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Bianconi I, Spath M, Aschbacher R, Pedron R, Wieser S, Pagani E. Characterization of Verona Integron-Encoded Metallo-β-Lactamase-Type Carbapenemase-Producing Escherichia coli Isolates Collected over a 16-Year Period in Bolzano (Northern Italy). Microb Drug Resist 2024; 30:91-100. [PMID: 38150043 DOI: 10.1089/mdr.2023.0197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
Multidrug-resistant Escherichia coli, particularly carbapenemase producers, are a major source of concern. This study aims to investigate the long-term epidemiology of Verona integron-encoded metallo-β-lactamase (VIM)-producing E. coli in the health district of Bolzano, Northern Italy, by examining the phenotypic and genotypic characteristics of 26 isolates obtained during 2005-2020. Isolates were identified with matrix-assisted laser desorption/ionization time-of-flight, susceptibility testing was by Vitek 2, Sensititre, and Etest; carbapenemase activity was confirmed by Etest and Carbapenemase Inactivation Method (CIM) test; and the VIM-antigen was identified by the NG-Test CARBA 5. Genome sequencing was performed on an Illumina MiSeq platform. Carbapenem minimum inhibitory concentrations varied across methodologies, and overall category agreement between phenotypic methods was low. All 23 sequenced isolates contained blaVIM-1. Eleven (47.8%) isolates belonged to the clonal lineage ST131, with fimH30 being the most common subclone. In Bolzano ST131-fimH30 was present as early as 2005. While the ST131 clonal lineage predominated for the first 10 years, various clonal lineages were present, especially in subsequent years, indicating the concurrent circulation of multiple clonal lineages. Future efforts should focus on the implementation of surveillance methods, including genomic analysis, as well as the use of updated infection control strategies and antibiotic stewardship programs to prevent the spread of these carbapenem-resistant strains.
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Affiliation(s)
- Irene Bianconi
- Laboratorio Aziendale di Microbiologia e Virologia Bolzano, Azienda Sanitaria dell'Alto Adige, Trentino-Alto Adige, Italy
- CIBIO-Department of Cellular, Computational and Integrative BiologyTrento, University of Trento, Trentino-Alto Adige, Italy
| | - Manuela Spath
- Laboratorio Aziendale di Microbiologia e Virologia Bolzano, Azienda Sanitaria dell'Alto Adige, Trentino-Alto Adige, Italy
| | - Richard Aschbacher
- Laboratorio Aziendale di Microbiologia e Virologia Bolzano, Azienda Sanitaria dell'Alto Adige, Trentino-Alto Adige, Italy
| | - Renato Pedron
- CIBIO-Department of Cellular, Computational and Integrative BiologyTrento, University of Trento, Trentino-Alto Adige, Italy
| | - Stefanie Wieser
- Claudiana Higher Provincial School of Health Professions Bolzano, Trentino-Alto Adige, Italy
| | - Elisabetta Pagani
- Laboratorio Aziendale di Microbiologia e Virologia Bolzano, Azienda Sanitaria dell'Alto Adige, Trentino-Alto Adige, Italy
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Nitti MT, Sleghel F, Kaczor M, Aschbacher R, Moroder E, Di Pierro AM, Piscopiello F, Spalla M, Piazza A, Migliavacca R, Pagani E. Colonization of Residents and Staff of an Italian Long-Term Care Facility and an Adjacent Acute Care Hospital Geriatrics Unit by Multidrug-Resistant Bacteria. Microb Drug Resist 2023; 29:477-484. [PMID: 37389822 DOI: 10.1089/mdr.2023.0019] [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: 07/01/2023] Open
Abstract
In 2022, we undertook a point prevalence screening study for Enterobacterales with extended-spectrum β-lactamases (ESBLs), high-level AmpC cephalosporinases and carbapenemases, and also methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) in a long-term care facility (LTCF) and the associated acute-care hospital Geriatrics unit in Bolzano, Northern Italy. Urine samples and rectal, inguinal, oropharyngeal, and nasal swabs were plated on selective agar plates. Metadata of the patients, including demographic data, were collected, and risk factors for colonization were determined. ESBL, AmpC, carbapenemase, and quinolone resistance genes were investigated by the HybriSpot 12 PCR AUTO System. The following colonization percentages by multidrug-resistant (MDR) bacteria have been found in LTCF residents: all MDR organisms, 59.5%; ESBL producers, 46.0% (mainly CTX-M-type enzymes); carbapenemase producers, 1.1% (one Klebsiella pneumoniae with KPC-type); MRSA, 4.5%; VRE, 6.7%. Colonization by MDR bacteria was 18.9% for LTCF staff and 45.0% for Geriatrics unit patients. Peripheral vascular disease, the presence of any medical device, cancer, and a Katz Index of 0 were significant risk factors for colonization of LTCF residents by MDR bacteria in univariate and/or multivariate regression analysis. To conclude, the ongoing widespread diffusion of MDR bacteria in the LTCF suggests that efforts should be strengthened on MDR screening, implementation of infection control strategies, and antibiotic stewardship programs targeting the unique aspects of LTCFs. ClinicalTrials.gov ID: 0530250-BZ Reg01 30/08/2022.
