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Wranne MS, Karami N, Sriram KK, 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.
| | - K K Sriram
- 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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Zhao QY, Cai RM, Cai P, Zhang L, Jiang HX, Zeng ZL. Characterization of Salmonella Phage P1-CTX and the Potential Mechanism Underlying the Acquisition of the blaCTX-M-27 Gene. Antibiotics (Basel) 2024; 13:446. [PMID: 38786174 PMCID: PMC11117986 DOI: 10.3390/antibiotics13050446] [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: 04/08/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
The P1 phage has garnered attention as a carrier of antibiotic resistance genes (ARGs) in Enterobacteriaceae. However, the transferability of ARGs by P1-like phages carrying ARGs, in addition to the mechanism underlying ARG acquisition, remain largely unknown. In this study, we elucidated the biological characteristics, the induction and transmission abilities, and the acquisition mechanism of the blaCTX-M-27 gene in the P1 phage. The P1-CTX phage exhibited distinct lytic plaques and possessed a complete head and tail structure. Additionally, the P1-CTX phage was induced successfully under various conditions, including UV exposure, heat treatment at 42 °C, and subinhibitory concentrations (sub-MICs) of antibiotics. Moreover, the P1-CTX phage could mobilize the blaCTX-M-27 gene into three strains of Escherichia coli (E. coli) and the following seven different serotypes of Salmonella: Rissen, Derby, Kentucky, Typhimurium, Cerro, Senftenberg, and Muenster. The mechanism underlying ARG acquisition by the P1-CTX phage involved Tn1721 transposition-mediated movement of blaCTX-M-27 into the ref and mat genes within its genome. To our knowledge, this is the first report documenting the dynamic processes of ARG acquisition by a phage. Furthermore, this study enriches the research on the mechanism underlying the phage acquisition of drug resistance genes and provides a basis for determining the risk of drug resistance during phage transmission.
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Affiliation(s)
- Qiu-Yun Zhao
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.-Y.Z.); (R.-M.C.); (P.C.); (L.Z.); (H.-X.J.)
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou 311300, China
| | - Run-Mao Cai
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.-Y.Z.); (R.-M.C.); (P.C.); (L.Z.); (H.-X.J.)
| | - Ping Cai
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.-Y.Z.); (R.-M.C.); (P.C.); (L.Z.); (H.-X.J.)
| | - Lin Zhang
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.-Y.Z.); (R.-M.C.); (P.C.); (L.Z.); (H.-X.J.)
| | - Hong-Xia Jiang
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.-Y.Z.); (R.-M.C.); (P.C.); (L.Z.); (H.-X.J.)
| | - Zhen-Ling Zeng
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Q.-Y.Z.); (R.-M.C.); (P.C.); (L.Z.); (H.-X.J.)
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3
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Tóth K, Damjanova I, Laczkó L, Buzgó L, Lesinszki V, Ungvári E, Jánvári L, Hanczvikkel A, Tóth Á, Szabó D. Genomic Epidemiology of C2/H30Rx and C1-M27 Subclades of Escherichia coli ST131 Isolates from Clinical Blood Samples in Hungary. Antibiotics (Basel) 2024; 13:363. [PMID: 38667039 PMCID: PMC11047377 DOI: 10.3390/antibiotics13040363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/10/2024] [Accepted: 04/14/2024] [Indexed: 04/29/2024] Open
Abstract
Extended-spectrum β-lactamase-producing Escherichia coli ST131 has become widespread worldwide. This study aims to characterize the virulome, resistome, and population structure of E. coli ST131 isolates from clinical blood samples in Hungary. A total of 30 C2/H30Rx and 33 C1-M27 ST131 isolates were selected for Illumina MiSeq sequencing and 30 isolates for MinION sequencing, followed by hybrid de novo assembly. Five C2/H30Rx and one C1-M27 cluster were identified. C1-M27 isolates harbored the F1:A2:B20 plasmid in 93.9% of cases. Long-read sequencing revealed that blaCTX-M-27 was on plasmids. Among the C2/H30Rx isolates, only six isolates carried the C2-associated F2:A1:B- plasmid type. Of 19 hybrid-assembled C2/H30Rx genomes, the blaCTX-M-15 gene was located on plasmid only in one isolate, while in the other isolates, ISEcp1 or IS26-mediated chromosomal integration of blaCTX-M-15 was detected in unique variations. In one isolate a part of F2:A1:B- plasmid integrated into the chromosome. These results suggest that CTX-M-15-producing C2/H30Rx and CTX-M-27-producing C1-M27 subclades may have emerged and spread in different ways in Hungary. While blaCTX-M-27 was carried mainly on the C1/H30R-associated F1:A2:B20 plasmid, the IncF-like plasmids of C2/H30Rx or its composite transposons have been incorporated into the chromosome through convergent evolutionary processes.
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Affiliation(s)
- Kinga Tóth
- Institute of Medical Microbiology, Faculty of Medicine, Semmelweis University, 1089 Budapest, Hungary
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Ivelina Damjanova
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Levente Laczkó
- One Health Institute, Faculty of Health Sciences, University of Debrecen, 4032 Debrecen, Hungary
- HUN-REN-DE Conservation Biology Research Group, University of Debrecen, 4032 Debrecen, Hungary
| | - Lilla Buzgó
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Virág Lesinszki
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Erika Ungvári
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Laura Jánvári
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Adrienn Hanczvikkel
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Ákos Tóth
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Dóra Szabó
- Institute of Medical Microbiology, Faculty of Medicine, Semmelweis University, 1089 Budapest, Hungary
- HUN-REN-SE Human Microbiota Research Group, 1052 Budapest, Hungary
- Neurosurgical and Neurointervention Clinic, Semmelweis University, 1083 Budapest, Hungary
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4
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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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5
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Garcia CR, Norfolk WA, Howard AK, Glatter AL, Beaudry MS, Mallis NA, Welton M, Glenn TC, Lipp EK, Ottesen EA. Long-term gut colonization with ESBL-producing Escherichia coli in participants without known risk factors from the southeastern United States. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.03.24302254. [PMID: 38370669 PMCID: PMC10871458 DOI: 10.1101/2024.02.03.24302254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
We evaluated gut carriage of extended spectrum beta lactamase producing Enterobacteriaceae (ESBL-E) in southeastern U.S. residents without recent in-patient healthcare exposure. Study enrollment was January 2021-February 2022 in Athens, Georgia, U.S. and included a diverse population of 505 adults plus 50 child participants (age 0-5). Based on culture-based screening of stool samples, 4.5% of 555 participants carried ESBL-Es. This is slightly higher than reported in studies conducted 2012-2015, which found carriage rates of 2.5-3.9% in healthy U.S. residents. All ESBL-E confirmed isolates (n=25) were identified as Escherichia coli. Isolates belonged to 11 sequence types, with 48% classified as ST131. Ninety six percent of ESBL-E isolates carried a blaCTX-M gene. Isolated ESBL-Es frequently carried virulence genes as well as multiple classes of antibiotic resistance genes. Long-term colonization was common, with 64% of ESBL-E positive participants testing positive when rescreened three months later. One participant yielded isolates belonging to two different E. coli sequence types that carried blaCTX-M-1 genes on near-identical plasmids, suggesting intra-gut plasmid transfer. Isolation of E. coli on media without antibiotics revealed that ESBL-E. coli typically made up a minor fraction of the overall gut E. coli population, although in some cases they were the dominant strain. ESBL-E carriage was not associated with a significantly different stool microbiome composition. However, some microbial taxa were differentially abundant in ESBL-E carriers. Together, these results suggest that a small subpopulation of US residents are long-term, asymptomatic carriers of ESBL-Es, and may serve as an important reservoir for community spread of these ESBL genes.
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Affiliation(s)
| | - William A. Norfolk
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
- Center for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Amanda K. Howard
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Amanda L. Glatter
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Megan S. Beaudry
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
- Daicel Arbor Biosciences, Ann Arbor, MI, USA
| | - Nicholas A. Mallis
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, USA
| | - Michael Welton
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, USA
| | - Travis C. Glenn
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
| | - Erin K. Lipp
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
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Hosaka Y, Muraki Y, Kajihara T, Kawakami S, Hirabayashi A, Shimojima M, Ohge H, Sugai M, Yahara K. Antimicrobial use and combination of resistance phenotypes in bacteraemic Escherichia coli in primary care: a study based on Japanese national data in 2018. J Antimicrob Chemother 2024; 79:312-319. [PMID: 38084874 PMCID: PMC10832589 DOI: 10.1093/jac/dkad379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 11/26/2023] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Antimicrobial use (AMU) in primary care is a contributing factor to the emergence of antimicrobial-resistant bacteria. We assessed the potential effects of AMU on the prevalence of a combination of resistance phenotypes in bacteraemic Escherichia coli in outpatient care settings between primary care facilities ('clinics') and hospitals. METHODS Population-weighted total AMU calculated from the national database was expressed as DDDs per 1000 inhabitants per day (DID). National data for all routine microbiological test results were exported from the databases of a major commercial clinical laboratory, including 16 484 clinics, and the Japan Nosocomial Infections Surveillance, including 1947 hospitals. AMU and the prevalence of combinations of resistance phenotypes in bacteraemic E. coli isolates were compared between clinics and hospitals. RESULTS The five most common bacteria isolated from patients with bacteraemia were the same in clinics, outpatient settings and inpatient settings in hospitals, with E. coli as the most frequent. Oral third-generation cephalosporins and fluoroquinolones were the top two AMU outpatient drugs, except for macrolides, and resulted in at least three times higher AMU in clinics than in hospitals. The percentage of E. coli isolates resistant to both drugs in clinics (18.7%) was 5.6% higher than that in hospitals (13.1%) (P < 10-8). CONCLUSIONS Significant AMU, specifically of oral third-generation cephalosporins and fluoroquinolones, in clinics is associated with a higher prevalence of E. coli isolates resistant to both drugs. This study provides a basis for national interventions to reduce inappropriate AMU in primary care settings.
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Affiliation(s)
- Yumiko Hosaka
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuichi Muraki
- Department of Clinical Pharmacoepidemiology, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Toshiki Kajihara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sayoko Kawakami
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Aki Hirabayashi
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Hiroki Ohge
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan
| | - Motoyuki Sugai
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
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Cho ST, Mills EG, Griffith MP, Nordstrom HR, McElheny CL, Harrison LH, Doi Y, Van Tyne D. Evolution of extended-spectrum β-lactamase-producing ST131 Escherichia coli at a single hospital over 15 years. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.571174. [PMID: 38168243 PMCID: PMC10760032 DOI: 10.1101/2023.12.11.571174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Escherichia coli belonging to sequence type ST131 constitute a globally distributed pandemic lineage that causes multidrug-resistant extra-intestinal infections. ST131 E. coli frequently produce extended-spectrum β-lactamases (ESBLs), which confer resistance to many β-lactam antibiotics and make infections difficult to treat. We sequenced the genomes of 154 ESBL-producing E. coli clinical isolates belonging to the ST131 lineage from patients at the University of Pittsburgh Medical Center (UPMC) between 2004 and 2018. Isolates belonged to the well described ST131 clades A (8%), B (3%), C1 (33%), and C2 (54%). An additional four isolates belonged to another distinct subclade within clade C and encoded genomic characteristics that have not been previously described. Time-dated phylogenetic analysis estimated that the most recent common ancestor (MRCA) for all clade C isolates from UPMC emerged around 1989, consistent with previous studies. We identified multiple genes potentially under selection in clade C, including the cell wall assembly gene ftsI, the LPS biosynthesis gene arnC, and the yersiniabactin uptake receptor fyuA. Diverse ESBL genes belonging to the blaCTX-M, blaSHV, and blaTEM families were identified; these genes were found at varying numbers of loci and in variable numbers of copies across isolates. Analysis of ESBL flanking regions revealed diverse mobile elements that varied by ESBL type. Overall, our findings show that ST131 subclades C1 and C2 dominated and were stably maintained among patients in the same hospital and uncover possible signals of ongoing adaptation within the clade C ST131 lineage.
