springs Hospital, Central Australian Health Service, Alice Springs, NT, Australia.
| | - Danny Tsai
- Alice Springs Hospital, Central Australian Health Service, Alice Springs, NT, Australia; Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia; University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Qld, Australia
| | - Brian M Forde
- University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Qld, Australia
| | - Shayne Camilleri
- Alice Springs Hospital, Central Australian Health Service, Alice Springs, NT, Australia; Department of Infectious Diseases, Austin Health, Melbourne, Vic, Australia
| | - Patrick N A Harris
- University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Qld, Australia; Central Microbiology, Pathology Queensland, Royal Brisbane & Women's Hospital, Brisbane, Qld, Australia
| | - Jason A Roberts
- University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Qld, Australia; Herston Infectious Diseases Institute, Metro North Health, Brisbane, Qld, Australia; Division of Anaesthesiology, Critical Care, Emergency and Pain Medicine, Nîmes University Hospital, University of Montpellier, Nîmes, France
| | - Fabian Chiong
- Alice Springs Hospital, Central Australian Health Service, Alice Springs, NT, Australia; Department of Infectious Diseases, The Canberra Hospital, Canberra, ACT, Australia
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Wranne MS, Karami N, Kk S, Jaén-Luchoro D, Yazdanshenas S, Lin YL, Kabbinale A, Flach CF, Westerlund F, Åhrén C. Comparison of CTX-M encoding plasmids present during the early phase of the ESBL pandemic in western Sweden. Sci Rep 2024; 14:11880. [PMID: 38789462 PMCID: PMC11126669 DOI: 10.1038/s41598-024-62663-2] [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: 02/09/2024] [Accepted: 05/20/2024] [Indexed: 05/26/2024] Open
Abstract
Plasmids encoding blaCTX-M genes have greatly shaped the evolution of E. coli producing extended-spectrum beta-lactamases (ESBL-E. coli) and adds to the global threat of multiresistant bacteria by promoting horizontal gene transfer (HGT). Here we screened the similarity of 47 blaCTX-M -encoding plasmids, from 45 epidemiologically unrelated and disperse ESBL-E. coli strains, isolated during the early phase (2009-2014) of the ESBL pandemic in western Sweden. Using optical DNA mapping (ODM), both similar and rare plasmids were identified. As many as 57% of the plasmids formed five ODM-plasmid groups of at least three similar plasmids per group. The most prevalent type (28%, IncIl, pMLST37) encoded blaCTX-M-15 (n = 10), blaCTX-M-3 (n = 2) or blaCTX-M-55 (n = 1). It was found in isolates of various sequence types (STs), including ST131. This could indicate ongoing local HGT as whole-genome sequencing only revealed similarities with a rarely reported, IncIl plasmid. The second most prevalent type (IncFII/FIA/FIB, F1:A2:B20) harboring blaCTX-M-27, was detected in ST131-C1-M27 isolates, and was similar to plasmids previously reported for this subclade. The results also highlight the need for local surveillance of plasmids and the importance of temporospatial epidemiological links so that detection of a prevalent plasmid is not overestimated as a potential plasmid transmission event in outbreak investigations.
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Affiliation(s)
- Moa S Wranne
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Nahid Karami
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden.
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden.
| | - Sriram Kk
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Shora Yazdanshenas
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Yii-Lih Lin
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Arpitha Kabbinale
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Carl-Fredrik Flach
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Christina Åhrén
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
- Swedish Strategic Program Against Antimicrobial Resistance (Strama), Region Västra Götaland, Gothenburg, Sweden
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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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Peirano G, Matsumara Y, Nobrega D, Church D, Pitout JDD. Population-based genomic surveillance of Pseudomonas aeruginosa causing bloodstream infections in a large Canadian health region. Eur J Clin Microbiol Infect Dis 2024; 43:501-510. [PMID: 38197977 DOI: 10.1007/s10096-024-04750-w] [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: 11/01/2023] [Accepted: 01/04/2024] [Indexed: 01/11/2024]
Abstract
PURPOSE Population-based surveillance was undertaken to determine clinical factors, susceptibility patterns, and incidence rates (IR) of Pseudomonas aeruginosa causing bloodstream infections (BSIs) in a Canadian region (2010-2018). METHODS We combined clinical data with genomics to characterize P. aeruginosa (BSIs) (n = 167) in a well-defined Canadian (Calgary) human population over a 9-year period (2010-2018). RESULTS The annual population IR per 100,000 patient years increased from 3.4/100,000 in 2010 to 5.9/100,000 in 2018, with the highest IRs in elderly males from the hospital setting. Over a quarter of patients presented with febrile neutropenia, followed by urinary tract infections and pneumonia. Antimicrobial resistance (AMR) rates and determinants were rare. The P. aeruginosa population was polyclonal consisting of three dominant sequence types (STs), namely ST244, ST111, and ST17. Antimicrobial-susceptible ST244 was the most common clone and belonged to three clades (A, B, C). The ST244 IR/100,000 increased over time due to the expansion of clade C. Multidrug-resistant ST111 was the second most common clone and IR/100,000 decreased over time. ST111 belonged to three clades (A, B, C) with clade C containing blaVIM-2. Different serotypes were linked to various STs. The IR/100,000 of P. aeruginosa that belonged to serotypes O6 increased significantly over time. CONCLUSION An effective multivalent vaccine consisting of five serotypes (O1, O3, O5, O6, O11) would confer protection to > 70% of Calgary residents with P. aeruginosa BSIs. This study has provided a unique perspective of the population dynamics over time of P. aeruginosa STs, clades, and serotypes responsible for BSIs.