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Affiliation(s)
| | - Ferisa Sleghel
- Reparto di Geriatria, Comprensorio Sanitario di Bolzano, Bolzano, Italy
| | - Malgorzata Kaczor
- Reparto di Geriatria, Comprensorio Sanitario di Bolzano, Bolzano, Italy
| | - Richard Aschbacher
- Laboratorio Aziendale di Microbiologia e Virologia, Comprensorio Sanitario di Bolzano, Bolzano, Italy
| | - Elena Moroder
- Laboratorio Aziendale di Microbiologia e Virologia, Comprensorio Sanitario di Bolzano, Bolzano, Italy
| | - Angela Maria Di Pierro
- Laboratorio Aziendale di Microbiologia e Virologia, Comprensorio Sanitario di Bolzano, Bolzano, Italy
| | - Francesca Piscopiello
- Dipartimento SCCDP, Unità di Microbiologia e Microbiologia clinica, Università degli Studi di Pavia, Pavia, Italy
| | - Melissa Spalla
- Dipartimento SCCDP, Unità di Microbiologia e Microbiologia clinica, Università degli Studi di Pavia, Pavia, Italy
| | - Aurora Piazza
- Dipartimento SCCDP, Unità di Microbiologia e Microbiologia clinica, Università degli Studi di Pavia, Pavia, Italy
| | - Roberta Migliavacca
- Dipartimento SCCDP, Unità di Microbiologia e Microbiologia clinica, Università degli Studi di Pavia, Pavia, Italy
| | - Elisabetta Pagani
- Laboratorio Aziendale di Microbiologia e Virologia, Comprensorio Sanitario di Bolzano, Bolzano, Italy
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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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Gatya Al-Mayahie SM, Al-Guranie DRT, Hussein AA, Bachai ZA. Prevalence of common carbapenemase genes and multidrug resistance among uropathogenic Escherichia coli phylogroup B2 isolates from outpatients in Wasit Province/ Iraq. PLoS One 2022; 17:e0262984. [PMID: 35077517 PMCID: PMC8789106 DOI: 10.1371/journal.pone.0262984] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 01/10/2022] [Indexed: 01/04/2023] Open
Abstract
Carbapenems are the last resort antimicrobials for the treatment of extended spectrum β-lactamases (ESBLs) producing Enterobacteriaceae. Emergence of carbapenems resistant group B2 uropathogenic E. coli (UPEC) is a major concern because of their high virulence. Prevalence of these enzymes and multidrug resistance (MDR) among B2 UPEC isolates from Iraqi outpatients with acute urinary tract infection (UTI) was evaluated in this research. Urine cultures were performed and the isolates were identified biochemically. Escherichia coli isolates were tested for phylogroup reference by quadraplex PCR, then B2 isolates were detected for antimicrobial resistance by disc diffusion test and carbapenemase genes by PCR. Escherichia coli was the most prevalent among Gram-negative isolates (66.6%) and B2 was the most detected phylogroup among E. coli isolates (33.9%). Most of B2 isolates showed high resistance rates to tested antimicrobials, especially β-lactams with MDR revealed in 100% of them. Whereas, low resistance rates were noted against carbapenems, aminoglycosides and nitrofurantoin. Carbapenemase genes were detected in 76.3% of B2 isolates. Of which, blaOXA-48 was the most frequent (57.8%), followed by blaPER (47.3%), blaKPC (15.7%), blaVEB and blaVIM (10.5%, for each). Whereas, blaGES and blaIMP genes were not found. Coproduction of these genes occurred among 17 isolates. The combination of blaOXA-48 and blaPER was the most frequent (41.1%). All carbapenemase producing isolates were MDR. These results revealed high prevalence of carbapenemase genes and MDR among B2 UPEC recovered in this study. In the study area. it is strongly advised to use aminoglycosides and nitrofurantoin for empirical treatment of UPEC.
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Affiliation(s)
| | | | - Aya Aziz Hussein
- Department of Biology, College of Science, Wasit University, Al-Kut City, Wasit Province, Iraq
| | - Zaineb Ali Bachai
- Department of Biology, College of Science, Wasit University, Al-Kut City, Wasit Province, Iraq
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OUP accepted manuscript. J Antimicrob Chemother 2022; 77:2199-2208. [DOI: 10.1093/jac/dkac142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 03/25/2022] [Indexed: 11/14/2022] Open
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Yang X, Qi Y, Li G, Wang Y, Lou Z, Jiang Y. Characterization of the genetic environment of blaKPC in Escherichia coli isolates from hospitals in China. FEMS Microbiol Lett 2021; 367:5819958. [PMID: 32286617 DOI: 10.1093/femsle/fnaa064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 04/09/2020] [Indexed: 11/13/2022] Open
Abstract
Carbapenem resistance in Enterobacteriaceae members has become a major challenge, and the genetic environment of blaKPC, encoding Klebsiella pneumoniae carbapenemases, has not been fully clarified in China. In this study, we aimed to explore the genetic environment of blaKPC in 25 carbapenem-resistant E. coli isolates from hospitals in Hangzhou Province, China. Antimicrobial susceptibility against 22 common antimicrobial agents was tested. Polymerase chain reaction (PCR) analysis was performed for screening of the resistent genes, such as blaKPC, blaCTX-M, blaTEM, blaSHV, blaNDM, qnrA, qnrB, qnrS, aac(6')-Ib, armA and rmtB. The genetic environment of blaKPC were determinedin one isolate. blaKPC was detected by PCR in all the clinical E. coli isolates. There were no strains carrying blaNDM, qnrA and armA. The genetic environment of blaKPC showed that blaKPC dissemination is plasmid mediated and that it is located in the Tn3-Tn4401 transposon complex. Encoding of blaKPC-2 was responsible for carbapenem resistance in the 25 E. coli isolates. The genetic environment of blaKPC was characterized by the Tn3-Tn4401 complex. Our findings may provide a theoretical basis for clinical drug-resistance monitoring, anti-infection treatment and hospital infection control.