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Affiliation(s)
- Shu-Ting Cho
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Emma G. Mills
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marissa P. Griffith
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hayley R. Nordstrom
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Christi L. McElheny
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lee H. Harrison
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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Byarugaba DK, Erima B, Wokorach G, Alafi S, Kibuuka H, Mworozi E, Musinguzi AK, Kiyengo J, Najjuka F, Wabwire-Mangen F. Resistome and virulome of high-risk pandemic clones of multidrug-resistant extra-intestinal pathogenic Escherichia coli (ExPEC) isolated from tertiary healthcare settings in Uganda. PLoS One 2023; 18:e0294424. [PMID: 37992119 PMCID: PMC10664879 DOI: 10.1371/journal.pone.0294424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/01/2023] [Indexed: 11/24/2023] Open
Abstract
Multi-drug resistant (MDR) globally disseminated extraintestinal pathogenic high-risk Escherichia coli (ExPEC) clones are threatening the gains in bacterial disease management. In this study, we evaluated the genomic structure including the resistome and virulome of the E. coli isolates from extraintestinal infections using whole genome sequencing (WGS). The results highlight that isolates were highly resistant (≥ 90.0%) to commonly used antibiotics (Ampicillin, Trimethoprim-Sulfamethoxazole, Nalidixic acid, and Piperacillin) and were less (<14%) resistant to last resort antibiotics; Imipenem (10.94%) and Meropenem (10.20%). A greater proportion of the E. coli isolates belonged to phylogroup B2 (30.52%) and phylogroup A (27.37%). The sequence types ST131 of phylogroup B2 (21.05%) and ST648 of phylogroup F (9.3%) were the dominant pandemic high-risk clones identified in addition to the ST1193, ST410, ST69, ST38, ST405, and ST10. Many of the isolates were MDR and most (64.58%) carried the blaCTX-M-15 gene for extended-spectrum β-lactamases. There was a high correlation between phylogroups and the occurrence of both antimicrobial resistance and virulence genes. The cephalosporin-resistance gene blaEC-5 was only found in phylogroup B2 while blaEC-8 and blaEC-19, were only found within phylogroup D and phylogroup F respectively. Aminoglycoside gene (aadA1) was only associated with phylogroups D and C. The isolates were armed with a broad range of virulence genes including adhesins, toxins, secreted proteases, iron uptake genes, and others. The yfcv, chuA, and kpsE genes preferentially occurred among isolates of phylogroup B2. The study underlines the predominance of MDR internationally disseminated high-risk ExPEC clones with a broad range of virulence genes known to be highly transmissible in healthcare and community settings.
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Affiliation(s)
- Denis K. Byarugaba
- Makerere University Walter Reed Project, Kampala, Uganda
- College of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Bernard Erima
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Godfrey Wokorach
- Makerere University Walter Reed Project, Kampala, Uganda
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda
| | - Stephen Alafi
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Hannah Kibuuka
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Edison Mworozi
- Makerere University Walter Reed Project, Kampala, Uganda
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - James Kiyengo
- Uganda Peoples’ Defence Forces, Ministry of Defence, Kampala, Uganda
| | - Florence Najjuka
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Fred Wabwire-Mangen
- Makerere University Walter Reed Project, Kampala, Uganda
- College of Health Sciences, Makerere University, Kampala, Uganda
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Salamzade R, McElheny CL, Manson AL, Earl AM, Shaikh N, Doi Y. Genomic epidemiology and antibiotic susceptibility profiling of uropathogenic Escherichia coli among children in the United States. mSphere 2023; 8:e0018423. [PMID: 37581436 PMCID: PMC10597468 DOI: 10.1128/msphere.00184-23] [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: 06/15/2023] [Indexed: 08/16/2023] Open
Abstract
Escherichia coli is the most common cause of urinary tract infections (UTIs) in children, and yet the underlying mechanisms of virulence and antibiotic resistance and the overall population structure of the species is poorly understood within this age group. To investigate whether uropathogenic E. coli (UPEC) from children who developed pyelonephritis carried specific genetic markers, we generated whole-genome sequence data for 96 isolates from children with UTIs. This included 57 isolates from children with either radiologically confirmed pyelonephritis or cystitis and 27 isolates belonging to the well-known multidrug-resistant sequence type ST131, selected to investigate their population structure and antibiotic resistance characteristics. We observed a UPEC population structure that is similar to those reported in adults. In comparison with prior investigations, we found that the full pap operon was more common among UPEC from pediatric cases of pyelonephritis. Further, in contrast with recent reports that the P-fimbriae adhesin-encoding papGII allele is substantially more prevalent in invasive UPEC from adults, we found papGII was common to both invasive and non-invasive UPEC from children. Among the set of ST131 isolates from children with UTIs, we found antibiotic resistance was correlated with known genetic markers of resistance, as in adults. Unexpectedly, we observed that fimH30, an allele of the fimbrial gene fimH often used as a proxy to type ST131 isolates into the most drug-resistant subclade C, was carried by some of the subclade A and subclade B isolates, suggesting that the fimH30 allele could confer a selective advantage for UPEC. IMPORTANCE Urinary tract infections (UTIs), which are most often caused by Escherichia coli, are not well studied in children. Here, we examine genetic characteristics that differentiate UTI-causing bacteria in children that either remain localized to the bladder or are involved in more serious kidney infections. We also examine patterns of antibiotic resistance among strains from children that are part of E. coli sequence type 131, a group of bacteria that commonly cause UTIs and are known to have high levels of drug resistance. This work provides new insight into the virulence and antibiotic resistance characteristics of the bacteria that cause UTIs in children.
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Affiliation(s)
- Rauf Salamzade
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Christi L. McElheny
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Abigail L. Manson
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Ashlee M. Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Nader Shaikh
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Fujita Health University School of Medicine, Aichi, Japan
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10
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Hayakawa K, Matsumura Y, Uemura K, Tsuzuki S, Sakurai A, Tanizaki R, Shinohara K, Hashimoto T, Hase R, Matono T, Kato H, Mawatari M, Hara H, Hamada Y, Saito S, Ohmagari N, Doi Y. Effectiveness of cefmetazole versus meropenem for invasive urinary tract infections caused by extended-spectrum β-lactamase-producing Escherichia coli. Antimicrob Agents Chemother 2023; 67:e0051023. [PMID: 37702483 PMCID: PMC10583665 DOI: 10.1128/aac.00510-23] [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: 04/21/2023] [Accepted: 07/12/2023] [Indexed: 09/14/2023] Open
Abstract
Cefmetazole is active against extended-spectrum β-lactamase-producing Escherichia coli (ESBLEC) and is a potential candidate for carbapenem-sparing therapy. This multicenter, observational study included patients hospitalized for invasive urinary tract infection due to ESBLEC between March 2020 and November 2021 at 10 facilities in Japan, for whom either cefmetazole or meropenem was initiated as a definitive therapy within 96 h of culture collection and continued for at least 3 d. Outcomes included clinical and microbiological effectiveness, recurrence within 28 d, and all-cause mortality (14 d, 30 d, in-hospital). Outcomes were adjusted for the inverse probability of propensity scores for receiving cefmetazole or meropenem. Eighty-one and forty-six patients were included in the cefmetazole and meropenem groups, respectively. Bacteremia accounted for 43% of the cefmetazole group, and 59% of the meropenem group. The crude clinical effectiveness, 14 d, 30 d, and in-hospital mortality for patients in the cefmetazole and meropenem groups were 96.1% vs 90.9%, 0% vs 2.3%, 0% vs 12.5%, and 2.6% vs 13.3%, respectively. After propensity score adjustment, clinical effectiveness, the risk of in-hospital mortality, and the risk of recurrence were similar between the two groups (P = 0.54, P = 0.10, and P = 0.79, respectively). In all cases with available data (cefmetazole : n = 61, meropenem : n = 22), both drugs were microbiologically effective. In all isolates, bla CTX-M was detected as the extended-spectrum β-lactamase gene. The predominant CTX-M subtype was CTX-M-27 (47.6%). Cefmetazole showed clinical and bacteriological effectiveness comparable to meropenem against invasive urinary tract infection due to ESBLECs.
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Affiliation(s)
- Kayoko Hayakawa
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yasufumi Matsumura
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kohei Uemura
- Interfaculty Initiative in Information Studies, The University of Tokyo, Tokyo, Japan
| | - Shinya Tsuzuki
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
- Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Aki Sakurai
- Departments of Microbiology and Infectious Diseases, Fujita Health University School of Medicine, Aichi, Japan
| | - Ryutaro Tanizaki
- Department of Internal Medicine and General Medicine, Ise Municipal General Hospital, Mie, Japan
| | - Koh Shinohara
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | | | - Ryota Hase
- Department of Infectious Diseases, Japanese Red Cross Narita Hospital, Chiba, Japan
| | - Takashi Matono
- Department of Infectious Diseases, Aso Iizuka Hospital, Fukuoka, Japan
| | - Hideaki Kato
- Infection Prevention and Control Department, Yokohama City University Hospital, Kanagawa, Japan
| | - Momoko Mawatari
- Department of Infectious Diseases, Japanese Red Cross Medical Center, Tokyo, Japan
| | - Hiroshi Hara
- Department of pharmacy, Yokohama Brain and Spine Center, Kanagawa, Japan
| | - Yukihiro Hamada
- Department of pharmacy, Tokyo Women’s Medical University Hospital, Tokyo, Japan
| | - Sho Saito
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Norio Ohmagari
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yohei Doi
- Departments of Microbiology and Infectious Diseases, Fujita Health University School of Medicine, Aichi, Japan
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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11
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Becerra-Aparicio F, Gómez-Zorrilla S, Hernández-García M, Gijón D, Siverio A, Berbel D, Sánchez-Carrillo C, Cercenado E, Rivera A, de Malet A, Xercavins M, Ruiz de Gopegui E, Canoura-Fernández L, Martínez JA, Seral C, Del Pozo JL, Cotarelo M, Díaz-Regañón J, Cantón R, Oliver A, Horcajada JP, Ruiz-Garbajosa P. Significant increase of CTX-M-15-ST131 and emergence of CTX-M-27-ST131 Escherichia coli high-risk clones causing healthcare-associated bacteraemia of urinary origin in Spain (ITUBRAS-2 project). J Antimicrob Chemother 2023; 78:2291-2296. [PMID: 37533351 DOI: 10.1093/jac/dkad234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/13/2023] [Indexed: 08/04/2023] Open
Abstract
OBJECTIVES To assess the microbiological characteristics of Escherichia coli causing healthcare-associated bacteraemia of urinary origin (HCA-BUO) in Spain (ITUBRAS-2 project), with particular focus on ESBL producers and isolates belonging to ST131 high-risk clone (HiRC). Clinical characteristics and outcomes associated with ST131 infection were investigated. METHODS A total of 222 E. coli blood isolates were prospectively collected from patients with HCA-BUO from 12 tertiary-care hospitals in Spain (2017-19). Antimicrobial susceptibility and ESBL/carbapenemase production were determined. ST131 subtyping was performed. A subset of 115 isolates were selected for WGS to determine population structure, resistome and virulome. Clinical charts were reviewed. RESULTS ESBL-producing E. coli prevalence was 30.6% (68/222). ST131 represented 29.7% (66/222) of E. coli isolates and accounted for the majority of ESBL producers (46/68, 67.6%). The C2/H30-Rx subclone accounted for most ST131 isolates (44/66) and was associated with CTX-M-15 (37/44) and OXA-1 enzymes (27/44). Cluster C1-M27 was identified in 4/10 isolates belonging to subclade C1/H30-R1 and associated with CTX-M-27. Additionally, ST131 isolates showed a high content of other acquired resistance genes, and clade C/ST131 isolates carried characteristic QRDR mutations. They were categorized as uropathogenic E. coli and had higher aggregate virulence scores. ST131 infection was associated with more complex patients, prior use of cephalosporins and inadequate empirical treatment but was not associated with worse clinical outcomes. CONCLUSIONS ST131 HiRC is the main driver of ESBL-producing E. coli causing HCA-BUO in Spain, mainly associated with the expansion of subclade CTX-M-15-C2/H30-Rx and the emergence of CTX-M-27-C1/H30-R1 (Cluster C1-M27).