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Affiliation(s)
- Gisele Peirano
- Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, Calgary, Alberta, T2L 2K8, Canada
- Alberta Precision Laboratories, Calgary, Alberta, Canada
| | | | - Diego Nobrega
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Deirdre Church
- Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, Calgary, Alberta, T2L 2K8, Canada
- Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Johann D D Pitout
- Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, Calgary, Alberta, T2L 2K8, 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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Shropshire WC, Strope B, Selvaraj Anand S, Bremer J, McDaneld P, Bhatti MM, Flores AR, Kalia A, Shelburne SA. Temporal dynamics of genetically heterogeneous extended-spectrum cephalosporin-resistant Escherichia coli bloodstream infections. mSphere 2023; 8:e0018323. [PMID: 37427953 PMCID: PMC10449519 DOI: 10.1128/msphere.00183-23] [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: 04/10/2023] [Accepted: 05/24/2023] [Indexed: 07/11/2023] Open
Abstract
Extended-spectrum cephalosporin-resistant Escherichia coli (ESC-R-Ec) is an urgent public health threat with sequence type clonal complex 131 (STc131), phylogroup B2 strains being particularly concerning as the dominant cause of ESC-R-Ec infections. To address the paucity of recent ESC-R-Ec molecular epidemiology data in the United States, we used whole-genome sequencing (WGS) to fully characterize a large cohort of invasive ESC-R-Ec at a tertiary care cancer center in Houston, Texas, collected from 2016 to 2020. During the study time frame, there were 1,154 index E. coli bloodstream infections (BSIs) of which 389 (33.7%) were ESC-R-Ec. Using time series analyses, we identified a temporal dynamic of ESC-R-Ec distinct from ESC-susceptible E. coli (ESC-S-Ec), with cases peaking in the last 6 months of the calendar year. WGS of 297 ESC-R-Ec strains revealed that while STc131 strains accounted for ~45% of total BSIs, the proportion of STc131 strains remained stable across the study time frame with infection peaks driven by genetically heterogeneous ESC-R-Ec clonal complexes. bla CTX-M variants accounted for most β-lactamases conferring the ESC-R phenotype (89%; 220/248 index ESC-R-Ec), and amplification of bla CTX-M genes was widely detected in ESC-R-Ec strains, particularly in carbapenem non-susceptible, recurrent BSI strains. Bla CTX-M-55 was significantly enriched within phylogroup A strains, and we identified bla CTX-M-55 plasmid-to-chromosome transmission occurring across non-B2 strains. Our data provide important information regarding the current molecular epidemiology of invasive ESC-R-Ec infections at a large tertiary care cancer center and provide novel insights into the genetic basis of observed temporal variability for these clinically important pathogens. IMPORTANCE Given that E. coli is the leading cause of worldwide ESC-R Enterobacterales infections, we sought to assess the current molecular epidemiology of ESC-R-Ec using a WGS analysis of many BSIs over a 5-year period. We identified fluctuating temporal dynamics of ESC-R-Ec infections, which have also recently been identified in other geographical regions such as Israel. Our WGS data allowed us to visualize the stable nature of STc131 over the study period and demonstrate a limited but genetically diverse group of ESC-R-Ec clonal complexes are detected during infection peaks. Additionally, we provide a widespread assessment of β-lactamase gene copy number in ESC-R-Ec infections and delineate mechanisms by which such amplifications are achieved in a diverse array of ESC-R-Ec strains. These data suggest that serious ESC-R-Ec infections are driven by a diverse array of strains in our cohort and impacted by environmental factors suggesting that community-based monitoring could inform novel preventative measures.
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Affiliation(s)
- William C. Shropshire
- Department of Infectious Diseases and Infection Control, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Benjamin Strope
- Program in Diagnostic Genetics and Genomics, MD Anderson Cancer Center School of Health Professions, Houston, Texas, USA
| | - Selvalakshmi Selvaraj Anand
- Program in Diagnostic Genetics and Genomics, MD Anderson Cancer Center School of Health Professions, Houston, Texas, USA
| | - Jordan Bremer
- Department of Infectious Diseases and Infection Control, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Patrick McDaneld
- Division of Pharmacy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Micah M. Bhatti
- Department of Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Anthony R. Flores
- Division of Infectious Diseases, Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Awdhesh Kalia
- Program in Diagnostic Genetics and Genomics, MD Anderson Cancer Center School of Health Professions, Houston, Texas, USA
| | - Samuel A. Shelburne
- Department of Infectious Diseases and Infection Control, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Jaén-Luchoro D, Kahnamouei A, Yazdanshenas S, Lindblom A, Samuelsson E, Åhrén C, Karami N. Comparative Genomic Analysis of ST131 Subclade C2 of ESBL-Producing E. coli Isolates from Patients with Recurrent and Sporadic Urinary Tract Infections. Microorganisms 2023; 11:1622. [PMID: 37512795 PMCID: PMC10384980 DOI: 10.3390/microorganisms11071622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/31/2023] [Accepted: 06/17/2023] [Indexed: 07/30/2023] Open
Abstract
The global emergence of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli), mainly causing urinary tract infections (UTI), is a major threat to human health. ESBL-E. coli sequence type (ST) 131 is the dominating clone worldwide, especially its subclade C2. Patients developing recurrent UTI (RUTI) due to ST131 subclade C2 appear to have an increased risk of recurrent infections. We have thus compared the whole genome of ST131 subclade C2 isolates from 14 patients with RUTI to those from 14 patients with sporadic UTI (SUTI). We aimed to elucidate if isolates causing RUTI can be associated with specific genomic features. Paired isolates from patients with RUTI were identical, presenting 2-18 single nucleotide polymorphism (SNP) differences for all six patients investigated. Comparative genomic analyses, including virulence factors, antibiotic resistance, pangenome and SNP analyses did not find any pattern associated with isolates causing RUTI. Despite extensive whole genome analyses, an increased risk of recurrences seen in patients with UTI due to ST131 subclade C2 isolates could not be explained by bacterial genetic differences in the two groups of isolates. Hence, additional factors that could aid in identifying bacterial properties contributing to the increased risk of RUTI due to ESBL-E. coli ST131 subclade C2 remains to be explored.