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Affiliation(s)
- Xuejing Yang
- Department of Clinical Laboratory, the First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Yan Qi
- Department of Clinical Laboratory, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang, China
| | - Guoping Li
- Department of Respiratory Medicine, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yuying Wang
- Department of Clinical Laboratory, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang, China
| | - Zhengqing Lou
- Department of Clinical Laboratory, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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Piazza A, Principe L, Comandatore F, Perini M, Meroni E, Mattioni Marchetti V, Migliavacca R, Luzzaro F. Whole-Genome Sequencing Investigation of a Large Nosocomial Outbreak Caused by ST131 H30Rx KPC-Producing Escherichia coli in Italy. Antibiotics (Basel) 2021; 10:antibiotics10060718. [PMID: 34203731 PMCID: PMC8232337 DOI: 10.3390/antibiotics10060718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 11/16/2022] Open
Abstract
KPC-producing Escherichia coli (KPC-Ec) remains uncommon, being mainly reported as the cause of sporadic episodes of infection rather than outbreak events. Here we retrospectively describe the dynamics of a large hospital outbreak sustained by KPC-Ec, involving 106 patients and 25 hospital wards, during a six-month period. Twenty-nine representative KPC-Ec isolates (8/29 from rectal swabs; 21/29 from other clinical specimens) have been investigated by Whole-Genome Sequencing (WGS). Outbreak isolates showed a multidrug-resistant profile and harbored several resistance determinants, including blaCTX-M-27, aadA5, dfrA17, sulI, gyrA1AB and parC1aAB. Phylogenomic analysis identified the ST131 cluster 1 (23/29 isolates), H30Rx clade C, as responsible for the epidemic event. A further two KPC-Ec ST131 clusters were identified: cluster 2 (n = 2/29) and cluster 3 (n = 1/29). The remaining KPC-Ec resulted in ST978 (n = 2/29) and ST1193 (n = 1/29), and were blaKPC-3 associated. The KPC-Ec ST131 cluster 1, originated in a previous KPC-Kp endemic context probably by plasmid transfer, and showed a clonal dissemination strategy. Transmission of the blaKPC gene to the globally disseminated high-risk ST131 clone represents a serious cause of concern. Application of WGS in outbreak investigations could be useful to better understand the evolution of epidemic events in order to address infection control and contrast interventions, especially when high-risk epidemic clones are involved.
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Affiliation(s)
- Aurora Piazza
- Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, Unit of Microbiology and Clinical Microbiology, University of Pavia, 27100 Pavia, Italy;
- Correspondence:
| | - Luigi Principe
- Clinical Pathology and Microbiology Unit, S. Giovanni di Dio Hospital, 88900 Crotone, Italy;
| | - Francesco Comandatore
- Romeo and Enrica Invernizzi Pediatric Research Center, Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, 20157 Milan, Italy; (F.C.); (M.P.)
| | - Matteo Perini
- Romeo and Enrica Invernizzi Pediatric Research Center, Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, 20157 Milan, Italy; (F.C.); (M.P.)
| | - Elisa Meroni
- Microbiology and Virology Unit, A. Manzoni Hospital, 23900 Lecco, Italy; (E.M.); (F.L.)
| | | | - Roberta Migliavacca
- Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, Unit of Microbiology and Clinical Microbiology, University of Pavia, 27100 Pavia, Italy;
| | - Francesco Luzzaro
- Microbiology and Virology Unit, A. Manzoni Hospital, 23900 Lecco, Italy; (E.M.); (F.L.)
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Adekanmbi AO, Usidamen S, Onilude AA. Molecular characterization of ESBL- producing uropathogenic Escherichia coli recovered from urine samples of patients attending a University Teaching hospital in Nigeria. Acta Microbiol Immunol Hung 2021. [PMID: 33964125 DOI: 10.1556/030.2021.01380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 02/09/2021] [Indexed: 11/19/2022]
Abstract
Infection of the urinary tract ranks as one of the most common infections affecting people worldwide and its treatment is made complicated by the rising incidence of antibiotic resistance. This study aimed to detect extended spectrum beta-lactamase (ESBL) genes and antibiotic resistance profile of uropathogenic Escherichia coli (E. coli) recovered from patients attending a University Teaching hospital in Nigeria. Uropathogenic E. coli isolates were obtained from the culture collection of Department of Microbiology and Parasitology of the University Teaching hospital for a period of four months (October 2019-January, 2020). Antibiotic susceptibility testing was done using the disc diffusion method while phenotypic ESBL production was detected using double disc synergy test (DDST). Detection of β-lactamase genes was done using Real-Time PCR. Forty-nine E. coli isolates were recovered from 120 urine samples, with 24 (49%) being ESBL positive. The resistance to antibiotics in the ESBL producers was: ciprofloxacin (100%), cefotaxime (100%), cefpodoxime (100%), tetracycline (95.7%), ceftazidime (56.7%), amoxicillin-clavulanate (50%), gentamicin (33.3%), and imipenem (0%). All the ESBL producers carried blaTEM, blaCTX-M-1 and blaCTX-M-9, 75% (18/24) carried blaSHV, while blaCTX-M-2, blaCTX-M-8 and blaCTX-M-25 groups were detected in 20.8% (5/24) of the isolates. There was co-occurrence of CTX-M, SHV and TEM β-lactamases in 79.2% (19/24) isolates, while five isolates (20.8%) co-harbored blaCTX-M and blaTEM. This study showed a high level of multidrug resistance and ESBL gene carriage in uropathogenic E. coli obtained in this study, suggesting a likely review of therapeutic options in the treatment of UTI to clamp down on the rising cases of antibiotic resistance.
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Affiliation(s)
- Abimbola Olumide Adekanmbi
- 1Environmental Microbiology and Biotechnology Laboratory, Department of Microbiology, University of Ibadan, Nigeria
| | - Sandra Usidamen
- 2Pathogenic Microbiology Laboratory, Department of Microbiology, University of Ibadan, Nigeria
| | - Anthony Abiodun Onilude
- 3Microbial Physiology and Biochemistry Laboratory, Department of Microbiology, University of Ibadan, Nigeria
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Taati Moghadam M, Mirzaei M, Fazel Tehrani Moghaddam M, Babakhani S, Yeganeh O, Asgharzadeh S, Farahani HE, Shahbazi S. The Challenge of Global Emergence of Novel Colistin-Resistant Escherichia coli ST131. Microb Drug Resist 2021; 27:1513-1524. [PMID: 33913748 DOI: 10.1089/mdr.2020.0505] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Escherichia coli ST131 is one of the high-risk multidrug-resistant clones with a global distribution and the ability to persist and colonize in a variety of niches. Carbapenemase-producing E. coli ST131 strains with the ability to resist last-line antibiotics (i.e., colistin) have been recently considered a significant public health. Colistin is widely used in veterinary medicine and therefore, colistin-resistant bacteria can be transmitted from livestock to humans through food. There are several mechanisms of resistance to colistin, which include chromosomal mutations and plasmid-transmitted mcr genes. E. coli ST131 is a great model organism to investigate the emergence of superbugs. This microorganism has the ability to cause intestinal and extraintestinal infections, and its accurate identification as well as its antibiotic resistance patterns are vitally important for a successful treatment strategy. Therefore, further studies are required to understand the evolution of this resistant organism for drug design, controlling the evolution of other nascent emerging pathogens, and developing antibiotic stewardship programs. In this review, we will discuss the importance of E. coli ST131, the mechanisms of resistance to colistin as the last-resort antibiotic against resistant Gram-negative bacteria, reports from different regions regarding E. coli ST131 resistance to colistin, and the most recent therapeutic approaches against colistin-resistance bacteria.