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Affiliation(s)
| | - Silvia Gómez-Zorrilla
- Servicio de Enfermedades Infecciosas, Hospital del Mar-IMIM, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Hernández-García
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Desiré Gijón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
| | - Ana Siverio
- Servicio de Enfermedades Infecciosas, Hospital del Mar-IMIM, Barcelona, Spain
- Servicio de Microbiología, Laboratorio de Referencia de Cataluña, Hospital del Mar, Barcelona, Spain
| | - Dàmaris Berbel
- Servicio de Microbiología, Hospital de Bellvitge, Barcelona, Spain
| | | | - Emilia Cercenado
- Servicio de Microbiología, Hospital Gregorio Marañón, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Alba Rivera
- Servicio de Microbiología, Hospital Santa Creu i San Pau, Barcelona, Spain
| | - Ana de Malet
- Servicio de Microbiología, Hospital Universitario Lucus Augusti, Lugo, Spain
| | - Mariona Xercavins
- Microbiología-CATLAB, Hospital Universitari Mútua Terrassa, Barcelona, Spain
| | - Enrique Ruiz de Gopegui
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Son Espases, IdISBa, Mallorca, Spain
| | | | | | - Cristina Seral
- Servicio de Microbiología, Hospital Clínico Lozano Blesa, Zaragoza, Spain
| | - José Luis Del Pozo
- Servicio de Microbiología, Clínica Universitaria de Navarra, Pamplona, Spain
| | | | | | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Antonio Oliver
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Son Espases, IdISBa, Mallorca, Spain
| | - Juan Pablo Horcajada
- Servicio de Enfermedades Infecciosas, Hospital del Mar-IMIM, Barcelona, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Patricia Ruiz-Garbajosa
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
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12
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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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13
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Yang JT, Zhang LJ, Lu Y, Zhang RM, Jiang HX. Genomic Insights into Global blaCTX-M-55-Positive Escherichia coli Epidemiology and Transmission Characteristics. Microbiol Spectr 2023; 11:e0108923. [PMID: 37358409 PMCID: PMC10434037 DOI: 10.1128/spectrum.01089-23] [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: 03/13/2023] [Accepted: 05/10/2023] [Indexed: 06/27/2023] Open
Abstract
In recent years, blaCTX-M-55-positive Escherichia coli has been widely reported in multiple locations with an increasing trend in prevalence, yet few studies have comprehensively analyzed the transmission characteristics and epidemiological patterns of blaCTX-M-55-positive E. coli. Here, we constructed a blaCTX-M-55-positive E. coli global genomic data set as completely as possible and explored the epidemiology and potential impact of blaCTX-M-55-positive E. coli on a global scale by high-resolution bioinformatics methods. The results show that blaCTX-M-55-positive E. coli has spread widely worldwide, especially in Asia, with the rich sequence typing (ST) diversity and high proportion of auxiliary genome occupancy indicating a high degree of openness. The phylogenetic tree suggests that blaCTX-M-55-positive E. coli is frequently clonally transmitted between the three human-animal environments and often cotransmitted with fosA, mcr, blaNDM, and tet(X). The stable presence of InclI1 and InclI2 in different hosts from different sources suggests that this part of the plasmid drives the widespread transmission of blaCTX-M-55-positive E. coli. We inductively clustered all blaCTX-M-55 flanking environmental gene structures and obtained five types. Notably, "ISEcp1-blaCTX-M-55-orf477-(Tn2)" and "IS26(IS15DI)-hp-hp-blaCTX-M-55-orf477-hp-blaTEM-IS26-hp-IS26-Tn2" are dominant in "humans" and in "animals and related foods," respectively. Overall, our findings highlight the importance of whole-genome sequencing-based surveillance in exploring the transmission and evolution of blaCTX-M-55-positive E. coli in the context of "One Health," and they serve as a reminder to strengthen the surveillance of blaCTX-M-55-positive E. coli in order to address the potential risk of future large outbreaks. IMPORTANCE CTX-M-55 was first discovered in Thailand in 2004, and today, this enzyme is the most common CTX-M subtype in E. coli of animal origin in China. Thus, blaCTX-M-55-positive E. coli getting widely spread is a growing public health problem. Although prevalence surveys of blaCTX-M-55-positive E. coli in different hosts have been widely reported in recent years, they remain insufficient in "One Health" context and from a global comprehensive perspective. Here, we constructed a genomic database of 2144 blaCTX-M-55-positive E. coli and used bioinformatics methods to resolve the spread and evolution of blaCTX-M-55-positive E. coli. The results suggest a potential risk of rapid transmission of blaCTX-M-55-positive E. coli and that long-term continuous surveillance of blaCTX-M-55-positive E. coli should be emphasized.
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Affiliation(s)
- Jin-Tao Yang
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Li-Juan Zhang
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, China
| | - Yang Lu
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Rong-Min Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Hong-Xia Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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14
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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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15
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Pitout JD, Peirano G, DeVinney R. The contributions of multidrug resistant clones to the success of pandemic extra-intestinal Pathogenic Escherichia coli. Expert Rev Anti Infect Ther 2023; 21:343-353. [PMID: 36822840 DOI: 10.1080/14787210.2023.2184348] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
INTRODUCTION High-risk multidrug (MDR) clones have played essential roles in the global emergence and spread of antimicrobial resistance (AMR), especially among Extra-intestinal Escherichia coli (ExPEC). AREAS COVERED Successful global ExPEC MDR clones are linked with the acquisition of fluoroquinolone resistance, CTX-M enzymes, and with carbapenemases. This article described the underlying mechanisms of fluoroquinolone resistance, the acquisition of CTX-M and carbapenemase genes among three global ExPEC high-risk MDR clones, namely i) ST1193 as being an example of a fluoroquinolone resistant clone. ii) ST131 as an example of a fluoroquinolone resistant and CTX-M clone. iii) ST410 as an example of a fluoroquinolone resistant, CTX-M and carbapenemase clone. This article also highlighted the contributions of these MDR determinants in the evolution of these high-risk MDR clones. EXPERT OPINION There is an enormous public health burden due to E. coli MDR high-risk clones such as ST1193, ST131 and ST410. These clones have played pivotal roles in the global spread of AMR. Sparse information is available on which specific features of these high-risk MDR clones have enabled them to become such successful global pathogens in relative short time periods.
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Affiliation(s)
- Johann Dd Pitout
- University of Calgary, Calgary, Alberta, Canada.,Dynalife Laboratories, University of Calgary, Calgary, Alberta, Canada.,University of Pretoria, Pretoria, Gauteng, South Africa
| | - Gisele Peirano
- University of Calgary, Calgary, Alberta, Canada.,Dynalife Laboratories, University of Calgary, Calgary, Alberta, Canada
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16
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Pitout JDD, Chen L. The Significance of Epidemic Plasmids in the Success of Multidrug-Resistant Drug Pandemic Extraintestinal Pathogenic Escherichia coli. Infect Dis Ther 2023; 12:1029-1041. [PMID: 36947392 PMCID: PMC10147871 DOI: 10.1007/s40121-023-00791-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/06/2023] [Indexed: 03/23/2023] Open
Abstract
Epidemic IncF plasmids have been pivotal in the selective advantage of multidrug-resistant (MDR) extraintestinal pathogenic Escherichia coli (ExPEC). These plasmids have offered several advantages to their hosts that allowed them to coevolve with the bacterial host genomes and played an integral role in the success of ExPEC. IncF plasmids are large, mosaic, and often contain various types of antimicrobial resistance (AMR) and virulence associated factor (VAF) genes. The presence of AMR, VAF genes, several addition/restriction systems combined with truncated transfer regions, led to the fixation of IncF plasmids in certain ExPEC MDR clones, such as ST131 and ST410. IncF plasmids entered the ST131 ancestral lineage in the mid 1900s and different ST131 clade/CTX-M plasmid combinations coevolved over time. The IncF_CTX-M-15/ST131-C2 subclade combination emerged during the early 2000s, spread rapidly across the globe, and is one of the greatest clone/plasmid successes of the millennium. The ST410-B3 subclade containing blaCTX-M-15 incorporated the NDM-5 carbapenemase gene into existing IncF platforms, providing an additional positive selective advantage that included the carbapenems. A "plasmid-replacement" clade scenario occurred in the histories of ST131 and ST410 as different subclades gained different AMR genes on different IncF platforms. The use of antimicrobial agents will generate selection pressures that enhance the risks for the continuous emergence of MDR ExPEC clone/IncF plasmid combinations. The reasons for clade/IncF replacements and associations between certain clades and specific IncF plasmid types are unknown. Such information will aid in designing management and prevention strategies to combat AMR.
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Affiliation(s)
- Johann D D Pitout
- Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, Calgary, AB, T2L 2K8, Canada.
- Dynacare Laboratories, Alberta, Canada.
- University of Pretoria, Pretoria, Gauteng, South Africa.
| | - Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Hackensack Meridian School of Medicine, Nutley, NJ, USA
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17
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Shibuki R, Nishiyama M, Mori M, Baba H, Kanamori H, Watanabe T. Characterization of extended-spectrum β-lactamase-producing Escherichia coli isolated from municipal and hospital wastewater in Japan. J Glob Antimicrob Resist 2023; 32:145-151. [PMID: 36842459 DOI: 10.1016/j.jgar.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 01/24/2023] [Accepted: 02/03/2023] [Indexed: 02/27/2023] Open
Abstract
OBJECTIVES The purpose of this study was to characterize the strains of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) isolated from municipal and hospital wastewater by detecting antibiotic resistance genes (ARGs) as well as antibiotic susceptibility. To identify the source of ESBL-EC, multi-locus sequence typing and typing plasmids that may carry ESBL-producing genes were conducted. METHODS Wastewater was sampled twice a month from February 2019 to February 2020 from a municipal wastewater treatment plant and hospital located in a city in northeastern Japan. Throughout the study period, 279 and 37 strains of ESBL-EC were isolated from municipal and hospital wastewater, respectively. RESULTS All 316 isolates were resistant to ampicillin and cefotaxime and susceptible to imipenem and tigecycline. Almost all (98.1%) of the ESBL-EC isolates possessed blaCTX-M, and the blaCTX-M-9 group was detected most frequently (62.3%). Multi-locus sequence typing revealed a higher diversity of sequence types (STs) in the isolates from municipal wastewater than in those from hospital wastewater; although ST131, which recently caused nosocomial- and community-associated infections worldwide, was dominant in both types of wastewater. All ST131 isolates possessed the IncFII plasmid, which is often reported to carry blaCTX-M. CONCLUSIONS These results demonstrated that healthy people carry clinically important antibiotic-resistant bacteria and ARGs, motivating routine monitoring of municipal wastewater to detect such antibiotic-resistant bacteria and ARGs from a variety of sources supported by the high diversity of STs in the present study.
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Affiliation(s)
- Rio Shibuki
- Graduate School of Agricultural Sciences, Yamagata University, Yamagata, Japan
| | | | - Masaya Mori
- Graduate School of Agricultural Sciences, Yamagata University, Yamagata, Japan
| | - Hiroaki Baba
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Hajime Kanamori
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Toru Watanabe
- Faculty of Agriculture, Yamagata University, Yamagata, Japan
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18
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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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19
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Chao CM, Lai CC, Yu WL. Epidemiology of extended-spectrum β-lactamases in Enterobacterales in Taiwan for over two decades. Front Microbiol 2023; 13:1060050. [PMID: 36762100 PMCID: PMC9905819 DOI: 10.3389/fmicb.2022.1060050] [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: 10/02/2022] [Accepted: 12/22/2022] [Indexed: 01/28/2023] Open
Abstract
The emergence of antimicrobial resistance among microorganisms is a serious public health concern, and extended-spectrum β-lactamases (ESBL)-producing Enterobacterales is one of the major concerns among antibiotic-resistant bacteria. Although the prevalence of ESBL in Enterobacterales has been increasing with time, the prevalence of ESBL could differ according to the species, hospital allocation, sources of infections, nosocomial or community acquisitions, and geographic regions. Therefore, we conducted a comprehensive review of the epidemiology of ESBL-producing Enterobacterales in Taiwan. Overall, the rates of ESBL producers are higher in northern regions than in other parts of Taiwan. In addition, the genotypes of ESBL vary according to different Enterobacterales. SHV-type ESBLs (SHV-5 and SHV-12) were the major types of Enterobacter cloacae complex, but Serratia marcescens, Proteus mirabilis, Escherichia coli, and Klebsiella pneumoniae were more likely to possess CTX-M-type ESBLs (CTX-M-3 and CTX-M-14). Moreover, a clonal sequence type of O25b-ST131 has been emerging among urinary or bloodstream E. coli isolates in the community in Taiwan, and this clone was potentially associated with virulence, ESBL (CTX-M-15) production, ciprofloxacin resistance, and mortality. Finally, the evolution of the genetic traits of the ESBL-producing Enterobacterales isolates helps us confirm the interhospital and intrahospital clonal dissemination in several regions of Taiwan. In conclusion, continuous surveillance in the investigation of ESBL production among Enterobacterales is needed to establish its long-term epidemiology.