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Affiliation(s)
- Daniel Jaén-Luchoro
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, 40530 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 40530 Gothenburg, Sweden
| | - Arezou Kahnamouei
- Department of Life Sciences and Systems Biology, University of Turin, 10124 Turin, Italy
| | - Shora Yazdanshenas
- Sahlgrenska University Hospital, Department of Clinical Microbiology, Region Västra Götaland, 41345 Gothenburg, Sweden
| | - Anna Lindblom
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, 40530 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 40530 Gothenburg, Sweden
- Sahlgrenska University Hospital, Department of Clinical Microbiology, Region Västra Götaland, 41345 Gothenburg, Sweden
| | - Emma Samuelsson
- Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Region Västra Götaland, 41345 Gothenburg, Sweden
| | - Christina Åhrén
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, 40530 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 40530 Gothenburg, Sweden
- Swedish Strategic Program against Antimicrobial Resistance (Strama), Region Västra Götaland, 40544 Gothenburg, Sweden
| | - Nahid Karami
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, 40530 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 40530 Gothenburg, Sweden
- Sahlgrenska University Hospital, Department of Clinical Microbiology, Region Västra Götaland, 41345 Gothenburg, Sweden
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Aljohani RH, ElFeky DS, Alswaji AA, Alrashidi E, Okdah L, Alalwan B, Aljohani SM, Balkhy HH, Redhwan A, Alghoribi MF. Genomic Characterization of Uropathogenic Escherichia coli Isolates from Tertiary Hospitals in Riyadh, Saudi Arabia. Int J Mol Sci 2023; 24:7582. [PMID: 37108743 PMCID: PMC10141978 DOI: 10.3390/ijms24087582] [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: 02/25/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infections (UTIs) in hospitalised and non-hospitalised patients. Genomic analysis was used to gain further insight into the molecular characteristics of UPEC isolates from Saudi Arabia. A total of 165 isolates were collected from patients with UTIs between May 2019 and September 2020 from two tertiary hospitals in Riyadh, Saudi Arabia. Identification and antimicrobial susceptibility testing (AST) were performed using the VITEK system. Extended-spectrum β-lactamase (ESBL)-producing isolates (n = 48) were selected for whole genome sequencing (WGS) analysis. In silico analysis revealed that the most common sequence types detected were ST131 (39.6%), ST1193 (12.5%), ST73 (10.4%), and ST10 (8.3%). Our finding showed that blaCTX-M-15 gene was detected in the majority of ESBL isolates (79.2%), followed by blaCTX-M-27 (12.5%) and blaCTX-M-8 (2.1%). ST131 carried blaCTX-M-15 or blaCTX-M-27, and all ST73 and ST1193 carried blaCTX-M-15. The relatively high proportion of ST1193 in this study was notable as a newly emerged lineage in the region, which warrants further monitoring.
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Affiliation(s)
- Rawan H. Aljohani
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11564, Saudi Arabia
| | - Dalia S. ElFeky
- Department of Basic Medical Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh 11564, Saudi Arabia
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Cairo University, Cairo 12613, Egypt
| | - Abdulrahman A. Alswaji
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
| | - Eisa Alrashidi
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
| | - Liliane Okdah
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
| | - Bassam Alalwan
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia
| | - Sameera M. Aljohani
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia
- Department of Basic Science, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences, Riyadh 14611, Saudi Arabia
| | | | - Alya Redhwan
- Department of Health, College of Health and Rehabilitation Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11564, Saudi Arabia
| | - Majed F. Alghoribi
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia
- Department of Basic Science, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences, Riyadh 14611, Saudi Arabia
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10
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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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11
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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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12
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Shropshire WC, Strope B, Anand SS, Bremer J, McDaneld P, Bhatti MM, Flores AR, Kalia A, Shelburne SA. Dynamic Periodicity of Extended-Spectrum Cephalosporin Resistant Bloodstream Escherichia coli Infections Driven by Non-CC131 Strains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527510. [PMID: 36798241 PMCID: PMC9934547 DOI: 10.1101/2023.02.07.527510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Extended-spectrum cephalosporin resistant (ESC-R) Escherichia coli (ESC-R- Ec ) is an urgent public health threat with clonal complex (CC) 131, phylogroup B2 strains being particularly concerning as the dominant cause of ESC-R- Ec infections. To address the paucity of recent ESC-R- Ec molecular epidemiology data in the United States (US), we used whole genome sequencing (WGS) to fully characterize a large cohort of invasive ESC-R- Ec at a tertiary care cancer center in Houston, Texas collected from 2016-2020. During the study timeframe, there were 1154 index E. coli bloodstream infections (BSIs) of which 389 (33.7%) were ESC-R. Using time series analyses, we identified a temporal dynamic of ESC-R E. coli BSIs ( Ec -BSIs), distinct from ESC-susceptible Ec -BSIs, with cases peaking in the last 6 months of the calendar year. WGS of 297 ESC-R Ec -BSI strains revealed that while CC131 strains accounted for ∼45% of total infections, the proportion of CC131 strains remained stable across the time-period, and infection peaks were driven by genetically diverse, non-CC131 isolates. Bla CTX-M variants accounted for most β-lactamases conferring the ESC-R phenotype (89%; 220/248 index ESC-R Ec -BSIs), and amplification of bla CTX-M genes was widely detected in ESC-R Ec -BSI strains, particularly in carbapenem non-susceptible strains and in strains causing recurrent BSIs. Bla CTX- M-55 was significantly enriched within phylogroup A strains, and we identified bla CTX-M-55 plasmid-to-chromosome transmission occurring across non-B2 strains. Our data provide important information regarding the current molecular epidemiology of invasive ESC-R E. coli and provide novel insights into the genetic basis of observed temporal variability for these clinically important pathogens. IMPORTANCE Given that E. coli is the leading cause of ESC-R Enterobacterales infection, we sought to assess the current molecular epidemiology of ESC-R- Ec using a WGS based analysis of many BSIs over a several year period. We identified a clear temporal dynamic of ESC-R- Ec infections, which has also recently been identified in other geographical regions such as Israel. Our WGS data allowed us to visualize the stable nature of CC131 over the study period and demonstrate that non-CC131 strains drove the infection peaks. Additionally, we provide the first widespread assessment of β-lactamase gene copy number in ESC-R- Ec infections and delineate mechanisms by which such amplifications are achieved in a diverse array of ESC-R- Ec strains. These data suggest that even for a tertiary care center, serious ESC-R- Ec infections are driven by a diverse array of strains and impacted by environmental factors suggesting that community-based monitoring could inform novel preventative measures.