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Affiliation(s)
- Majid Taati Moghadam
- Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, Iran University of Medical Sciences, Tehran, Iran
| | - Mehrnaz Mirzaei
- Department of Microbiology, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
| | | | - Sajad Babakhani
- Department of Microbiology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Omid Yeganeh
- Department of Microbiology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Sajad Asgharzadeh
- Department of Microbiology, Iran University of Medical Sciences, Tehran, Iran
| | | | - Shahla Shahbazi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran
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Escherichia coli Sequence Type 457 Is an Emerging Extended-Spectrum-β-Lactam-Resistant Lineage with Reservoirs in Wildlife and Food-Producing Animals. Antimicrob Agents Chemother 2020; 65:AAC.01118-20. [PMID: 33020161 DOI: 10.1128/aac.01118-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/18/2020] [Indexed: 01/16/2023] Open
Abstract
Silver gulls carry phylogenetically diverse Escherichia coli, including globally dominant extraintestinal pathogenic E. coli (ExPEC) sequence types and pandemic ExPEC-ST131 clades; however, our large-scale study (504 samples) on silver gulls nesting off the coast of New South Wales identified E. coli ST457 as the most prevalent. A phylogenetic analysis of whole-genome sequences (WGS) of 138 ST457 samples comprising 42 from gulls, 2 from humans (Australia), and 14 from poultry farmed in Paraguay were compared with 80 WGS deposited in public databases from diverse sources and countries. E. coli ST457 strains are phylogenetic group F, carry fimH145, and partition into five main clades in accordance to predominant flagella H-antigen carriage. Although we identified considerable phylogenetic diversity among the 138 ST457 strains, closely related subclades (<100 SNPs) suggested zoonotic or zooanthroponosis transmission between humans, wild birds, and food-producing animals. Australian human clinical and gull strains in two of the clades were closely related (≤80 SNPs). Regarding plasmid content, country, or country/source, specific connections were observed, including I1/ST23, I1/ST314, and I1/ST315 disseminating bla CMY-2 in Australia, I1/ST113 carrying bla CTX-M-8 and mcr-5 in Paraguayan poultry, and F2:A-:B1 plasmids of Dutch origin being detected across multiple ST457 clades. We identified a high prevalence of nearly identical I1/ST23 plasmids carrying bla CMY-2 among Australian gull and clinical human strains. In summary, ST457 is a broad host range, geographically diverse E. coli lineage that can cause human extraintestinal disease, including urinary tract infection, and displays a remarkable ability to capture mobile elements that carry and transmit genes encoding resistance to critically important antibiotics.
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11
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Apostolakos I, Feudi C, Eichhorn I, Palmieri N, Fasolato L, Schwarz S, Piccirillo A. High-resolution characterisation of ESBL/pAmpC-producing Escherichia coli isolated from the broiler production pyramid. Sci Rep 2020; 10:11123. [PMID: 32636426 PMCID: PMC7341882 DOI: 10.1038/s41598-020-68036-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 05/29/2020] [Indexed: 12/16/2022] Open
Abstract
The presence of extended-spectrum β-lactamase (ESBL) or plasmid-mediated AmpC β-lactamase (pAmpC)-producing Escherichia coli (ESBL/pAmpC-EC) in livestock is a public health risk given the likelihood of their transmission to humans via the food chain. We conducted whole genome sequencing on 100 ESBL/pAmpC-EC isolated from the broiler production to explore their resistance and virulence gene repertoire, characterise their plasmids and identify transmission events derived from their phylogeny. Sequenced isolates carried resistance genes to four antimicrobial classes in addition to cephalosporins. Virulence gene analysis assigned the majority of ESBL/pAmpC-EC to defined pathotypes. In the complex genetic background of ESBL/pAmpC-EC, clusters of closely related isolates from various production stages were identified and indicated clonal transmission. Phylogenetic comparison with publicly available genomes suggested that previously uncommon ESBL/pAmpC-EC lineages could emerge in poultry, while others might contribute to the maintenance and dissemination of ESBL/pAmpC genes in broilers. The majority of isolates from diverse E. coli lineages shared four dominant plasmids (IncK2, IncI1, IncX3 and IncFIB/FII) with identical ESBL/pAmpC gene insertion sites. These plasmids have been previously reported in diverse hosts, including humans. Our findings underline the importance of specific plasmid groups in the dissemination of cephalosporin resistance genes within the broiler industry and across different reservoirs.
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Affiliation(s)
- Ilias Apostolakos
- Department of Comparative Biomedicine and Food Science, University of Padua, 35020, Padua, Italy
| | - Claudia Feudi
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
| | - Inga Eichhorn
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
| | - Nicola Palmieri
- Department for Farm Animals and Veterinary Public Health, University Clinic for Poultry and Fish Medicine, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Luca Fasolato
- Department of Comparative Biomedicine and Food Science, University of Padua, 35020, Padua, Italy
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
| | - Alessandra Piccirillo
- Department of Comparative Biomedicine and Food Science, University of Padua, 35020, Padua, Italy.