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Affiliation(s)
- Chien-Ming Chao
- Department of Intensive Care Medicine, Chi Mei Medical Center, Liouying, Taiwan,Department of Dental Laboratory Technology, Min-Hwei College of Health Care Management, Tainan, Taiwan
| | - Chih-Cheng Lai
- Division of Hospital Medicine, Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Wen-Liang Yu
- Department of Intensive Care Medicine, Chi Mei Medical Center, Tainan, Taiwan,Department of Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan,*Correspondence: Wen-Liang Yu,
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20
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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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21
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Mills EG, Martin MJ, Luo TL, Ong AC, Maybank R, Corey BW, Harless C, Preston LN, Rosado-Mendez JA, Preston SB, Kwak YI, Backlund MG, Bennett JW, Mc Gann PT, Lebreton F. A one-year genomic investigation of Escherichia coli epidemiology and nosocomial spread at a large US healthcare network. Genome Med 2022; 14:147. [PMID: 36585742 PMCID: PMC9801656 DOI: 10.1186/s13073-022-01150-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Extra-intestinal pathogenic Escherichia coli (ExPEC) are a leading cause of bloodstream and urinary tract infections worldwide. Over the last two decades, increased rates of antibiotic resistance in E. coli have been reported, further complicating treatment. Worryingly, specific lineages expressing extended-spectrum β-lactamases (ESBLs) and fluoroquinolone resistance have proliferated and are now considered a serious threat. Obtaining contemporary information on the epidemiology and prevalence of these circulating lineages is critical for containing their spread globally and within the clinic. METHODS Whole-genome sequencing (WGS), phylogenetic analysis, and antibiotic susceptibility testing were performed for a complete set of 2075 E. coli clinical isolates collected from 1776 patients at a large tertiary healthcare network in the USA between October 2019 and September 2020. RESULTS The isolates represented two main phylogenetic groups, B2 and D, with six lineages accounting for 53% of strains: ST-69, ST-73, ST-95, ST-131, ST-127, and ST-1193. Twenty-seven percent of the primary isolates were multidrug resistant (MDR) and 5% carried an ESBL gene. Importantly, 74% of the ESBL-E.coli were co-resistant to fluoroquinolones and mostly belonged to pandemic ST-131 and emerging ST-1193. SNP-based detection of possible outbreaks identified 95 potential transmission clusters totaling 258 isolates (12% of the whole population) from ≥ 2 patients. While the proportion of MDR isolates was enriched in the set of putative transmission isolates compared to sporadic infections (35 vs 27%, p = 0.007), a large fraction (61%) of the predicted outbreaks (including the largest cluster grouping isolates from 12 patients) were caused by the transmission of non-MDR clones. CONCLUSION By coupling in-depth genomic characterization with a complete sampling of clinical isolates for a full year, this study provides a rare and contemporary survey on the epidemiology and spread of E. coli in a large US healthcare network. While surveillance and infection control efforts often focus on ESBL and MDR lineages, our findings reveal that non-MDR isolates represent a large burden of infections, including those of predicted nosocomial origins. This increased awareness is key for implementing effective WGS-based surveillance as a routine technology for infection control.
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Affiliation(s)
- Emma G. Mills
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Melissa J. Martin
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Ting L. Luo
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Ana C. Ong
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Rosslyn Maybank
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Brendan W. Corey
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Casey Harless
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Lan N. Preston
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Joshua A. Rosado-Mendez
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Scott B. Preston
- grid.414467.40000 0001 0560 6544Department of Pathology, Walter Reed National Military Medical Center, Bethesda, MD USA
| | - Yoon I. Kwak
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Michael G. Backlund
- grid.414467.40000 0001 0560 6544Department of Pathology, Walter Reed National Military Medical Center, Bethesda, MD USA
| | - Jason W. Bennett
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Patrick T. Mc Gann
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Francois Lebreton
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
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22
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Li C, Chen X, Ju Z, Li C, Xu Y, Ding J, Wang Y, Ma P, Gu K, Lei C, Tang Y, Wang H. Comparative Analysis of Phylogenetic Relationships and Virulence Factor Characteristics between Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates Derived from Clinical Sites and Chicken Farms. Microbiol Spectr 2022; 10:e0255722. [PMID: 36374015 PMCID: PMC9769871 DOI: 10.1128/spectrum.02557-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance in bacteria is the most urgent global threat to public health, with extended-spectrum β-lactamase-producing Escherichia coli (ESBL-E. coli) being one of the most documented examples. Nonetheless, the ESBL-E. coli transmission relationship among clinical sites and chicken farms remains unclear. Here, 408 ESBL-E. coli strains were isolated from hospitals and chicken farms in Sichuan Province and Yunnan Province in 2021. We detected blaCTX-M genes in 337 (82.62%) ESBL-E. coli strains. Although the isolation rate, prevalent sequence type (ST) subtypes, and blaCTX-M gene subtypes of ESBL-E. coli varied based on regions and sources, a few strains of CTX-ESBL-E. coli derived from clinical sites and chicken farms in Sichuan Province displayed high genetic similarity. This indicates a risk of ESBL-E. coli transmission from chickens to humans. Moreover, we found that the high-risk clonal strains ST131 and ST1193 primarily carried blaCTX-M-27. This indicates that drug-resistant E. coli from animal and human sources should be monitored. As well, the overuse of β-lactam antibiotics should be avoided in poultry farms to ensure public health and build an effective regulatory mechanism of "farm to fork" under a One Health perspective. IMPORTANCE Bacterial drug resistance has become one of the most significant threats to human health worldwide, especially for extended-spectrum β-lactamase-producing E. coli (ESBL-E. coli). Timely and accurate epidemiological surveys can provide scientific guidance for the adoption of treatments in different regions and also reduce the formation of drug-resistant bacteria. Our study showed that the subtypes of ESBL-E. coli strains prevalent in different provinces are somewhat different, so it is necessary to individualize treatment regimens in different regions, and it is especially important to limit and reduce antibiotic use in poultry farming since chicken-derived ESBL-E. coli serves as an important reservoir of drug resistance genes and has the potential to spread to humans, thus posing a threat to human health. The use of antibiotics in poultry farming should be particularly limited and reduced.
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Affiliation(s)
- Chao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xuan Chen
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Zijing Ju
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Cui Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Ying Xu
- The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Jiawei Ding
- Clinical Laboratory Department, Yan’an Hospital Affiliated with Kunming Medical University, Kunming, Yunnan, China
| | - Yuting Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Peng Ma
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Kui Gu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Changwei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yizhi Tang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
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Neffe L, Forde TL, Oravcova K, Köhler U, Bautsch W, Tomasch J, Häussler S. Genomic epidemiology of clinical ESBL-producing Enterobacteriaceae in a German hospital suggests infections are primarily community- and regionally-acquired. Microb Genom 2022; 8:mgen000901. [PMID: 36748515 PMCID: PMC9837565 DOI: 10.1099/mgen.0.000901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Clinical Enterobacteriaceae isolates that produce extended-spectrum β-lactamases (ESBLs) have been increasingly reported at a global scale. However, comprehensive data on the molecular epidemiology of ESBL-producing strains are limited and few studies have been conducted in non-outbreak situations.We used whole-genome sequencing to describe the population structure of 294 ESBL-producing Escherichia coli and Klebsiella pneumoniae isolates that were recovered from a German community hospital throughout a 1 year sampling period in a non-outbreak situation.We found a high proportion of E. coli isolates (61.5 %) belonged to the globally disseminated extraintestinal pathogenic ST131, whereas a wider diversity of STs was observed among K. pneumoniae isolates. The E. coli ST131 population in this study was shaped by multiple introductions of strains as demonstrated by contextual genomic analysis including ST131 strains from other geographical sources. While no recent common ancestor of the isolates of the current study and other international isolates was found, our clinical isolates clustered with those previously recovered in the region. Furthermore, we found that the isolation of ESBL-producing clinical strains in hospitalized patients could only rarely be associated with likely patient-to-patient transmission, indicating primarily a community and regional acquisition of strains.Further genomic analyses of clinical, carriage and environmental isolates is needed to uncover hidden transmissions and thus discover the most common sources of ESBL-producing pathogen infections in our hospitals.
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Affiliation(s)
- Lisa Neffe
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany,Institute for Molecular Bacteriology, TWINCORE GmbH, Center of Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover, Germany
| | - Taya L. Forde
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Katarina Oravcova
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Ute Köhler
- Städtisches Klinikum Braunschweig gGmbH, Germany
| | | | - Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany,Institute for Molecular Bacteriology, TWINCORE GmbH, Center of Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover, Germany,Department of Clinical Microbiology, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany,*Correspondence: Susanne Häussler,
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24
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Zamudio R, Boerlin P, Beyrouthy R, Madec JY, Schwarz S, Mulvey MR, Zhanel GG, Cormier A, Chalmers G, Bonnet R, Haenni M, Eichhorn I, Kaspar H, Garcia-Fierro R, Wood JLN, Mather AE. Dynamics of extended-spectrum cephalosporin resistance genes in Escherichia coli from Europe and North America. Nat Commun 2022; 13:7490. [PMID: 36509735 PMCID: PMC9744880 DOI: 10.1038/s41467-022-34970-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022] Open
Abstract
Extended-spectrum cephalosporins (ESCs) are critically important antimicrobial agents for human and veterinary medicine. ESC resistance (ESC-R) genes have spread worldwide through plasmids and clonal expansion, yet the distribution and dynamics of ESC-R genes in different ecological compartments are poorly understood. Here we use whole genome sequence data of Enterobacterales isolates of human and animal origin from Europe and North America and identify contrasting temporal dynamics. AmpC β-lactamases were initially more dominant in North America in humans and farm animals, only later emerging in Europe. In contrast, specific extended-spectrum β-lactamases (ESBLs) were initially common in animals from Europe and later emerged in North America. This study identifies differences in the relative importance of plasmids and clonal expansion across different compartments for the spread of different ESC-R genes. Understanding the mechanisms of transmission will be critical in the design of interventions to reduce the spread of antimicrobial resistance.
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Affiliation(s)
- Roxana Zamudio
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Patrick Boerlin
- Department of Pathobiology, University of Guelph, Guelph, N1G 2W1, Canada
| | - Racha Beyrouthy
- Microbes Intestin Inflammation et Susceptibilité de l'Hôte (M2ISH), Faculté de Médecine, Université Clermont Auvergne, Clermont-Ferrand, 63001, France.,Centre National de Référence de la résistance aux antibiotiques, Centre Hospitalier Universitaire de Clermont-Ferrand, Clermont-Ferrand, 63000, France
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, Anses Laboratoire de Lyon, Université de Lyon, Lyon, 69007, France
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, 14163, Germany.,Veterinary Centre for Resistance Research (TZR), Department of Veterinary Medicine, Freie Universität Berlin, Berlin, 14163, Germany
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, R3E 3R2, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
| | - Ashley Cormier
- Department of Pathobiology, University of Guelph, Guelph, N1G 2W1, Canada
| | - Gabhan Chalmers
- Department of Pathobiology, University of Guelph, Guelph, N1G 2W1, Canada
| | - Richard Bonnet
- Microbes Intestin Inflammation et Susceptibilité de l'Hôte (M2ISH), Faculté de Médecine, Université Clermont Auvergne, Clermont-Ferrand, 63001, France.,Centre National de Référence de la résistance aux antibiotiques, Centre Hospitalier Universitaire de Clermont-Ferrand, Clermont-Ferrand, 63000, France
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Anses Laboratoire de Lyon, Université de Lyon, Lyon, 69007, France
| | - Inga Eichhorn
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, 14163, Germany.,Veterinary Centre for Resistance Research (TZR), Department of Veterinary Medicine, Freie Universität Berlin, Berlin, 14163, Germany
| | - Heike Kaspar
- Department Method Standardisation, Resistance to Antibiotics Unit Monitoring of Resistance to Antibiotics, Federal Office of Consumer Protection and Food Safety, Berlin, 12277, Germany
| | - Raquel Garcia-Fierro
- Unité Antibiorésistance et Virulence Bactériennes, Anses Laboratoire de Lyon, Université de Lyon, Lyon, 69007, France
| | - James L N Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK. .,University of East Anglia, Norwich, NR4 7TJ, UK.
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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: 11] [Impact Index Per Article: 5.5] [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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Mhaya A, Trabelsi R, Aillerie S, M’Zali F, Bégu D, Tounsi S, Gdoura R, Arpin C. Detection of Clones B2-ST131-C2 and A-ST617 in Escherichia coli Producing Both CTX-M-15 and CTX-M-27 from Tunisian Community Patients. Antibiotics (Basel) 2022; 11:antibiotics11101329. [PMID: 36289987 PMCID: PMC9598323 DOI: 10.3390/antibiotics11101329] [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: 07/27/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 01/18/2023] Open
Abstract
During a two-month period (2017–2018), 336 urine samples positive for Escherichia coli were collected from Tunisian patients. Of the 336 samples, 266 were collected from community patients and 70 from hospital settings. In all, 15 ESBL producers were identified (8 and 7, respectively) and assigned to 13 pulsotypes, including four ESBL-producing E. coli (ESBL-E) with E1 and E2 profiles (2 isolates each) from community patients. The two strains E1 were identified as B2-ST131 subclade C2 and the two isolates E2, A-ST617. The four strains carrying both CTX-M-15 and CTX-M-27, exhibited the multireplicon IncFII/F1A/F1B with the same formula F31:A4:B1. Two isolates with patterns E3 and E4 (Dice coefficient, 78.7%) isolated from community and hospital settings of two geographic areas were assigned to the emerging ST131 C1-M27 subclade and contained the replicon F1:A-:B20. The remaining ESBL-E divided into different sequence types/associated CTX-M: 2 ST131-C2/CTX-M-15 and ST744/CTX-M-55, ST617/CTM-15, ST2973/CTX-M-55, ST6448/CTX-M-15, ST224/CTX-M-15, ST1431/CTX-M-15, and ST38/CTX-M-27, one isolate each. Our study reports for the first time the presence in the Tunisian community of two clones of E. coli, including the virulent clone ST131-C2 harboring both CTX-M-15 and CTX-M-27, and confirms the spread of the emergent clone ST131-C1-M-27, notably in community urinary tract infections.