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Yang C, Diarra MS, Attiq Rehman M, Li L, Yu H, Yin X, Aslam M, Carrillo CD, Yang C, Gong J. Virulence potential of antimicrobial-resistant extraintestinal pathogenic Escherichia coli from retail poultry meat in a Caenorhabditis elegans model. J Food Prot 2023; 86:100008. [PMID: 36916583 DOI: 10.1016/j.jfp.2022.11.001] [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: 03/09/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 12/23/2022]
Abstract
Healthy poultry can be a reservoir for extraintestinal pathogenic Escherichia coli (ExPEC), some of which could be multidrug resistant to antimicrobials. These ExPEC strains could contaminate the environment and/or food chain representing thus, food safety and human health risk. However, few studies have shown the virulence of poultry-source antimicrobial-resistant (AMR) ExPEC in humans. This study characterized AMR ExPEC and investigated the virulence potential of some of their isolates in a Caenorhabditis elegans infection model. A total of 46 E. coli isolates from poultry (chicken, n = 29; turkey, n = 12) retail meats and chicken feces (n = 4), or humans (n = 1) were sequenced and identified as ExPEC. Except eight, all remaining 38 ExPEC isolates were resistant to at least one antibiotic and carried corresponding antimicrobial resistance genes (ARGs). About 27 of the 46 ExPEC isolates were multidrug-resistant (≥3 antibiotic classes). Seven ExPEC isolates from chicken or turkey meats were of serotype O25:H4 and sequence type (ST) 131 which clustered with an isolate from a human urinary tract infection (UTI) case having the same serotype and ST. The C. elegans challenge model using eight of studied ExPEC isolates harboring various ARGs and virulence genes (VGs) showed that regardless of their ARG or VG numbers in tested poultry meat and feces, ExPEC significantly reduced the life span of the nematode (P < 0.05) similarly to a human UTI isolate. This study indicated the pathogenic potential of AMR ExPEC from retail poultry meat or feces, but more studies are warranted to establish their virulence in poultry and human. Furthermore, relationships between specific resistance profiles and/or VGs in these E. coli isolates for their pathogenicity deserve investigations.
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Affiliation(s)
- Chongwu Yang
- Guelph Research and Development Centre, Agriculture Agri-Food Canada (AAFC), Guelph, Ontario, Canada N1G 5C9; Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Moussa S Diarra
- Guelph Research and Development Centre, Agriculture Agri-Food Canada (AAFC), Guelph, Ontario, Canada N1G 5C9.
| | - Muhammad Attiq Rehman
- Guelph Research and Development Centre, Agriculture Agri-Food Canada (AAFC), Guelph, Ontario, Canada N1G 5C9
| | - Linyan Li
- Guelph Research and Development Centre, Agriculture Agri-Food Canada (AAFC), Guelph, Ontario, Canada N1G 5C9; State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Hai Yu
- Guelph Research and Development Centre, Agriculture Agri-Food Canada (AAFC), Guelph, Ontario, Canada N1G 5C9
| | - Xianhua Yin
- Guelph Research and Development Centre, Agriculture Agri-Food Canada (AAFC), Guelph, Ontario, Canada N1G 5C9
| | - Mueen Aslam
- Lacombe Research Centre, AAFC, Lacombe, Alberta, Canada T4L1W1
| | - Catherine D Carrillo
- Canadian Food Inspection Agency (CFIA), Ottawa Laboratory (Carling), Ottawa, Ontario, Canada K1Y 4K7
| | - Chengbo Yang
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Joshua Gong
- Guelph Research and Development Centre, Agriculture Agri-Food Canada (AAFC), Guelph, Ontario, Canada N1G 5C9.
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Emergence and Dissemination of Extraintestinal Pathogenic High-Risk International Clones of Escherichia coli. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122077. [PMID: 36556442 PMCID: PMC9780897 DOI: 10.3390/life12122077] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Multiresistant Escherichia coli has been disseminated worldwide, and it is one of the major causative agents of nosocomial infections. E. coli has a remarkable and complex genomic plasticity for taking up and accumulating genetic elements; thus, multiresistant high-risk clones can evolve. In this review, we summarise all available data about internationally disseminated extraintestinal pathogenic high-risk E. coli clones based on whole-genome sequence (WGS) data and confirmed outbreaks. Based on genetic markers, E. coli is clustered into eight phylogenetic groups. Nowadays, the E. coli ST131 clone from phylogenetic group B2 is the predominant high-risk clone worldwide. Currently, strains of the C1-M27 subclade within clade C of ST131 are circulating and becoming prominent in Canada, China, Germany, Hungary and Japan. The C1-M27 subclade is characterised by blaCTX-M-27. Recently, the ST1193 clone has been reported as an emerging high-risk clone from phylogenetic group B2. ST38 clone carrying blaOXA-244 (a blaOXA-48-like carbapenemase gene) caused several outbreaks in Germany and Switzerland. Further high-risk international E. coli clones include ST10, ST69, ST73, ST405, ST410, ST457. High-risk E. coli strains are present in different niches, in the human intestinal tract and in animals, and persist in environment. These strains can be transmitted easily within the community as well as in hospital settings. WGS analysis is a useful tool for tracking the dissemination of resistance determinants, the emergence of high-risk mulitresistant E. coli clones and to analyse changes in the E. coli population on a genomic level.