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Ripabelli G, Sammarco ML, Scutellà M, Felice V, Tamburro M. Carbapenem-Resistant KPC- and TEM-Producing Escherichia coli ST131 Isolated from a Hospitalized Patient with Urinary Tract Infection: First Isolation in Molise Region, Central Italy, July 2018. Microb Drug Resist 2019; 26:38-45. [PMID: 31386590 DOI: 10.1089/mdr.2019.0085] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In July 2018, a Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli ST131 was isolated from a patient admitted to the Vascular Surgery Unit of the main hospital of Molise region, Central Italy. Sequencing and alignment with the available sequences revealed that the isolate harbored the KPC-2 variant and TEM-1 beta-lactamase. This observation raises great concerns about the spread of carbapenem resistance in national and local settings with high endemicity level of KPC in K. pneumoniae, and underlines the importance of strengthening a proactive surveillance.
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Affiliation(s)
- Giancarlo Ripabelli
- Department of Medicine and Health Sciences "Vincenzo Tiberio," University of Molise, Campobasso, Italy
| | - Michela Lucia Sammarco
- Department of Medicine and Health Sciences "Vincenzo Tiberio," University of Molise, Campobasso, Italy
| | - Massimiliano Scutellà
- Laboratory Medicine Unit, "Antonio Cardarelli" Hospital, Azienda Sanitaria Regionale del Molise, Campobasso, Italy
| | - Valentina Felice
- Laboratory Medicine Unit, "Antonio Cardarelli" Hospital, Azienda Sanitaria Regionale del Molise, Campobasso, Italy
| | - Manuela Tamburro
- Department of Medicine and Health Sciences "Vincenzo Tiberio," University of Molise, Campobasso, Italy
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Simoni S, Caucci S, Brenciani A, Morroni G, Giovanetti E, Menzo S, Facinelli B, Mingoia M. Increase and diversity of carbapenemase-producing Escherichia coli isolates, Italy. Future Microbiol 2019; 14:1035-1042. [DOI: 10.2217/fmb-2019-0069] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: This study reports on a surveillance in an Italian hospital focused on carbapenemase-producing Escherichia coli (CP-Ec). Materials & methods: Eighteen isolates (nine from clinical specimens and nine from rectal swab) were characterized for antibiotic susceptibilities, typing features, main carbapenemase, extended-spectrum ß-lactamases (ESBLs) and other bla genes, and their transferability by conjugation and transformation. Results: An increase in CP-Ec isolates was observed during 3-year surveillance period. Compared with the clinical isolates, all belonging to one sequence type (ST), ST131, those from rectal swab were very heterogeneous and belonged to eight STs. Transfer data confirmed the role of conjugative plasmids in the spreading of carbapenemase genes. Conclusion: The prevalence of CP-Ec in Italy has risen, with a substantial increase over the last year.
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Affiliation(s)
- Serena Simoni
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
| | - Sara Caucci
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
| | - Andrea Brenciani
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
| | - Gianluca Morroni
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
| | - Eleonora Giovanetti
- Unit of Microbiology, Department of Life & Environmental Sciences Polytechnic University of Marche, Ancona, Italy
| | - Stefano Menzo
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
| | - Bruna Facinelli
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
| | - Marina Mingoia
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
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Prevalence of Multidrug Resistance and Extended-Spectrum β-Lactamase Carriage of Clinical Uropathogenic Escherichia coli Isolates in Riyadh, Saudi Arabia. Int J Microbiol 2018; 2018:3026851. [PMID: 30305814 PMCID: PMC6165594 DOI: 10.1155/2018/3026851] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 08/17/2018] [Indexed: 12/30/2022] Open
Abstract
The prevalence of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-producing E. coli) has recently increased worldwide. This study aims at determining the antimicrobial susceptibility patterns of a collection of clinical E. coli urine isolates and evaluating the ESBL carriage of these isolates at phenotypic and genotypic levels. A total of 100 E. coli urine isolates were collected at a tertiary healthcare centre in Riyadh from January 2018 to March 2018. Antimicrobial susceptibility testing was carried out for all isolates. ESBL production was characterized at phenotypic and genotypic levels using double-disc synergy test and polymerase chain reaction, respectively. Detection of different ESBL variants was performed using DNA sequencing. Of 100 E. coli isolates, 67 were associated with multidrug resistance (MDR) phenotype. All isolates showed variable resistance levels to all antibiotics used here expect to imipenem, where they were all imipenem-sensitive. 33 out of 100 E. coli isolates were positive for ESBLs by phenotypic and genotypic methods. Among all ESBL-positive E. coli isolates, the CTX-M was the most prevalent ESBL type (31/33 isolates; 93.94%). CTX-M-15 variant was detected in all isolates associated with CTX-M carriage. Multiple ESBL gene carriage was detected in 15/33 isolates (45.45%), where 11 (33.33%) isolates produced two different ESBL types while 4 isolates (12.12%) associated with carrying three different ESBL types. Our study documented the high antimicrobial resistance of ESBL-producing E. coli to many front-line antibiotics currently used to treat UTI patients, and this implies the need to continuously revise the local guidelines used for optimal empirical therapy for UTI patients. It also showed the high prevalence of ESBL carriage in E. coli urine isolates, with CTX-M-15 being the most predominant CTX-M variant.
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TEM-184, a Novel TEM-Derived Extended-Spectrum β-Lactamase with Enhanced Activity against Aztreonam. Antimicrob Agents Chemother 2018; 62:AAC.00688-18. [PMID: 29941651 DOI: 10.1128/aac.00688-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/19/2018] [Indexed: 11/20/2022] Open
Abstract
TEM-184, a novel TEM-derived extended-spectrum β-lactamase (ESBL), was isolated from an Escherichia coli ST354 clinical strain. Compared to TEM-1, TEM-184 contains the mutations Q6K, E104K, I127V, R164S, and M182T. Kinetic analysis of this enzyme revealed extended-spectrum activity against aztreonam in particular. TEM-184 was also susceptible to inhibitors, including clavulanic acid, tazobactam, and avibactam.