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Affiliation(s)
- Amel Mhaya
- University of Bordeaux, Department of Biological and Medical Sciences, UMR CNRS 5234, 146 Rue Léo Saignat, 33076 Bordeaux, France
- Centre of Biotechnology of Sfax, Laboratory of Biopesticides, Road of Sidi Mansour Km 6, 3018 Sfax, Tunisia
| | - Rahma Trabelsi
- University of Sfax, Department of Life Science, Research Laboratory of Environmental Toxicology-Microbiology and Health, Road of Soukra Km 3.5, 3000 Sfax, Tunisia
| | - Sabine Aillerie
- University of Bordeaux, Department of Biological and Medical Sciences, UMR CNRS 5234, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Fatima M’Zali
- University of Bordeaux, Aquitaine Microbiologie, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Dominique Bégu
- University of Bordeaux, Department of Biological and Medical Sciences, UMR CNRS 5234, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Slim Tounsi
- Centre of Biotechnology of Sfax, Laboratory of Biopesticides, Road of Sidi Mansour Km 6, 3018 Sfax, Tunisia
| | - Radhouane Gdoura
- University of Sfax, Department of Life Science, Research Laboratory of Environmental Toxicology-Microbiology and Health, Road of Soukra Km 3.5, 3000 Sfax, Tunisia
| | - Corinne Arpin
- University of Bordeaux, Department of Biological and Medical Sciences, UMR CNRS 5234, 146 Rue Léo Saignat, 33076 Bordeaux, France
- Correspondence:
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Sekizuka T, Tanaka R, Hashino M, Yatsu K, Kuroda M. Comprehensive Genome and Plasmidome Analysis of Antimicrobial Resistant Bacteria in Wastewater Treatment Plant Effluent of Tokyo. Antibiotics (Basel) 2022; 11:antibiotics11101283. [PMID: 36289941 PMCID: PMC9598598 DOI: 10.3390/antibiotics11101283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/16/2022] [Accepted: 09/16/2022] [Indexed: 01/01/2023] Open
Abstract
To characterize environmental antimicrobial resistance (AMR) in urban areas, extended-spectrum β-lactamase- (ESBL)/carbapenemase-producing bacteria (EPB/CPB, respectively) from urban wastewater treatment plant effluents in Tokyo were isolated on CHROMagar ESBL plate. Complete genome sequence analysis, including plasmids, indicated that 126 CTX-M-positive isolates (31%) were identified among the 404 obtained isolates. The CTX-M-9 group was predominant (n = 65, 52%), followed by the CTX-M-1 group (n = 44, 35%). Comparative genome analysis revealed that CTX-M-27-positive E. coli O16:H5-ST131-fimH41 exhibited a stable genome structure and clonal-global dissemination. Plasmidome network analysis revealed that 304 complete plasmid sequences among 85 isolates were grouped into 14 incompatibility (Inc) network communities (Co1 to Co14). Co10 consisted of primarily IncFIA/IncFIB plasmids harboring blaCTX-M in E. coli, whereas Co12 consisted primarily of IncFIA(HI1)/Inc FIB(K) plasmids harboring blaCTX-M, blaKPC, and blaGES in Klebsiella spp. Co11 was markedly located around Co10 and Co12. Co11 exhibited blaCTX-M, blaKPC, and blaNDM, and was mainly detected in E. coli and Klebsiella spp. from human and animal sources, suggesting a mutual role of Co11 in horizontal gene transfer between E. coli and Klebsiella spp. This comprehensive resistome analysis uncovers the mode of relational transfer among bacterial species, highlighting the potential source of AMR burden on public health in urban communities.
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Azuma T, Uchiyama T, Zhang D, Usui M, Hayashi T. Distribution and characteristics of carbapenem-resistant and extended-spectrum β-lactamase (ESBL) producing Escherichia coli in hospital effluents, sewage treatment plants, and river water in an urban area of Japan. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 839:156232. [PMID: 35623520 DOI: 10.1016/j.scitotenv.2022.156232] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/21/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
Occurrence of profiles of the carbapenem-resistant Escherichia coli (CRE-E) and extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-E) in an urban river in a sub-catchment of the Yodo River Basin, one of the representative water systems of Japan was investigated. We conducted seasonal and year-round surveys for the antimicrobial-resistant bacteria (AMRB) and antimicrobial-resistance genes (AMRGs) in hospital effluents, sewage treatment plant (STP) wastewater, and river water; subsequently, contributions to wastewater discharge into the rivers were estimated by analyses based on the mass flux. Furthermore, the characteristics of AMRB in the water samples were evaluated on the basis of antimicrobial susceptibility tests. CRE-E and ESBL-E were detected in all water samples with mean values 11 and 1900 CFU/mL in the hospital effluent, 58 and 4550 CFU/mL in the STP influent, not detected to 1 CFU/mL in the STP effluent, and 1 and 1 CFU/mL in the STP discharge into the river, respectively. Contributions of the pollution load derived from the STP effluent discharged into the river water were 1 to 21%. The resistome profiles for blaIMP, blaTEM, and blaCTX-M genes in each water sample showed that AMRGs were not completely removed in the wastewater treatment process in the STP, and the relative abundances of blaIMP, blaTEM, and blaCTX-M genes were almost similar (P<0.05). Susceptibility testing of antimicrobial-resistant E. coli isolates showed that CRE-E and ESBL-E detected in wastewaters and river water were linked to the prevalence of AMRB in clinical settings. These results suggest the importance of conducting environmental risk management of AMRB and AMRGs in the river environment. To our knowledge, this is the first detailed study that links the medical environment to CRE-E and ESBL-E for evaluating the AMRB and AMRGs in hospital effluents, STP wastewater, and river water at the basin scale on the basis of mass flux as well as the contributions of CRE-E and ESBL-E to wastewater discharge into the river.
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Affiliation(s)
- Takashi Azuma
- Department of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
| | - Tomoharu Uchiyama
- Food Microbiology and Food Safety, Department of Health and Environmental Sciences, School of Veterinary Medicine, Rakuno Gakuen University, 582 Midorimachi, Bunkyodai, Ebetsu, Hokkaido 069-8501, Japan
| | - Dongsheng Zhang
- Food Microbiology and Food Safety, Department of Health and Environmental Sciences, School of Veterinary Medicine, Rakuno Gakuen University, 582 Midorimachi, Bunkyodai, Ebetsu, Hokkaido 069-8501, Japan
| | - Masaru Usui
- Food Microbiology and Food Safety, Department of Health and Environmental Sciences, School of Veterinary Medicine, Rakuno Gakuen University, 582 Midorimachi, Bunkyodai, Ebetsu, Hokkaido 069-8501, Japan
| | - Tetsuya Hayashi
- Department of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan; Faculty of Human Development, Department of Food and Nutrition Management Studies, Soai University, 4-4-1 Nankonaka, Osaka Suminoeku, Osaka 559-0033, Japan
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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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Comparison of the Treatment Outcome of Piperacillin-Tazobactam versus Carbapenems for Patients with Bacteremia Caused by Extended-Spectrum β-Lactamase-Producing Escherichia coli in Areas with Low Frequency of Coproduction of OXA-1: a Preliminary Analysis. Microbiol Spectr 2022; 10:e0220622. [PMID: 35916524 PMCID: PMC9430612 DOI: 10.1128/spectrum.02206-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although piperacillin-tazobactam (TZP) was shown to be less effective than carbapenems in treating bacteremia due to extended-spectrum β-lactamase-producing (ESBL)-producing organisms in a randomized controlled trial, the fact that many of the causative organisms co-produced inhibitor-resistant OXA-1 along with ESBLs may have influenced the results. In this study, we compared the therapeutic effectiveness of TZP and carbapenem in treating ESBL-producing Escherichia coli bacteremia in areas with low frequency of OXA-1 co-production. Forty patients, 14 in the TZP treatment group and 26 in the carbapenem treatment group, were included in the analysis. There were no significant differences in patient background between the two groups. Urinary tract infection or cholangitis was the source of bacteremia in 26 patients (65%), and the Pitt bacteremia score was zero or one in 35 patients (87.5%). Only four (11.4%) of the 35 causative isolates available for microbiological analysis harbored blaOXA-1, and only three (8.6%) were non-susceptible to TZP. Seventeen (48.6%) isolates carried blaCTX-M-27, none of which carried other β-lactamase genes. No significant difference in the frequency of treatment failure on day 14 of bacteremia was documented between the TZP and carbapenem treatment groups in both the crude analysis and the inverse probability of treatment weighting-adjusted analysis. This study demonstrates that TZP may be a treatment option for non-severe cases of ESBL-producing E. coli bacteremia in areas with low frequency of OXA-1 co-production. IMPORTANCE Although carbapenems are considered the drug of choice for severe infections caused by extended-spectrum β-lactamase-producing (ESBL)-producing organisms, other therapeutic options are being explored to avoid increasing the selective pressure for carbapenem-resistant organisms. In this study, it was suggested that piperacillin-tazobactam may be as effective as carbapenems for the treatment of mild bacteremia caused by ESBL-producing Escherichia coli in areas where OXA-1 co-production by ESBL-producing E. coli is rare. The genetic background of each regional epidemic clone differs even among multidrug-resistant bacteria classified under the same name (e.g., ESBL-producing organisms), resulting in possible differences in the efficacy of therapeutic agents. Exploration of treatment options for multidrug-resistant organisms according to local epidemiology is worthwhile from the perspective of antimicrobial stewardship.
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Perestrelo S, Correia Carreira G, Valentin L, Fischer J, Pfeifer Y, Werner G, Schmiedel J, Falgenhauer L, Imirzalioglu C, Chakraborty T, Käsbohrer A. Comparison of approaches for source attribution of ESBL-producing Escherichia coli in Germany. PLoS One 2022; 17:e0271317. [PMID: 35839265 PMCID: PMC9286285 DOI: 10.1371/journal.pone.0271317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 06/28/2022] [Indexed: 11/19/2022] Open
Abstract
Extended-spectrum beta-lactamase (ESBL)-producing Escherichia (E.) coli have been widely described as the cause of treatment failures in humans around the world. The origin of human infections with these microorganisms is discussed controversially and in most cases hard to identify. Since they pose a relevant risk to human health, it becomes crucial to understand their sources and the transmission pathways. In this study, we analyzed data from different studies in Germany and grouped ESBL-producing E. coli from different sources and human cases into subtypes based on their phenotypic and genotypic characteristics (ESBL-genotype, E. coli phylogenetic group and phenotypic antimicrobial resistance pattern). Then, a source attribution model was developed in order to attribute the human cases to the considered sources. The sources were from different animal species (cattle, pig, chicken, dog and horse) and also from patients with nosocomial infections. The human isolates were gathered from community cases which showed to be colonized with ESBL-producing E. coli. We used the attribution model first with only the animal sources (Approach A) and then additionally with the nosocomial infections (Approach B). We observed that all sources contributed to the human cases, nevertheless, isolates from nosocomial infections were more related to those from human cases than any of the other sources. We identified subtypes that were only detected in the considered animal species and others that were observed only in the human population. Some subtypes from the human cases could not be allocated to any of the sources from this study and were attributed to an unknown source. Our study emphasizes the importance of human-to-human transmission of ESBL-producing E. coli and the different role that pets, livestock and healthcare facilities may play in the transmission of these resistant bacteria. The developed source attribution model can be further used to monitor future trends. A One Health approach is necessary to develop source attribution models further to integrate also wildlife, environmental as well as food sources in addition to human and animal data.