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15
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Salamanca-Rivera E, López-Cerero L, Rodríguez-Martínez JM, Pascual A, Rodríguez-Baño J. Prevalence, Incidence, and Risk Factors for Intestinal Colonization Due to Fluoroquinolone-Resistant ST131 Escherichia coli: a Longitudinal Study in Highly Dependent, Long-Term Care Facility Residents. Microbiol Spectr 2022; 10:e0167322. [PMID: 35943257 PMCID: PMC9431526 DOI: 10.1128/spectrum.01673-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/13/2022] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli ST131 clade C is an important driver for fluoroquinolone resistance (FQ-R). We conducted a prospective observational study in residents from two long-term care facilities (LTCFs) in Seville, Spain, in 2018. Fecal swabs and environmental samples were obtained. E. coli isolates were screened for clade C, FQ-R ST131 by PCR, and molecular typing by PFGE; representatives from pulsotypes were studied by whole-genome-sequencing (WGS) and assigned to lineages (cgSTs). Prevalence of colonization at each time point, incidence density, and risk factors for acquisition were studied. Seventy-six FQ-R ST131 E. coli isolates belonging to 34 cgSTs were obtained; 24 belonging to subclade C1 (116 isolates, 65.9%) and 10 to C2 (60, 34.1%). C1 lineages showed lower virulence scores than C2 (median [IQR], 19 [18 to 20] versus 21 [20 to 21.5], P = 0.001) and higher number of plasmids (4 [3 to 5] versus 2 [2 to 3], P = 0.01). aac(6')-Ib-cr and blaOXA-1 were less frequent in C1 than C2 (2 [8.3%] versus 6 [60%], P = 0.003 for both); ESBL genes were detected in eight (33.3%) C1 (5 blaCTX-M-27) and three (30%) C2 (all blaCTX-M-15). Of the 82 residents studied, 49 were colonized at some point (59.7%), with a pooled prevalence of 38.6%. Incidence density of new lineage acquisition was 2.22 per 100 resident weeks (1.28 and 0.93 C1 and C2 subclades, respectively). Independent risk factors for acquisitions were having a colonized roommate (HR = 4.21; 95% CI = 1.71 to 10.36; P = 0.002) and urinary or fecal incontinence (HR = 2.82; 95% CI = 1.21 to 6.56; P = 0.01). LTCFs are important reservoirs of clade C ST131 E. coli. The risk factors found suggest that cross-transmission is the most relevant transmission mechanisms. IMPORTANCE We aimed at investigating the microbiological and epidemiological features of clade C fluoroquinolone-resistant ST131 E. coli isolates colonizing highly dependent residents in long-term care facilities (LTCFs) during 40 weeks and the risk factors of acquisition. Isolates from C1 and C2 subclades were characterized in this environment. The clonality of the isolates was characterized and they were assigned to lineages (cgSTs), Resistance genes, virulence factors, and plasmids were also described. This study suggests that cross-transmission is the most relevant transmission mechanisms; however, environmental colonization might also play a role. We believe the data provide useful information to depict the epidemiology of these bacteria by merging detailed microbiological and epidemiological information.
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Affiliation(s)
- Elena Salamanca-Rivera
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
- Instituto de Biomedicina de Sevilla and CSIC, Seville, Spain
- Centro de Investigación en Red en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Lorena López-Cerero
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
- Instituto de Biomedicina de Sevilla and CSIC, Seville, Spain
- Departamento de Microbiología, Universidad de Sevilla, Seville, Spain
- Centro de Investigación en Red en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Jose Manuel Rodríguez-Martínez
- Instituto de Biomedicina de Sevilla and CSIC, Seville, Spain
- Departamento de Microbiología, Universidad de Sevilla, Seville, Spain
- Centro de Investigación en Red en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Alvaro Pascual
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
- Instituto de Biomedicina de Sevilla and CSIC, Seville, Spain
- Departamento de Microbiología, Universidad de Sevilla, Seville, Spain
- Centro de Investigación en Red en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Jesús Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
- Instituto de Biomedicina de Sevilla and CSIC, Seville, Spain
- Departamento de Medicina, Universidad de Sevilla, Seville, Spain
- Centro de Investigación en Red en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
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The impact of the ST131 clone on recurrent ESBL-producing E. coli urinary tract infection: a prospective comparative study. Sci Rep 2022; 12:10048. [PMID: 35710924 PMCID: PMC9203711 DOI: 10.1038/s41598-022-14177-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/02/2022] [Indexed: 11/24/2022] Open
Abstract
The global emergence of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli), mainly causing urinary tract infections (UTI), is of great concern. Almost one third of patients with UTI, develop recurrent UTI (RUTI). We followed 297 patients for one year after their first episode of UTI due to ESBL-E. coli. Our aim was to evaluate the impact of the globally dominant sequence type (ST)131 clone and its clades, on the risk of subsequent recurrences with ESBL-E. coli. Isolates from patients developing RUTI (68/297) were compared with those from patients with sporadic UTI (SUTI, 229/297). No association was found between RUTI and the two most prevalent phylogroups B2 and D, blaCTX-M genes, or resistance profile. Half of the patients with RUTI were infected with ST131 isolates. Clade C2 were in dominance (50/119) among ST131 isolates. They were more common in patients with RUTI than SUTI (28% vs 13%) and multivariate analysis showed an increased odds-ratio (OR = 2.21, p = 0.033) for recurrences in patients infected with these isolates as compared to non-ST131 isolates. Detecting specific biomarkers, as ST131 clade C2, in ESBL-E. coli UTI isolates may aid in prediction of RUTI and improve diagnostics and care of patients with a risk of ESBL-E. coli recurrences.
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17
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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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18
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Escherichia coli ST1193: Following in the Footsteps of E. coli ST131. Antimicrob Agents Chemother 2022; 66:e0051122. [PMID: 35658504 DOI: 10.1128/aac.00511-22] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Escherichia coli ST1193 is an emerging global multidrug (MDR) high-risk clone and an important cause of community-onset urinary and bloodstream infections. ST1193 is imitating E. coli ST131, the most successful MDR clone of all time. Both clones emerged in the early 1990s by acquiring quinolone resistance-determining region (QRDR) mutations, IncF plasmids, virulence factors, and type 1 pilus (fimH) recombination. They are the only MDR clones that are dominant among unselected E. coli populations. ST131 is the most frequent clone and ST1193 the second most frequent clone among fluoroquinolone/cephalosporin-resistant E. coli isolates. Both clones have played pivotal roles in the global spread of MDR E. coli. ST1193 originated from ST clonal complex 14 (STc14), is lactose nonfermenting, belongs to phylogenetic group B2, and contains the O type O75. Global ST1193 prevalence has been increasing since 2012, even replacing ST131 in certain regions. blaCTX-M genes are rapidly expanding among ST1193 isolates, a scenario that occurred with ST131 during the 2000s. A validated PCR will enable global surveys to determine the extent of ST1193 among One Health E. coli isolates. The rapid emergence of ST1193 is concerning and is adding to the public health burden of MDR E. coli clones. Basic mechanistic, evolutionary, surveillance, and clinical studies are urgently required to investigate the success of ST1193. Such information will aid with management and prevention strategies. The medical community can ill afford to ignore the spread of another global successful MDR high-risk E. coli clone, especially one that is following in the footsteps of E. coli ST131.