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Bozcal E, Eldem V, Aydemir S, Skurnik M. The relationship between phylogenetic classification, virulence and antibiotic resistance of extraintestinal pathogenic Escherichia coli in İzmir province, Turkey. PeerJ 2018; 6:e5470. [PMID: 30155366 PMCID: PMC6110251 DOI: 10.7717/peerj.5470] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/21/2018] [Indexed: 12/25/2022] Open
Abstract
Background Extraintestinal pathogenic Escherichia coli (ExPEC) is an important bacterium and responsible for many bloodstream infections, including urinary tract infections and even fatal bacteremia. The aim of this research was to investigate whether ExPEC strains isolated from Turkish blood cultures have a relationship between 16S rRNA based phylogenetic clusters and antibiotic resistance profiles, virulence factors or clonal lineages. Methods Phenotypically identified ExPEC blood culture isolates (n = 104) were included in this study. The 16S rRNA partial sequence analysis was performed for genotypic identification of ExPEC isolates. Antibiotic susceptibility and Extended-Spectrum β-Lactamase testing of isolates were performed. Phylogenetic classification (A, B1, B2 and D), Multi Locus Sequence Typing analysis and virulence-associated genes were investigated. Results Based on 16S rRNA partial sequence analysis, 97 out of 104 (93.26%) ExPEC isolates were confirmed as E. coli. Ampicillin (74.22%) and cefuroxime axetil (65.97%) resistances had the highest frequencies among the ExPEC isolates. In terms of phylogenetic classification of ExPEC, D (38.14%, 37/97) was the most prevalent group after A (29.89%, 29/97), B2 (20.61%, 20/97), and B1 (11.34%, 11/97). The sequence types of the 20 ExPEC isolates belonging to the B2 phylogenetic group were analyzed by Multi Locus Sequence Typing. Ten isolates out of 20 (50.0%) were identified as ST131. The other STs were ST95 (n = 1), ST14 (n = 1), ST10 (n = 1), ST69 (n = 1), ST1722 (n = 2), ST141 (n = 1), ST88 (n = 1), ST80 (n = 1), and ST998 (n = 1). Of the ST131 strains, six (60%, 6/10) represented serogroup O25. The most common virulence factor genes were serum resistance factor gene, traT (55.7%) aerobactin siderophore receptor and yersiniabactin encoding genes iutA (45.3%) and fyuA (50.5%), respectively. In addition, PAI (41.2%), iroN (23.7%), hlyA (15.4%), kpsII (13.4%), ompT (13.4%), papG (12.4%), iss (9.3%), cnf1 (7.2%), ibeA (2.06%), and sfaS (2.06%) genes were present in the ExPEC isolates. Conclusion The 16S rRNA-based phylogenetic relationship tree analysis showed that a large cluster was present among 97 ExPEC isolates along with related reference strains. There were 21 main clusters with 32 closely related subclusters. Based on our findings, different clonal lineages of ExPEC can display different antibiotic susceptibilities and virulence properties. We also concluded that virulence factors were not distributed depending on phylogenetic groups (A, B1, B2, and D). The ExPEC isolates belonging to the same phylogenetic group and sequence type could display different resistance and virulence characteristics.
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Affiliation(s)
- Elif Bozcal
- Department of Biology, Basic and Industrial Microbiology Section, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Vahap Eldem
- Department of Biology, Zoology Section, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Sohret Aydemir
- Department of Medical Microbiology, Faculty of Medicine, Ege University, İzmir, Turkey
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
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Gauthier L, Dortet L, Cotellon G, Creton E, Cuzon G, Ponties V, Bonnin RA, Naas T. Diversity of Carbapenemase-Producing Escherichia coli Isolates in France in 2012-2013. Antimicrob Agents Chemother 2018; 62:e00266-18. [PMID: 29866863 PMCID: PMC6105832 DOI: 10.1128/aac.00266-18] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/25/2018] [Indexed: 12/17/2022] Open
Abstract
With the dissemination of carbapenemase-producing Enterobacteriaceae (CPE) strains worldwide, carbapenem-hydrolyzing enzymes are increasingly reported among isolates of Escherichia coli, the first hospital and community-acquired opportunistic pathogen. Here, we have performed an epidemiological survey of carbapenemase-producing E. coli (CP-Ec) isolates received at the French National Reference Centre (F-NRC) in 2012 and 2013. Antimicrobial susceptibilities for last-resort antibiotics and antimicrobial compounds commonly used to treat urinary tract infections were determined by broth microdilution. Clonal relationship was assessed using repetitive sequence-based PCR (rep-PCR) and multilocus sequence typing (MLST). From this collection of 140 carbapenemase-producing E. coli isolates, 74% produced an OXA-48-like carbapenemase and 21% produced an NDM carbapenemase. A link with a foreign country was suspected for 37% of infected/colonized patients. Most of the isolates were from screening (56%) and from urine samples (26%). Colistin, fosfomycin, and nitrofurantoin possessed the most consistent activity, with 100%, 95%, and 96% isolates susceptible, respectively. A wide diversity of carbapenemase-producing E. coli isolates has been found (50 different sequence types [STs]). The most prevalent clones were (i) E. coli sequence type 38 (ST38) producing OXA-48 (n = 21), a clone linked to Turkey and North African countries, (ii) E. coli ST-90 producing OXA-204 (n = 9), which was responsible for an outbreak related to a contaminated duodenoscope, and (iii) E. coli ST-410 producing OXA-181 (n = 5), which was recovered from patients of different geographical origins. These specific clones might be considered high-risk clones for the dissemination of carbapenemases in E. coli The wide diversity of STs, combined with the increasing number of CP-Ec isolates received by the F-NRC, suggests a likely dissemination of CP-Ec isolates in the community.