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Affiliation(s)
- Sara Perestrelo
- Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
- * E-mail:
| | | | - Lars Valentin
- Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jennie Fischer
- Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Yvonne Pfeifer
- Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Guido Werner
- Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Judith Schmiedel
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Campus Giessen, Giessen, Germany
- Hessisches universitäres Kompetenzzentrum Krankenhaushygiene (HuKKH), Giessen, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Campus Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Campus Giessen, Giessen, Germany
| | - Annemarie Käsbohrer
- Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
- Veterinary Public Health and Epidemiology, University of Veterinary Medicine, Vienna, Austria
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Yoon EJ, Choi YJ, Kim D, Won D, Choi JR, Jeong SH. Amplification of the Chromosomal blaCTX-M-14 Gene in Escherichia coli Expanding the Spectrum of Resistance under Antimicrobial Pressure. Microbiol Spectr 2022; 10:e0031922. [PMID: 35467393 PMCID: PMC9241692 DOI: 10.1128/spectrum.00319-22] [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: 01/28/2022] [Accepted: 04/11/2022] [Indexed: 11/20/2022] Open
Abstract
Various forms of adaptive evolution occur in clinical isolates in response to the presence of antimicrobial drugs. Among a total of 171 CTX-M-9 group/family extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli blood isolates recovered between 2016 and 2017 in six general hospitals, 50.3% of the isolates possessed the blaCTX-M-14-like gene in their chromosome rather than in a plasmid. Focusing on this unprecedented way of the blaCTX-M ESBL gene possession, molecular epidemiology of the isolates was assessed and the chromosomal location of the acquired cephalosporinase gene was dissected in an evolutionary point of view. Taking advantage of a complete collection of E. coli blood isolates from a limited period, clonal relatedness of the E. coli isolates carrying the blaCTX-M-14-like gene was clarified and the dominant clone, ST131 H30R, was identified. To control the level of resistance and the resistance spectrum to oxyimino-cephalosporin drugs, transcription level of the blaCTX-M-14-like gene was tuned finely through positioning the gene near the chromosomal initiation dnaA gene and amplifying numbers of the gene in a chromosome using either the copy-and-paste or the tandem amplification methods. Inconspicuous fitness cost by chromosomal location of the gene and free adjustment of the oxyimino-cephalosporin resistance would urge the dominancy of E. coli clinical isolates harboring the blaCTX-M ESBL gene in their chromosome. IMPORTANCE Increasing prevalence of E. coli producing CTX-M ESBL is a major concern in clinical settings because it significantly limits treatment options. Thus, it is important to keep watching current molecular mechanisms of resistance and the scheme for dissemination. Recently, chromosomal locations of the blaCTX-M genes are often documented in clinical settings and the bacterial strategies were needed to be dissected in an evolutionary point of view. Both main mechanisms of fine tuning the chromosomal gene expression, bacterial gene amplification either by copy-and-paste or by tandem amplification and positioning the gene near the chromosomal initiation dnaA gene, were demonstrated in the study, and the fitness cost by the chromosomal location was evaluated.
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Affiliation(s)
- Eun-Jeong Yoon
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
- Division of Antimicrobial Resistance Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, South Korea
| | - You Jeong Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Dokyun Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Dongju Won
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
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33
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Johnston BD, Gordon DM, Burn S, Johnson TJ, Weber BP, Miller EA, Johnson JR. Novel Multiplex PCR Method and Genome Sequence-Based Analog for High-Resolution Subclonal Assignment and Characterization of Escherichia coli Sequence Type 131 Isolates. Microbiol Spectr 2022; 10:e0106422. [PMID: 35604132 PMCID: PMC9241916 DOI: 10.1128/spectrum.01064-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/30/2022] [Indexed: 12/01/2022] Open
Abstract
Escherichia coli sequence type 131 (ST131) is a pandemic, multidrug-resistant extraintestinal pathogen. The multiple distinctive ST131 subclones differ for rfb and fliC alleles (O and H antigens), fimH allele (type-1 fimbriae adhesin), resistance phenotype and genotype, clinical correlates, and host predilection. Current PCR assays for detecting ST131 and its main subclones offer limited sub-ST characterization. Here we combined 22 novel and 14 published primers for a multiplex PCR assay to detect and extensively characterize ST131 isolates. The primers target mdh36, gyrB47, trpA72, sbmA, plsB, nupC, rmuC, kefC, ybbW, the O16 and O25b rfb variants, five fimH alleles (fimH22, fimH27, fimH30, fimH35, and fimH41), two fliC alleles (H4 and H5), a (subclone-specific) fluoroquinolone resistance-associated parC allele, and a (subclone-specific) prophage marker. The resulting amplicons resolve 15 molecular subsets within ST131, including 3 within clade A (H41 subclone), 5 within clade B (H22 subclone), and 7 within clade C (H30 subclone), which includes subclones C0 (H30S: 2 subsets), C1 and C1-M27 (H30R1: 2 subsets), and C2 (H30Rx: 3 subsets). Validation in three laboratories showed that this assay provides a rapid, accurate, and portable method for rapidly detecting and characterizing E. coli ST131 and its key subsets. Additionally, for users with whole genome sequencing (WGS) capability, we developed a command-line executable called ST131Typer, an in silico version of the extended multiplex PCR assay. Its accuracy was 87.8%, with most issues due to incomplete or fragmented input genome assemblies. These two novel assays should facilitate detailed ST131 subtyping using either endpoint PCR or WGS. IMPORTANCE These novel assays provide greater subclonal resolution and characterization of E. coli ST131 isolates than do the available comparable PCR assays, plus offer a novel sequence-based alternative to PCR. They may prove useful for molecular epidemiological studies, surveillance, and, potentially, clinical management.
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Affiliation(s)
- Brian D. Johnston
- Minneapolis VA Health Care System, Minneapolis, Minnesota, USA
- University of Minnesota, Minneapolis, Minnesota, USA
| | - David M. Gordon
- Research School of Biology, The Australian National University Australia, Canberra, Australian Capital Territory, Australia
| | - Samantha Burn
- Research School of Biology, The Australian National University Australia, Canberra, Australian Capital Territory, Australia
| | - Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Bonnie P. Weber
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Elizabeth A. Miller
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - James R. Johnson
- Minneapolis VA Health Care System, Minneapolis, Minnesota, USA
- University of Minnesota, Minneapolis, Minnesota, USA
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Lopes R, Furlan JPR, Rodrigues Dos Santos LD, Stehling EG. Detection of CTX-M-27-positive endophytic Escherichia coli ST131 lineage C1/H30R subclade carrying bla KPC-2 on an IncX3-IncU plasmid in a fresh vegetable. J Glob Antimicrob Resist 2022; 30:178-179. [PMID: 35738387 DOI: 10.1016/j.jgar.2022.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/20/2022] [Accepted: 06/14/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Ralf Lopes
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brasil
| | - João Pedro Rueda Furlan
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brasil
| | - Lucas David Rodrigues Dos Santos
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brasil
| | - Eliana Guedes Stehling
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brasil.
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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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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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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: 23] [Impact Index Per Article: 11.5] [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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Sallem N, Hammami A, Mnif B. Trends in human intestinal carriage of ESBL- and carbapenemase-producing Enterobacterales among food handlers in Tunisia: emergence of C1-M27-ST131 subclades, blaOXA-48 and blaNDM. J Antimicrob Chemother 2022; 77:2142-2152. [PMID: 35640660 DOI: 10.1093/jac/dkac167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/06/2022] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVES To determine the prevalence of community intestinal carriage of ESBL-producing Enterobacterales (ESBL-E), acquired-AmpC-producing Enterobacterales (aAmpC-E) and carbapenemase-producing Enterobacterales (CPE) in Tunisia. METHODS From November 2012 to September 2017, stool samples from food handlers in Sfax, Tunisia, were screened for ESBL-E, AmpC-E and CPE using antibiotic-containing media. The genes encoding these β-lactamases were characterized by PCR, sequencing, and transfer assays. ST131 clonal groups were detected by PCR and characterized for antibiotic resistance, virulence genes and PFGE patterns. RESULTS Of 2135 participants, ESBL-E, aAmpC-E, and CPE carriage were detected in 419 (19.63%), 35 (1.63%) and 7 (0.33%) participants, respectively. CTX-M-15 (60%), CTX-M-1 (16.8%) and CTX-M-27 (12.8%) were the most common ESBL determinants. The ESBL-E carriage was significantly higher in summer (33%) and autumn (25.7%) than in winter (12.1%) and spring (11.4%). ST131 was detected in 50 (13.2%) of the 378 ESBL-producing Escherichia coli isolates; most of them (35; 70%) belonged to subclade C1 (cluster C1-M27: 23 isolates, 46%; cluster C1-non-M27: 12 isolates, 24%) followed by those belonging to subclade C2 (11; 22%). Although subclade C2 isolates, all harbouring blaCTX-M-15, had the highest resistance rates and virulence factor and addiction system scores, the subclade C1 isolates, mainly harbouring blaCTX-M-27 (94%), were predominant since 2015. The most frequently detected carbapenemase-encoding gene was blaOXA-48-like (85%) and acquired AmpC-encoding genes were blaDHA-1 (54%) and blaCMY-2 (46%). CONCLUSIONS This is the first large Tunisian study to reveal a high faecal ESBL carriage rate, a low CPE carriage rate, and the predominance of CTX-M-27-producing subclade C1 among faecal ESBL-ST131 isolates in the Tunisian community.
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Affiliation(s)
- Nesrine Sallem
- Habib Bourguiba University Hospital, Research Laboratory Microorganisms and Human Disease, University of Sfax, Route El Ain Km 0.5, 3029, Sfax, Tunisia
| | - Adnene Hammami
- Habib Bourguiba University Hospital, Research Laboratory Microorganisms and Human Disease, University of Sfax, Route El Ain Km 0.5, 3029, Sfax, Tunisia.,Faculty of Medicine Sfax, Laboratory of Microbiology, University of Sfax, Avenue Majida Boulila, 3027, Sfax, Tunisia
| | - Basma Mnif
- Habib Bourguiba University Hospital, Research Laboratory Microorganisms and Human Disease, University of Sfax, Route El Ain Km 0.5, 3029, Sfax, Tunisia.,Faculty of Medicine Sfax, Laboratory of Microbiology, University of Sfax, Avenue Majida Boulila, 3027, Sfax, Tunisia
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Porter SB, Johnston BD, Kisiela D, Clabots C, Sokurenko EV, Johnson JR. Bacteriophage Cocktail and Microcin-Producing Probiotic Escherichia coli Protect Mice Against Gut Colonization With Multidrug-Resistant Escherichia coli Sequence Type 131. Front Microbiol 2022; 13:887799. [PMID: 35547133 PMCID: PMC9082999 DOI: 10.3389/fmicb.2022.887799] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/06/2022] [Indexed: 11/24/2022] Open
Abstract
Non-antibiotic measures are needed to reduce the rate of infections due to multidrug-resistant organisms (MDROs), including by eliminating the commensal reservoir that underlies such strains’ dissemination and leads to recurrent infections. Here, we tested a cocktail of pre-selected bacteriophages and an engineered microcin C7-producing probiotic Escherichia coli Nissle-1917 strain for their ability to reduce gut colonization by an E. coli strain from sequence type 131 (ST131)-H30R, which is the major clonal group of MDROs among extraintestinal clinical E. coli isolates. Although the bacteriophage cocktail was highly effective against ST131-H30R strains both in vitro and in a murine model of subcutaneous sepsis, it was only weakly and transiently effective against gut colonization by the target ST131-H30R strain (0.5 log10 decrease on d + 1: p < 0.001; no significant effect on d + 4 and beyond). The probiotic strain, while also highly active against ST131-H30R in vitro, was ineffective against ST131-H30R gut colonization despite its abundant presence in feces. Nonetheless, despite failing as decolonizing agents when administered separately, when co-administered the bacteriophage cocktail and probiotic strain exhibited striking synergy against ST131-H30R gut colonization. This combinatory effect was most pronounced on d + 1 (3.3 log10 target strain decrease: p < 0.001), and persisted until d + 7 (0.5 log10 decrease; p < 0.02.). Although by d + 10 the ST131-H30R load was fully restored, these findings provide proof of concept for combined bacteriophage-plus-probiotic administration to reduce or, possibly, to prevent gut colonization with MDROs in high-risk individuals.