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Liu X, Li X, Yang AW, Tang B, Jian ZJ, Zhong YM, Li HL, Li YM, Yan Q, Liang XH, Liu WE. Community Fecal Carriage and Molecular Epidemiology of Extended-Spectrum β-Lactamase- and Carbapenemase-Producing Escherichia coli from Healthy Children in the Central South China. Infect Drug Resist 2022; 15:1601-1611. [PMID: 35418762 PMCID: PMC8995156 DOI: 10.2147/idr.s357090] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/26/2022] [Indexed: 12/25/2022] Open
Affiliation(s)
- Xuan Liu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Xin Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - A-Wen Yang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Bin Tang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Zi-Juan Jian
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Yi-Ming Zhong
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Hong-Ling Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Yan-Ming Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Qun Yan
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Xiang-Hui Liang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, People's Republic of China
| | - Wen-En Liu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, People's Republic of China
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20
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Abstract
Escherichia coli is a leading cause of community-acquired and health care-associated bloodstream infections (BSIs) worldwide. Limited information is available regarding the changes in population dynamics of human E. coli over extended time periods, especially among nonbiased E. coli isolates in large well-defined geographical regions. Coque and colleagues (I. Rodríguez, A. S. Figueiredo, M. Sousa, S. Aracil-Gisbert, et al., mSphere 6:e00868-21, 2021, https://doi.org/10.1128/msphere.00868-21) conducted a longitudinal study of E. coli BSIs in a Madrid hospital over a 21-year period (1996 to 2016). Certain E. coli B2 phylogroups (i.e., ST131 and ST73) dominated the community E. coli population in Madrid. These community clones were often introduced into the hospital setting. This study and other longitudinal surveys from England and Canada showed that ST131 subclades C1 and C2 were mainly responsible for the increase in fluoroquinolone and cephalosporin resistance among E. coli during the mid- to late 2000s.
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21
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Peirano G, Matsumara Y, Nobrega D, DeVinney R, Pitout J. Population-based epidemiology of Escherichia coli ST1193 causing blood stream infections in a centralized Canadian region. Eur J Clin Microbiol Infect Dis 2021:10.1007/s10096-021-04373-5. [PMID: 34750697 DOI: 10.1007/s10096-021-04373-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/27/2021] [Indexed: 11/29/2022]
Abstract
Escherichia coli ST1193 is an emerging global clone associated with fluoroquinolone resistance. A population-based study described genomics, clinical factors, susceptibility patterns, and incidence rates of ST1193 (n = 69) causing incident blood stream infections in a centralized Canadian region 2016-18. ST1193 was responsible for community-acquired upper urinary tract infections among the elderly. The incidence rate (IR) per 100,000 person-years among Calgary residents increased from 1.0 (95%confidence interval [95%CI] 0.7-1.5) in 2016, to 1.7 (95%CI 1.3-2.3) in 2018 (p = 0.05). This was mainly due to the significant increase of ST1193 blood stream infections among female long-term care (LTC) residents. ST1193 IR with blaCTX-Ms was 3.18 times higher in 2018 than in 2016 (CI 95% 0.98-13.49). We identified a ST1193 isolate with only a parC S80I mutation that is different from previously published data. The population-based study identified a significant increase over a 2-year period of E. coli ST1193 blood stream infections among elderly females residing in LTC centers. There was also a notable increase of ST1193 with bla CTX-Ms in 2018. The rapid emergence of ST1193 is concerning and adding to the public health burden of multidrug resistant E. coli blood stream infections in Calgary.
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Affiliation(s)
- Gisele Peirano
- Alberta Precision Laboratories, Calgary, Alberta, Canada
- Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, Calgary, Alberta, T2L 2K8, Canada
| | | | | | - Rebekah DeVinney
- Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, Calgary, Alberta, T2L 2K8, Canada
| | - Johann Pitout
- Alberta Precision Laboratories, Calgary, Alberta, Canada.
- Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, Calgary, Alberta, T2L 2K8, Canada.
- University of Pretoria, Pretoria, Gauteng, South Africa.
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22
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Martischang R, François P, Cherkaoui A, Gaïa N, Renzi G, Agostinho A, Perez M, Graf CE, Harbarth S. Epidemiology of ESBL-producing Escherichia coli from repeated prevalence studies over 11 years in a long-term-care facility. Antimicrob Resist Infect Control 2021; 10:148. [PMID: 34666836 PMCID: PMC8527759 DOI: 10.1186/s13756-021-01013-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/25/2021] [Indexed: 12/29/2022] Open
Abstract
Background Escherichia coli sequence type (ST) 131 H30 is an emerging multidrug resistant subclone, known to spread and cause outbreaks in long-term care facilities (LTCFs). Objectives and methods From 2010 through 2020, we performed 11 yearly surveillance studies for determining the prevalence of digestive carriage of ESBL-producing E. coli (ESBL-EC) among residents in a university-affiliated LCTF. Sequencing and genotyping of selected isolates were performed to characterize temporal trends in the prevalence and epidemic potential of ESBL-EC subclones, and for evaluating a potential rebound effect following discontinuation of contact precautions for ESBL-EC carriers in January 2019. Results This study included 2′403 LTCF residents, with 252 (10.5%) positive for ESBL-EC. Among the 236 ESBL-EC isolates available for typing, 58.0% belonged to the ST131 lineage, including 94/137 (68.6%) ST131 H30 isolates. An increasing yearly prevalence was observed for ESBL-EC (from 4.6 to 9.4%; p = 0.11), but not for the ST131 H30 subclone, which peaked in 2015 and declined thereafter. Multiple previously unnoticed ESBL-EC outbreaks occurred in the LTCF. Since 2018, we noted the clonal expansion of a rare ST131 H89 subclone (O16:H5) harboring CTX-M-14 and CTX-M-24. No rebound effect was observed in ESBL-EC prevalence nor in the different subclones following discontinuation of contact precautions for ESBL-EC carriers since 2019. Conclusion Clonal fluctuation was observed for ST131 H30 ESBL-EC with a current decline in prevalence. Surveillance should include the evolution of ST131 non-H30 subclones, which may spread in LTCFs. Our findings suggest that discontinuation of contact precautions for ESBL-EC carriers in LTCFs may be safely implemented, in support of European recommendations to limit ESBL-producing Enterobacteriaceae control measures in endemic settings to non-E. coli. Supplementary Information The online version contains supplementary material available at 10.1186/s13756-021-01013-7.