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Affiliation(s)
- Lauraine Gauthier
- Bactériologie-Hygiene unit, Bicêtre Hospital, Assistance Publique des Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- EA7361 "Structure, dynamic, function and expression of broad spectrum β-lactamases," Paris-Sud University, LabEx LERMIT, Faculty of Medecine, Le Kremlin-Bicêtre, France
- French National Reference Centre for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- Bactériologie-Hygiene unit, Bicêtre Hospital, Assistance Publique des Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- EA7361 "Structure, dynamic, function and expression of broad spectrum β-lactamases," Paris-Sud University, LabEx LERMIT, Faculty of Medecine, Le Kremlin-Bicêtre, France
- French National Reference Centre for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Garance Cotellon
- French National Reference Centre for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Elodie Creton
- French National Reference Centre for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Gaëlle Cuzon
- Bactériologie-Hygiene unit, Bicêtre Hospital, Assistance Publique des Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- EA7361 "Structure, dynamic, function and expression of broad spectrum β-lactamases," Paris-Sud University, LabEx LERMIT, Faculty of Medecine, Le Kremlin-Bicêtre, France
- French National Reference Centre for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | | | - Rémy A Bonnin
- EA7361 "Structure, dynamic, function and expression of broad spectrum β-lactamases," Paris-Sud University, LabEx LERMIT, Faculty of Medecine, Le Kremlin-Bicêtre, France
- French National Reference Centre for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Thierry Naas
- Bactériologie-Hygiene unit, Bicêtre Hospital, Assistance Publique des Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- EA7361 "Structure, dynamic, function and expression of broad spectrum β-lactamases," Paris-Sud University, LabEx LERMIT, Faculty of Medecine, Le Kremlin-Bicêtre, France
- French National Reference Centre for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
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Seni J, Peirano G, Okon KO, Jibrin YB, Mohammed A, Mshana SE, DeVinney R, Pitout JDD. The population structure of clinical extra-intestinal Escherichia coli in a teaching hospital from Nigeria. Diagn Microbiol Infect Dis 2018; 92:46-49. [PMID: 29859643 DOI: 10.1016/j.diagmicrobio.2018.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 04/01/2018] [Accepted: 04/05/2018] [Indexed: 10/17/2022]
Abstract
Limited information is available regarding the population structure of extra-intestinal pathogenic Escherichia coli (ExPEC) in Africa. Antimicrobial resistance profiles, sequence types (STs) and fimH types were determined on 60 clinical ExPEC from Nigeria using a 7-single nucleotide polymorphism quantitative PCR and sequencing of certain genes. Different ST131 clades were identified with a multiplex PCR. The isolates were mostly obtained from urines (58.3%). Not-susceptibility rates were as follows: trimethoprim-sulfamethoxazole (98%), cefotaxime (68%), gentamicin (55%), ciprofloxacin (62%) and piperacillin-tazobactam (2%). Dominant STs were associated with CTX-M-15 and included ST131-fimH30 (23%), ST457-fimH145 (20%), ST405-fimH27 (13%) and ST95-fimH41 (10%). We found the 7-SNP qPCR to be simple and cost-effective that can be utilized to tract different ExPEC clones on a global scale. This study provided insight into the population structure of ExPEC from Nigeria showing high prevalence of the rarely reported ST457 and the presence of multidrug resistant ST95.
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Affiliation(s)
- Jeremiah Seni
- Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania; Department of Microbiology, Immunology and Infectious Diseases, University of Calgary,Calgary, Alberta, Canada
| | - Giselle Peirano
- Department of Pathology & Laboratory Medicine, Cumming School of Medicine, University of Calgary,Calgary, Alberta, Canada; Division of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada
| | | | - Yusuf Bara Jibrin
- Department of Internal Medicine, Abubakar Tafawa Balewa University teaching hospital Bauchi
| | - Alkali Mohammed
- Department of Internal Medicine, Abubakar Tafawa Balewa University teaching hospital Bauchi
| | - Stephen E Mshana
- Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Rebekah DeVinney
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary,Calgary, Alberta, Canada
| | - Johann D D Pitout
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary,Calgary, Alberta, Canada; Department of Pathology & Laboratory Medicine, Cumming School of Medicine, University of Calgary,Calgary, Alberta, Canada; Division of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada; Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.
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Zogg AL, Simmen S, Zurfluh K, Stephan R, Schmitt SN, Nüesch-Inderbinen M. High Prevalence of Extended-Spectrum β-Lactamase Producing Enterobacteriaceae Among Clinical Isolates From Cats and Dogs Admitted to a Veterinary Hospital in Switzerland. Front Vet Sci 2018; 5:62. [PMID: 29662886 PMCID: PMC5890143 DOI: 10.3389/fvets.2018.00062] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/12/2018] [Indexed: 11/13/2022] Open
Abstract
Objectives This study aimed to identify and characterize extended-spectrum β-lactamase (ESBL) producing Enterobacteriaceae among clinical samples of companion animals. Methods A total of 346 non-duplicate Enterobacteriaceae isolates were collected between 2012 and 2016 from diseased cats (n = 115) and dogs (n = 231). The presence of blaESBL, PMQR genes, and the azithromycin resistance gene mph(A) was confirmed by PCR and sequencing of bla genes. Isolates were further characterized by antimicrobial resistance profiling, multilocus sequence typing, phylogenetic grouping, identification of mutations in the QRDR of gyrA and parC, and screening for virulence-associated genes. Results Among the 346 isolates, 72 (20.8%) were confirmed ESBL producers [58 Escherichia coli (E. coli), 11 Klebsiella pneumoniae (K. pneumoniae), and 3 Enterobacter cloacae]. The strains were cultured from urine (n = 45), skin and skin wounds (n = 8), abscesses (n = 6), surgical sites (n = 6), bile (n = 4), and other sites (n = 3). ESBL genes included blaCTX-M-1, 14, 15, 27, 55, and blaSHV-12, predominantly blaCTX-M-15 (54.8%, 40/73), and blaCTX-M-1 (24.7%, 18/73). Further genes included qnrB (4.2%, 3/72), qnrS (9.7%, 7/72), aac(6')-Ib-cr (47.2%, 34/72), and mph(A) (38.9%, 28/72). Seventeen (23.6%) isolates belonged to the major lineages of human pathogenic K. pneumoniae ST11, ST15, and ST147 and E. coli ST131. The most prevalent ST was E. coli ST410 belonging to phylogenetic group C. Conclusion The high prevalence of ESBL producing clinical Enterobacteriaceae from cats and dogs in Switzerland and the presence of highly virulent human-related K. pneumoniae and E. coli clones raises concern about transmission prevention as well as infection management and prevention in veterinary medicine.