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Affiliation(s)
- Stephen B Porter
- Minneapolis VA Health Care System, Veterans Health Administration, United States Department of Veterans Affairs, Minneapolis, MN, United States
| | - Brian D Johnston
- Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Dagmara Kisiela
- Department of Microbiology, University of Washington, Seattle, WA, United States
| | - Connie Clabots
- Minneapolis VA Health Care System, Veterans Health Administration, United States Department of Veterans Affairs, Minneapolis, MN, United States
| | - Evgeni V Sokurenko
- Department of Microbiology, University of Washington, Seattle, WA, United States
| | - James R Johnson
- Minneapolis VA Health Care System, Veterans Health Administration, United States Department of Veterans Affairs, Minneapolis, MN, United States.,Department of Medicine, University of Minnesota, Minneapolis, MN, United States
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Belas A, Marques C, Menezes J, da Gama LT, Cavaco-Silva P, Pomba C. ESBL/ pAmpC-Producing Escherichia coli Causing Urinary Tract Infections in Non-Related Companion Animals and Humans. Antibiotics (Basel) 2022; 11:antibiotics11050559. [PMID: 35625203 PMCID: PMC9137695 DOI: 10.3390/antibiotics11050559] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 11/29/2022] Open
Abstract
Urinary tract infections (UTI) caused by Escherichia coli are frequently diagnosed in humans and companion animals. Extended-spectrum beta-lactamase (ESBL)- and cephalosporinase (pAmpC)-producing Escherichia coli are worldwide-disseminated and frequently multidrug-resistant, hence leading to treatment failure and public health concerns. This study aimed to characterize and compare ESBL/pAmpC-producing E. coli strains causing community-acquired UTI in companion animals and non-related humans. Third-generation cephalosporin (3GC)-resistant E. coli (companion animals n = 35; humans n = 85) isolated from patients with UTI were tested against 14 antimicrobials following CLSI guidelines. PCR-based assays were used to detect the major E. coli phylogenetic groups, pathogenicity associated-islands (PAIs), virulence genes, and ESBLs/pAmpC resistance genes. ESBL/pAmpC-producing E. coli isolates were typed by multi-locus sequence typing (MLST) and PCR. E. coli strains from companion animals and humans shared two MDR high-risk clonal lineages: ST131 and ST648. To the best of our knowledge, this study reports the first description of E. coli ST131 clade C1-M27 and the clonal lineage ST131 clade A in humans with community-acquired UTI in Portugal. Considering that companion animals with UTI are generally treated at home by the owners, measures should be implemented to avoid the spread of multidrug-resistant high-risk clones to humans and their household environment.
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Affiliation(s)
- Adriana Belas
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal or (A.B.); or (C.M.); (J.M.); (L.T.d.G.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
- Faculty of Veterinary Medicine, Lusófona University, 1749-024 Lisbon, Portugal
| | - Cátia Marques
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal or (A.B.); or (C.M.); (J.M.); (L.T.d.G.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
- Faculty of Veterinary Medicine, Lusófona University, 1749-024 Lisbon, Portugal
| | - Juliana Menezes
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal or (A.B.); or (C.M.); (J.M.); (L.T.d.G.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Luís Telo da Gama
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal or (A.B.); or (C.M.); (J.M.); (L.T.d.G.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Patrícia Cavaco-Silva
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, 2829-511 Caparica, Portugal;
- Technophage, 1649-028 Lisboa, Portugal
| | - Constança Pomba
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal or (A.B.); or (C.M.); (J.M.); (L.T.d.G.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
- Correspondence:
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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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Tóth K, Tóth Á, Kamotsay K, Németh V, Szabó D. Population snapshot of the extended-spectrum β-lactamase-producing Escherichia coli invasive strains isolated from a Hungarian hospital. Ann Clin Microbiol Antimicrob 2022; 21:3. [PMID: 35144632 PMCID: PMC8829994 DOI: 10.1186/s12941-022-00493-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 01/12/2022] [Indexed: 11/25/2022] Open
Abstract
Background This study was carried out to determine the prevalence and the genetic background of extended-spectrum β-lactamase-producing Escherichia coli invasive isolates obtained from a tertiary-care hospital in Budapest, Hungary. Methods Between October–November 2018, all invasive ESBL-producing E. coli isolates were collected from Central Hospital of Southern Pest. The antimicrobial susceptibility testing was performed according to the EUCAST guidelines. The possible clonal relationships were investigated by core genome (cg)MLST (SeqSphere +) using whole-genome sequencing (WGS) data of isolates obtained from Illumina 251-bp paired-end sequencing. From WGS data acquired antimicrobial resistance genes, virulence genes and replicon types were retrieved using ResFinder3.1, PlasmidFinder2.1, pMLST-2.0, VirulenceFinder2.0 and Virulence Factors Database online tools. Results Overall, six E. coli isolates proved to be resistant to third-generation cephalosporins and ESBL-producers in the study period. Full genome sequence analysis showed that five E. coli isolates belonged to the ST131 clone: two to C1-M27 subclade with blaCTX-M-27 and three to C2/H30Rx subclade with blaCTX-M-15. One isolate belonged to ST1193 with blaCTX-M-27. According to cgMLST, all C2/H30Rx isolates formed a cluster (≤ 6 allele differences), while the blaCTX-M-27-producing C1-M27 isolates differed at least 35 alleles from each other. Both C2/H30Rx and C1-M27 ST131 isolates harbored similar antimicrobial resistance gene sets. However, only C2/H30Rx isolates had the qnrB and aac(3)-IIa. The isolates carried similar extraintestinal virulence gene set but differed in some genes encoding siderophores, protectins and toxins. Moreover, only one C2/H30Rx isolate carried salmochelin siderophore system and showed virotype B. All isolates showed resistance against ceftriaxone, cefotaxime, and ciprofloxacin, and the C2/H30Rx isolates were also resistant to gentamicin, tobramycin, and ceftazidime. Conclusions Out of six ESBL-producing E. coli, five belonged to the ST131 clone. This study indicates, that the C2/H30Rx and C1-M27 subclades of the ST131 appear to be the dominant clones collected in a Hungarian hospital.
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Affiliation(s)
- Kinga Tóth
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary. .,Department of Bacteriology, Mycology, and Parasitology, National Public Health Center, Budapest, Hungary.
| | - Ákos Tóth
- Department of Bacteriology, Mycology, and Parasitology, National Public Health Center, Budapest, Hungary
| | - Katalin Kamotsay
- Central Microbiology Laboratory, Central Hospital of Southern Pest National Institute of Hematology and Infectious Disease, Budapest, Hungary
| | - Viktória Németh
- Central Microbiology Laboratory, Central Hospital of Southern Pest National Institute of Hematology and Infectious Disease, Budapest, Hungary
| | - Dóra Szabó
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
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Resistome and Virulome of Multi-Drug Resistant E. coli ST131 Isolated from Residents of Long-Term Care Facilities in the Northern Italian Region. Diagnostics (Basel) 2022; 12:diagnostics12010213. [PMID: 35054380 PMCID: PMC8774598 DOI: 10.3390/diagnostics12010213] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/04/2022] [Accepted: 01/12/2022] [Indexed: 11/17/2022] Open
Abstract
Long-term care facilities (LTCFs) are important reservoirs of antimicrobial-resistant (AMR) bacteria which colonize patients transferred from the hospital, or they may emerge in the facility as a result of mutation or gene transfer. In the present study, we characterized, from a molecular point of view, 43 E. coli strains collected from residents of LTCFs in Northern Italy. The most common lineage found was ST131, followed by sporadic presence of ST12, ST69, ST48, ST95, ST410 and ST1193. All strains were incubators of several virulence factors, with iss, sat, iha and senB being found in 84%, 72%, 63% and 51% of E. coli, respectively. Thirty of the ST131 analyzed were of the O25b:H4 serotype and H30 subclone. The ST131 isolates were found to be mainly associated with IncF plasmids, CTX-M-1, CTX-M-3, CTX-M-15, CTX-M-27 and gyrA/parC/parE mutations. Metallo-β-lactamases were not found in ST131, whereas KPC-3 carbapenemase was found only in two ST131 and one ST1193. In conclusion, we confirmed the spread of extended-spectrum β-lactamase genes in E. coli ST131 isolated from colonized residents living inside LTCFs. The ST131 represents an incubator of fluoroquinolones, aminoglycosides and other antibiotic resistance genes in addition to different virulence factors.
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44
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Nagy BJ, Balázs B, Benmazouz I, Gyüre P, Kövér L, Kaszab E, Bali K, Lovas-Kiss Á, Damjanova I, Majoros L, Tóth Á, Bányai K, Kardos G. Comparison of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolates From Rooks (Corvus frugilegus) and Contemporary Human-Derived Strains: A One Health Perspective. Front Microbiol 2022; 12:785411. [PMID: 35095799 PMCID: PMC8792927 DOI: 10.3389/fmicb.2021.785411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/09/2021] [Indexed: 12/14/2022] Open
Abstract
During winter, a large number of rooks gather and defecate at the park of a university clinic. We investigated the prevalence of extended-spectrum beta-lactamase (ESBL)–producing Escherichia coli in these birds and compared recovered isolates with contemporary human isolates. In 2016, fecal samples were collected from 112 trap-captured rooks and investigated for presence of ESBL producers using eosin methylene blue agar supplemented by 2 mg/L cefotaxime; 2,455 contemporary human fecal samples of patients of the clinics sent for routine culturing were tested similarly. In addition, 42 ESBL-producing E. coli isolates collected during the same period from inpatients were also studied. ESBL genes were sought for by PCR and were characterized by sequencing; E. coli ST131 clones were identified. Epidemiological relatedness was determined by pulsed-field gel electrophoresis and confirmed using whole genome sequencing in selected cases. Thirty-seven (33%) of sampled rooks and 42 (1.7%) of human stools yielded ESBL-producing E coli. Dominant genes were blaCTX–M–55 and blaCTX–M–27 in corvid, blaCTX–M–15 and blaCTX–M–27 in human isolates. ST162 was common among rooks. Two rook-derived E. coli belonged to ST131 C1-M27, which was also predominant (10/42) among human fecal and (15/42) human clinical isolates. Another potential link between rooks and humans was a single ST744 rook isolate grouped with one human fecal and three clinical isolates. Despite possible contact, genotypes shared between rooks and humans were rare. Thus, rooks are important as long-distance vectors and reservoirs of ESBL-producing E. coli rather than direct sources of infections to humans in our setting.
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Affiliation(s)
- Bálint József Nagy
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Pharmaceutical Sciences, University of Debrecen, Debrecen, Hungary
| | - Bence Balázs
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Pharmaceutical Sciences, University of Debrecen, Debrecen, Hungary
| | - Isma Benmazouz
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Department of Nature Conservation, Zoology and Game Management, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Péter Gyüre
- Department of Nature Conservation, Zoology and Game Management, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - László Kövér
- Department of Nature Conservation, Zoology and Game Management, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Eszter Kaszab
- Institute for Veterinary Medical Research, Budapest, Hungary
| | - Krisztina Bali
- Institute for Veterinary Medical Research, Budapest, Hungary
| | - Ádám Lovas-Kiss
- Department for Tisza River Research, Centre for Ecological Research–DRI, Hungarian Academy of Sciences, Budapest, Hungary
| | | | - László Majoros
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Ákos Tóth
- National Public Health Center, Budapest, Hungary
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine Budapest, Budapest, Hungary
| | - Gábor Kardos
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine Budapest, Budapest, Hungary
- *Correspondence: Gábor Kardos,
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45
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Kurittu P, Khakipoor B, Jalava J, Karhukorpi J, Heikinheimo A. Whole-Genome Sequencing of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli From Human Infections in Finland Revealed Isolates Belonging to Internationally Successful ST131-C1-M27 Subclade but Distinct From Non-human Sources. Front Microbiol 2022; 12:789280. [PMID: 35058905 PMCID: PMC8764355 DOI: 10.3389/fmicb.2021.789280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/10/2021] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance (AMR) is a growing concern in public health, particularly for the clinically relevant extended-spectrum beta-lactamase (ESBL) and AmpC-producing Enterobacteriaceae. Studies describing ESBL-producing Escherichia coli clinical samples from Finland to the genomic level and investigation of possible zoonotic transmission routes are scarce. This study characterizes ESBL-producing E. coli from clinical samples in Finland using whole genome sequencing (WGS). Comparison is made between animal, food, and environmental sources in Finland to gain insight into potential zoonotic transmission routes and to recognize successful AMR genes, bacterial sequence types (STs), and plasmids. ESBL-producing E. coli isolates (n = 30) obtained from the Eastern Finland healthcare district between 2018 and 2020 underwent WGS and were compared to sequences from non-human and healthy human sources (n = 67) isolated in Finland between 2012 and 2018. A majority of the clinical isolates belonged to ST131 (n = 21; 70%), of which 19 represented O25:H4 and fimH30 allele, and 2 O16:H5 and fimH41 allele. Multidrug resistance was common, and the most common bla gene identified was bla CTX-M-27 (n = 14; 47%) followed by bla CTX-M-15 (n = 10; 33%). bla CTX-M-27 was identified in 13 out of 21 isolates representing ST131, with 12 isolates belonging to a recently discovered international E. coli ST131 C1-M27 subclade. Isolates were found to be genetically distinct from non-human sources with core genome multilocus sequence typing based analysis. Most isolates (n = 26; 87%) possessed multiple replicons, with IncF family plasmids appearing in 27 (90%) and IncI1 in 5 (17%) isolates. IncF[F1:A2:B20] replicon was identified in 11, and IncF[F-:A2:B20] in 4 isolates. The results indicate the ST131-C1-M27 clade gaining prevalence in Europe and provide further evidence of the concerning spread of this globally successful pathogenic clonal group. This study is the first to describe ESBL-producing E. coli in human infections with WGS in Finland and provides important information on global level of the spread of ESBL-producing E. coli belonging to the C1-M27 subclade. The results will help guide public health actions and guide future research.