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Affiliation(s)
- Romain Martischang
- Infection Control Programme and WHO Collaborating Centre on Patient Safety, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland.
| | - Patrice François
- Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | | | - Nadia Gaïa
- Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Gesuele Renzi
- Bacteriology Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Americo Agostinho
- Infection Control Programme and WHO Collaborating Centre on Patient Safety, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Monica Perez
- Infection Control Programme and WHO Collaborating Centre on Patient Safety, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Christophe E Graf
- Department of Rehabilitation and Geriatrics, Geneva University Hospitals, Geneva, Switzerland
| | - Stephan Harbarth
- Infection Control Programme and WHO Collaborating Centre on Patient Safety, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
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23
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Castanheira M, Simner PJ, Bradford PA. Extended-spectrum β-lactamases: an update on their characteristics, epidemiology and detection. JAC Antimicrob Resist 2021; 3:dlab092. [PMID: 34286272 PMCID: PMC8284625 DOI: 10.1093/jacamr/dlab092] [Citation(s) in RCA: 262] [Impact Index Per Article: 87.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Gram-negative pathogens are a major cause of resistance to expanded-spectrum β-lactam antibiotics. Since their discovery in the early 1980s, they have spread worldwide and an are now endemic in Enterobacterales isolated from both hospital-associated and community-acquired infections. As a result, they are a global public health concern. In the past, TEM- and SHV-type ESBLs were the predominant families of ESBLs. Today CTX-M-type enzymes are the most commonly found ESBL type with the CTX-M-15 variant dominating worldwide, followed in prevalence by CTX-M-14, and CTX-M-27 is emerging in certain parts of the world. The genes encoding ESBLs are often found on plasmids and harboured within transposons or insertion sequences, which has enabled their spread. In addition, the population of ESBL-producing Escherichia coli is dominated globally by a highly virulent and successful clone belonging to ST131. Today, there are many diagnostic tools available to the clinical microbiology laboratory and include both phenotypic and genotypic tests to detect β-lactamases. Unfortunately, when ESBLs are not identified in a timely manner, appropriate antimicrobial therapy is frequently delayed, resulting in poor clinical outcomes. Several analyses of clinical trials have shown mixed results with regards to whether a carbapenem must be used to treat serious infections caused by ESBLs or whether some of the older β-lactam-β-lactamase combinations such as piperacillin/tazobactam are appropriate. Some of the newer combinations such as ceftazidime/avibactam have demonstrated efficacy in patients. ESBL-producing Gram-negative pathogens will continue to be major contributor to antimicrobial resistance worldwide. It is essential that we remain vigilant about identifying them both in patient isolates and through surveillance studies.
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24
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Stokes W, Peirano G, Matsumara Y, Nobrega D, Pitout JDD. Population-based surveillance of Enterobacter cloacae complex causing blood stream infections in a centralized Canadian region. Eur J Clin Microbiol Infect Dis 2021; 41:119-125. [PMID: 34258687 DOI: 10.1007/s10096-021-04309-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/08/2021] [Indexed: 11/30/2022]
Abstract
Active population-based surveillance determined clinical factors, susceptibility patterns, incidence rates (IR), and genomics among Enterobacter cloacae complex (n = 154) causing blood stream infections in a centralized Canadian region (2015-2017). The annual population IR was 1.2/100,000 (95% CI 0.9-16) in 2015, 1.4/100,000 (95% CI 1.1-1.9) in 2016, and 1.5/100,000 (95% CI 1.2-2.0) in 2017, affecting mainly elderly males with underlying comorbid conditions in the hospital setting. E. cloacae complex was dominated by polyclonal subspecies (i.e., E. hormaechei subsp. steigerwaltii, subsp. hoffmanni and subsp. xiangfangesis). Antimicrobial resistant determinants were rare. This study provided novel information about Enterobacter genomics in a well-defined human population.
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Affiliation(s)
- William Stokes
- Alberta Precision Laboratories, Calgary, Alberta, Canada.,Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, Calgary, Alberta, T2L 2K8, Canada.,Department of Pathology and Laboratory Medicine, University of Alberta, Edmonton, Alberta, Canada.,Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Gisele Peirano
- Alberta Precision Laboratories, Calgary, Alberta, Canada.,Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, Calgary, Alberta, T2L 2K8, Canada
| | | | | | - Johann D D Pitout
- Alberta Precision Laboratories, Calgary, Alberta, Canada. .,Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, Calgary, Alberta, T2L 2K8, Canada. .,University of Pretoria, Pretoria, Gauteng, South Africa.
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25
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Nobrega D, Peirano G, Lynch T, Finn TJ, Devinney R, Pitout JDD. Spatial distribution of Escherichia coli ST131 C subclades in a centralized Canadian urban region. J Antimicrob Chemother 2021; 76:1135-1139. [PMID: 33547472 DOI: 10.1093/jac/dkab020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/11/2021] [Indexed: 11/14/2022] Open
Abstract
INTRODUCTION Escherichia coli ST131 is the most common multidrug-resistant (MDR) E. coli clone causing bloodstream infections (BSIs) in Calgary. This study describes patient characteristics and spatial distribution of ST131 subclades C1 and C2 causing BSIs in Calgary. METHODS E. coli from blood (n = 685) obtained in Calgary, Canada, (2016) were PCR screened for ST131 and positives (n = 141) underwent whole genome sequencing. Patient characteristics were analysed using Fisher's Exact/t-tests and spatial analysis was used to identify clusters. RESULTS Overall, 21% of E. coli was identified as ST131 and clade C dominated the population. ST131-C2 was associated with blaCTX-M-15 and significantly more MDR than ST131-C1. The spatial distribution in Calgary showed that ST131-C1 was mainly present in long-term care (LTC) residents whereas ST131-C2 clustered in a specific North East (NE) Calgary sector comprising of six neighbourhoods without LTC centres. This NE sector has high immigration and travel rates from the Indian subcontinent. CONCLUSIONS This study showed that ST131 C subclades have different geographical distribution patterns in Calgary. We believe that recent travel to and immigration from certain high-risk regions for antimicrobial resistance are responsible for the ST131-C2 NE Calgary clustering pattern.
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Affiliation(s)
- Diego Nobrega
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Gisele Peirano
- Division of Microbiology, Alberta Precision Laboratories, Calgary, Alberta, Canada.,Department of Pathology & Laboratory Medicine, University of Calgary, Cummings School of Medicine, Calgary, Alberta, Canada
| | - Tarah Lynch
- Division of Microbiology, Alberta Precision Laboratories, Calgary, Alberta, Canada.,Department of Pathology & Laboratory Medicine, University of Calgary, Cummings School of Medicine, Calgary, Alberta, Canada.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Cummings School of Medicine, Calgary, Alberta, Canada
| | - Thomas J Finn
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Cummings School of Medicine, Calgary, Alberta, Canada
| | - Rebekah Devinney
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Cummings School of Medicine, Calgary, Alberta, Canada
| | - Johann D D Pitout
- Division of Microbiology, Alberta Precision Laboratories, Calgary, Alberta, Canada.,Department of Pathology & Laboratory Medicine, University of Calgary, Cummings School of Medicine, Calgary, Alberta, Canada.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Cummings School of Medicine, Calgary, Alberta, Canada.,Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
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26
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Temporal Trend of ST131 Clone among Urinary Escherichia coli Isolates in the Community: A Taiwan National Surveillance from 2002 to 2016. Microorganisms 2021; 9:microorganisms9050963. [PMID: 33947027 PMCID: PMC8145988 DOI: 10.3390/microorganisms9050963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 11/17/2022] Open
Abstract
Sequence type (ST) 131 is a multidrug-resistant pandemic lineage of E. coli responsible for extraintestinal infections. Few surveillance data of ST131 included all antimicrobial-susceptible and -resistant isolates or focused on community-acquired urinary tract infection (UTI). From a population-based surveillance pool of 2997 outpatient urine E. coli isolates, 542 were selected for detection of ST131 based on ciprofloxacin and/or cefotaxime resistance. Pulsed-field gel electrophoresis (PFGE) was performed on all ST131 isolates to further determine their relatedness. The estimated overall ST131 prevalence in this community UTI cohort increased from 11.2% (in 2002-2004), 12.2% (in 2006-2008), 13.6% (in 2010-2012), to 17.4% in 2014-2016 (p < 0.01). In the ciprofloxacin-resistant/cefotaxime-resistant group, ST131 increased from 33.3% in 2002-2004 to 72.1% in 2014-2016 (p < 0.01). In the ciprofloxacin-resistant/cefotaxime-susceptible group, ST131 was found in 24.3% overall without significant increase in its prevalence over time. PFGE showed emergence of a cluster of ciprofloxacin-resistant/cefotaxime-resistant ST131 carrying Gr. 1 CTX-M ESBL in 2014-2016, especially 2016. Multivariate analysis revealed that age (≥65 y.o) and ciprofloxacin resistance were independent factors associated with ST131. This longitudinal surveillance showed that ciprofloxacin-resistant/cefotaxime-susceptible ST131 has been circulating in the community since 2002 but ciprofloxacin-resistant/cefotaxime-resistant ST131 increased rapidly in the later years.
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27
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Zhang Y, Sun YH, Wang JY, Chang MX, Zhao QY, Jiang HX. A Novel Structure Harboring blaCTX-M-27 on IncF Plasmids in Escherichia coli Isolated from Swine in China. Antibiotics (Basel) 2021; 10:antibiotics10040387. [PMID: 33916584 PMCID: PMC8065532 DOI: 10.3390/antibiotics10040387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/31/2021] [Accepted: 04/02/2021] [Indexed: 01/11/2023] Open
Abstract
The aim of this study was to elucidate the prevalence of blaCTX-M-27-producing Escherichia coli and transmission mechanisms of blaCTX-M-27 from swine farms in China. A total of 333 E. coli isolates were collected from two farms from 2013 to 2016. Thirty-two CTX-M-27-positive E. coli were obtained, and all were multidrug-resistant. Pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) profiles indicated a wide range of strain types that carried blaCTX-M-27, and the sequence type ST10 predominated. Conjugation, replicon typing, S1-PFGE and hybridization experiments confirmed that 28 out of 32 CTX-M-27 positive isolates carried blaCTX-M-27 genes on plasmids F18:A-:B10 (16) and F24:A-:B1 (12).The blaCTX-M-27 genes for 24 isolates were transmitted by plasmids with sizes ranging from 40 to 155 kb. A comparative analysis with blaCTX-M-27-plasmids indicated that the tra-trb region of F24:A-:B1 plasmids was destroyed by insertion of a complex region (eight isolates) and a novel structure containing blaCTX-M-27 in the F18:A-:B10 plasmids (12 isolates). The novel structure increased the stability of the blaCTX-M-27 gene in E. coli. This study indicated that the predominant vehicle for blaCTX-M-27 transmission has diversified over time and that control strategies to limit blaCTX-M-27 transmission in farm animals are necessary.
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Affiliation(s)
- Yan Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China;
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.-H.S.); (J.-Y.W.); (M.-X.C.); (Q.-Y.Z.)
| | - Yin-Huan Sun
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.-H.S.); (J.-Y.W.); (M.-X.C.); (Q.-Y.Z.)
| | - Jiang-Yang Wang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.-H.S.); (J.-Y.W.); (M.-X.C.); (Q.-Y.Z.)
| | - Man-Xia Chang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.-H.S.); (J.-Y.W.); (M.-X.C.); (Q.-Y.Z.)
| | - Qiu-Yun Zhao
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.-H.S.); (J.-Y.W.); (M.-X.C.); (Q.-Y.Z.)
| | - Hong-Xia Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China;
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.-H.S.); (J.-Y.W.); (M.-X.C.); (Q.-Y.Z.)
- Correspondence: ; Tel.: +86-20-8528-3934
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