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Affiliation(s)
- Paula Kurittu
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Banafsheh Khakipoor
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Jari Jalava
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Jari Karhukorpi
- Eastern Finland Laboratory Centre Joint Authority Enterprise (ISLAB), Joensuu, Finland
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Finnish Food Authority, Seinäjoki, Finland
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46
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Masui T, Nakano R, Nakano A, Saito K, Suzuki Y, Kakuta N, Horiuchi S, Tsubaki K, Kitahara T, Yano H. Predominance of CTX-M-9 Group Among ESBL-Producing Escherichia coli Isolated from Healthy Individuals in Japan. Microb Drug Resist 2022; 28:355-360. [PMID: 34990283 DOI: 10.1089/mdr.2021.0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The detection rate of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales, microorganisms associated with health care settings, has significantly increased worldwide. Moreover, their community incidence has increased in several countries. In this study, we investigated the prevalence and genetic diversity of ESBL-producing Escherichia coli isolated from 547 nonduplicated stool specimens from healthy Japanese individuals, between 2015 and 2019. E. coli were isolated on deoxycholate-hydrogen sulfide-lactose (DHL) agar and identified by MALDI-TOF MS, ESBL were screened through disk diffusion method (cefotaxime with or without clavulanate), and genetic detection and genotyping were performed by PCR and DNA sequencing. Clonal similarities between ESBL-producing and nonproducing isolates were assessed by multilocus sequence typing (MLST). The prevalence of ESBL-producing E. coli was 9.7% (53/547). These bacteria harbored CTX-M genes, from which CTX-M-9 (31/53, 58.5%) and CTX-M-1 (13/53, 24.5%) groups were the predominant. The MLST analysis revealed that ST131 genotype prevailed within ESBL-producing E. coli (15/53), whereas ST95 (10/53) and ST73 (8/53) prevailed among non-ESBL producers, with ST131 being present in only four isolates. Overall, a high prevalence rate of CTX-M-type ESBL-producing E. coli was detected. CTX-M-9 group-producing ST131 predominated among healthy Japanese individuals, similar to that observed in hospital isolates. CTX-M-type ESBL may disseminate clonally among hospital patients and subsequently, within the community.
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Affiliation(s)
- Takashi Masui
- Department of Otolaryngology-Head and Neck Surgery, Nara Medical University, Kashihara, Japan.,Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Ryuichi Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Akiyo Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Kai Saito
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Yuki Suzuki
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Naoki Kakuta
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Saori Horiuchi
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Kousuke Tsubaki
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Tadashi Kitahara
- Department of Otolaryngology-Head and Neck Surgery, Nara Medical University, Kashihara, Japan
| | - Hisakazu Yano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
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47
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Nguyen Q, Nguyen TTN, Pham P, Chau V, Nguyen LPH, Nguyen TD, Ha TT, Le NTQ, Vu DT, Baker S, Thwaites GE, Rabaa MA, Pham DT. Genomic insights into the circulation of pandemic fluoroquinolone-resistant extra-intestinal pathogenic Escherichia coli ST1193 in Vietnam. Microb Genom 2021; 7. [PMID: 34904942 PMCID: PMC8767341 DOI: 10.1099/mgen.0.000733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Extra-intestinal pathogenic Escherichia coli (ExPEC) ST1193, a globally emergent fluoroquinolone-resistant clone, has become an important cause of bloodstream infections (BSIs) associated with significant morbidity and mortality. Previous studies have reported the emergence of fluoroquinolone-resistant ExPEC ST1193 in Vietnam; however, limited data exist regarding the genetic structure, antimicrobial resistance (AMR) determinants and transmission dynamics of this pandemic clone. Here, we performed genomic and phylogenetic analyses of 46 ST1193 isolates obtained from BSIs and healthy individuals in Ho Chi Minh City, Vietnam, to investigate the pathogen population structure, molecular mechanisms of AMR and potential transmission patterns. We further examined the phylogenetic structure of ST1193 isolates in a global context. We found that the endemic E. coli ST1193 population was heterogeneous and highly dynamic, largely driven by multiple strain importations. Several well-supported phylogenetic clusters (C1-C6) were identified and associated with distinct bla CTX-M variants, including bla CTXM-27 (C1-C3, C5), bla CTXM-55 (C4) and bla CTXM-15 (C6). Most ST1193 isolates were multidrug-resistant and carried an extensive array of AMR genes. ST1193 isolates also exhibited the ability to acquire further resistance while circulating in Vietnam. There were phylogenetic links between ST1193 isolates from BSIs and healthy individuals, suggesting these organisms may both establish long-term colonization in the human intestinal tract and induce infections. Our study uncovers factors shaping the population structure and transmission dynamics of multidrug-resistant ST1193 in Vietnam, and highlights the urgent need for local One Health genomic surveillance to capture new emerging ExPEC clones and to better understand the origins and transmission patterns of these pathogens.
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Affiliation(s)
- Quynh Nguyen
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Phuong Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vinh Chau
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Tuyen Thanh Ha
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nhi Thi Quynh Le
- The University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | | | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Maia A Rabaa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Duy Thanh Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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48
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Li D, Wyrsch ER, Elankumaran P, Dolejska M, Marenda MS, Browning GF, Bushell RN, McKinnon J, Chowdhury PR, Hitchick N, Miller N, Donner E, Drigo B, Baker D, Charles IG, Kudinha T, Jarocki VM, Djordjevic SP. Genomic comparisons of Escherichia coli ST131 from Australia. Microb Genom 2021; 7:000721. [PMID: 34910614 PMCID: PMC8767332 DOI: 10.1099/mgen.0.000721] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Escherichia coli ST131 is a globally dispersed extraintestinal pathogenic E. coli lineage contributing significantly to hospital and community acquired urinary tract and bloodstream infections. Here we describe a detailed phylogenetic analysis of the whole genome sequences of 284 Australian ST131 E. coli isolates from diverse sources, including clinical, food and companion animals, wildlife and the environment. Our phylogeny and the results of single nucleotide polymorphism (SNP) analysis show the typical ST131 clade distribution with clades A, B and C clearly displayed, but no niche associations were observed. Indeed, interspecies relatedness was a feature of this study. Thirty-five isolates (29 of human and six of wild bird origin) from clade A (32 fimH41, 2 fimH89, 1 fimH141) were observed to differ by an average of 76 SNPs. Forty-five isolates from clade C1 from four sources formed a cluster with an average of 46 SNPs. Within this cluster, human sourced isolates differed by approximately 37 SNPs from isolates sourced from canines, approximately 50 SNPs from isolates from wild birds, and approximately 52 SNPs from isolates from wastewater. Many ST131 carried resistance genes to multiple antibiotic classes and while 41 (14 %) contained the complete class one integron-integrase intI1, 128 (45 %) isolates harboured a truncated intI1 (462-1014 bp), highlighting the ongoing evolution of this element. The module intI1-dfrA17-aadA5-qacEΔ1-sul1-ORF-chrA-padR-IS1600-mphR-mrx-mphA, conferring resistance to trimethoprim, aminoglycosides, quaternary ammonium compounds, sulphonamides, chromate and macrolides, was the most common structure. Most (73 %) Australian ST131 isolates carry at least one extended spectrum β-lactamase gene, typically blaCTX-M-15 and blaCTX-M-27. Notably, dual parC-1aAB and gyrA-1AB fluoroquinolone resistant mutations, a unique feature of clade C ST131 isolates, were identified in some clade A isolates. The results of this study indicate that the the ST131 population in Australia carries diverse antimicrobial resistance genes and plasmid replicons and indicate cross-species movement of ST131 strains across diverse reservoirs.
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Affiliation(s)
- Dmitriy Li
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Ethan R. Wyrsch
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | | | - Monika Dolejska
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic,Department of Biology and Wildlife Disease, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Czech Republic,Biomedical Center, Charles University, Czech Republic,Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno, Brno, Czech Republic
| | - Marc S. Marenda
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia
| | - Glenn F. Browning
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia
| | - Rhys N. Bushell
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia
| | - Jessica McKinnon
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | | | - Nola Hitchick
- San Pathology, Sydney Adventist Hospital, Wahroonga, NSW 2076, Australia
| | - Natalie Miller
- San Pathology, Sydney Adventist Hospital, Wahroonga, NSW 2076, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | | | | | - Timothy Kudinha
- Central West Pathology Laboratory, Charles Sturt University, Orange, NSW, 2800, Australia
| | - Veronica M. Jarocki
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia,*Correspondence: Veronica M. Jarocki,
| | - Steven Philip Djordjevic
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia,*Correspondence: Steven Philip Djordjevic,
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49
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Margalit A, Carolan JC, Walsh F. Global protein responses of multi-drug resistant plasmid containing Escherichia coli to ampicillin, cefotaxime, imipenem and ciprofloxacin. J Glob Antimicrob Resist 2021; 28:90-96. [PMID: 34922055 DOI: 10.1016/j.jgar.2021.12.006] [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: 10/26/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 10/19/2022] Open
Abstract
OBJECTIVES This study compared the proteomics of Escherichia coli containing the multi-drug resistance pEK499 plasmid under antimicrobial stress and no antimicrobial. METHODS We utilised mass spectrometry-based proteomics to compare the proteomes of the bacteria and plasmid under antimicrobial stress and no antimicrobial. RESULTS Our analysis identified statistically significant differentially abundant proteins common to groups exposed to the β-lactam antimicrobials but not ciprofloxacin, indicating a β-lactam stress response to exposure from this class of drugs, irrespective of β-lactam resistance or susceptibility. Data arising from comparisons of the proteomes of ciprofloxacin-treated E. coli and controls detected an increase in the relative abundance of proteins associated with ribosomes, translation, the TCA-cycle and several proteins associated with detoxification and a decrease in the relative abundances of proteins associated with stress response, including oxidative stress. We identified changes in proteins associated with persister formation in the presence of ciprofloxacin but not the β-lactams. The plasmid proteome differed across each treatment and did not follow the pattern of antimicrobial - AMR protein associations: a relative increase in the amount of blaCTX-M-15 in the presence of cefotaxime and ciprofloxacin but not the other β-lactams, suggesting regulation of the blaCTX-M-15 protein production. CONCLUSIONS The proteomic data from the this study provided novel insights into the proteins produced from the chromosome and plasmid under different antimicrobial stresses. These data also identified novel proteins not previously associated with AMR or antimicrobials responses in pathogens, which may well represent potential targets of AMR inhibition.
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Affiliation(s)
- Anatte Margalit
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| | - James C Carolan
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| | - Fiona Walsh
- Department of Biology, Maynooth University, Co. Kildare, Ireland.
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50
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Hapuarachchi IU, Hannaway RF, Roman T, Biswas A, Dyet K, Morgan X, Ussher JE. Genetic evaluation of ESBL-producing Escherichia coli urinary isolates in Otago, New Zealand. JAC Antimicrob Resist 2021; 3:dlab147. [PMID: 34778763 PMCID: PMC8578626 DOI: 10.1093/jacamr/dlab147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/01/2021] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVES The incidence of infections with ESBL-producing Escherichia coli (ESBL-Ec) in New Zealand is increasing. ESBL-Ec most commonly cause urinary tract infections and are seen in both community and hospitalized patients. The reason for the increasing incidence of ESBL-Ec infections is unknown. METHODS In this study, 65 urinary ESBL-Ec isolates from the Otago region in 2015 were fully genetically characterized to understand the mechanisms of transmission. The ESBL gene, E. coli STs, plasmid types and genetic context (e.g. insertion sequences) of ESBL genes were determined by a combination of whole genome and plasmid sequencing. The phylogenetic relationships of the isolates were compared with ESBL-Ec isolates sequenced as part of the 2016 nationwide survey. RESULTS Significant diversity of E. coli strains, plasmids, and the genetic context of ESBL genes was seen. However, there was evidence of common mobile genetic elements in unrelated ESBL-Ec. CONCLUSIONS Multiple introductions of ESBL resistance genes or resistant bacterial strains with limited horizontal transmission of mobile genetic elements accounts for the increased incidence of ESBL-Ec in this low prevalence area. Future studies should investigate modes of transmission of ESBL-Ec in the Otago region.
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Affiliation(s)
- Isuri U Hapuarachchi
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Rachel F Hannaway
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Tabatha Roman
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Ambarish Biswas
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- AgResearch, Palmerston North, New Zealand
| | | | - Xochitl Morgan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - James E Ussher
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Southern Community Laboratories, Dunedin, New Zealand
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