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Affiliation(s)
- Anna Lena Zogg
- National Centre for Enteropathogenic Bacteria and Listeria, Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zürich, Zürich, Switzerland
| | - Sabrina Simmen
- National Centre for Enteropathogenic Bacteria and Listeria, Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zürich, Zürich, Switzerland
| | - Katrin Zurfluh
- National Centre for Enteropathogenic Bacteria and Listeria, Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zürich, Zürich, Switzerland
| | - Roger Stephan
- National Centre for Enteropathogenic Bacteria and Listeria, Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zürich, Zürich, Switzerland
| | - Sarah N Schmitt
- Vetsuisse Faculty, Institute of Veterinary Bacteriology, University of Zürich, Zürich, Switzerland
| | - Magdalena Nüesch-Inderbinen
- National Centre for Enteropathogenic Bacteria and Listeria, Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zürich, Zürich, Switzerland
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Abstract
Ever since antibiotics were introduced into human and veterinary medicine to treat and prevent bacterial infections there has been a steady selection and increase in the frequency of antibiotic resistant bacteria. To be able to reduce the rate of resistance evolution, we need to understand how various biotic and abiotic factors interact to drive the complex processes of resistance emergence and transmission. We describe several of the fundamental factors that underlay resistance evolution, including rates and niches of emergence and persistence of resistant bacteria, time- and space-gradients of various selective agents, and rates and routes of transmission of resistant bacteria between humans, animals and other environments. Furthermore, we discuss the options available to reduce the rate of resistance evolution and/ or transmission and their advantages and disadvantages.
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Giufrè M, Errico G, Accogli M, Monaco M, Villa L, Distasi MA, Del Gaudio T, Pantosti A, Carattoli A, Cerquetti M. Emergence of NDM-5-producing Escherichia coli sequence type 167 clone in Italy. Int J Antimicrob Agents 2018; 52:76-81. [PMID: 29501819 DOI: 10.1016/j.ijantimicag.2018.02.020] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/23/2018] [Accepted: 02/24/2018] [Indexed: 11/29/2022]
Abstract
The emergence of carbapenemase-producing Enterobacteriaceae (CPE) is a critical concern worldwide. In Italy, CPE isolates are very frequent, with the KPC enzyme types strongly predominant whereas the New Delhi metallo-β-lactamase (NDM) enzymes are extremely rare. Here we report the first detection of NDM-5-producing Escherichia coli sequence type 167 (ST167) isolates from two patients with urinary tract infection (Ec001 and Ec002 from urines), including one with colonisation (Ec003 from faeces) admitted to the same hospital 2 months apart in 2017. Minimum inhibitory concentrations (MICs) were determined by broth microdilution. The carbapenemase type was identified both by phenotypic and genotypic methods. Isolate genotypes were investigated by phylogenetic typing, multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Next-generation sequencing (NGS) was used to obtain complete sequences of plasmids. The three E. coli isolates carried the blaNDM-5 gene, shared the same resistance phenotype and belonged to ST167. By PFGE, isolates showed the same profile, suggesting that they were the same strain. NGS revealed that the blaNDM-5 gene was located on a 99-kb multireplicon plasmid (designed pNDM-5-IT) with a peculiar scaffold constituted by four replicons of the IncF type (FIA, FIB and two copies of the FII replicon). pNDM-5-IT plasmid harboured multiple resistance and virulence determinants, including the arginine deaminase (ADI) cluster never found associated with plasmids before. Since NDM-5-producing E. coli ST167 has been regarded as a successful epidemic clone in China, the emergence of such a clone carrying a plasmid associated both with multiresistance and virulence could be a public-health threat.
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Affiliation(s)
- Maria Giufrè
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Giulia Errico
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Marisa Accogli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Monica Monaco
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Laura Villa
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | | | - Tito Del Gaudio
- U.O. Clinical Pathology Unit, Lorenzo Bonomo Hospital, Andria, Italy
| | - Annalisa Pantosti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Alessandra Carattoli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Marina Cerquetti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
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Giufrè M, Accogli M, Ricchizzi E, Barbanti F, Farina C, Fazii P, Mattei R, Sarti M, Barozzi A, Buttazzi R, Cosentino M, Nardone M, Savini V, Spigaglia P, Moro ML, Cerquetti M. Multidrug-resistant infections in long-term care facilities: extended-spectrum β-lactamase-producing Enterobacteriaceae and hypervirulent antibiotic resistant Clostridium difficile. Diagn Microbiol Infect Dis 2018; 91:275-281. [PMID: 29571838 DOI: 10.1016/j.diagmicrobio.2018.02.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 11/15/2017] [Accepted: 02/23/2018] [Indexed: 11/30/2022]
Abstract
Infections due to multidrug-resistant (MDR) organisms in long-term care facilities (LTCFs) residents constitute a public health concern. This multicenter study investigated the frequency of ESBL-producing pathogens and MDR Clostridium difficile in clinical specimens from LTCF residents in Italy. During October 2014-March 2015, all urine and diarrheic fecal samples from LTCF residents (≥65 years) with suspected urinary tract infection or C. difficile infection, respectively, received for diagnosis by 4 hospital laboratories located in different cities were analyzed. Antibiotic susceptibility testing, characterization of resistance genes, and molecular typing of pathogens were performed. Of 806 urine cultures collected from 626 residents at 44 different LTCFs, 492 were positive for microbial infection. Of these, 158 were positive for at least an ESBL-producing Enterobacteriaceae species (32.1%), with Escherichia coli as the most frequent ESBL pathogen (23.4%) followed by Klebsiella pneumoniae (4.5%). Furthermore, 4 carbapenemase producers (0.8%) (1 E. coli with VIM-1and 3 K. pneumoniae with KPC-3) were detected. The CTX-M-15 type ESBL predominated in both E. coli (71.3%) and K. pneumoniae (77.3%). Most E. coli isolates (82.6%) belonged to the ST131/H30 clone/subclone. For K. pneumoniae, ST307 and ST15 were frequent (31.8% and 22.7%, respectively), but isolates harboring blaKPC-3 belonged to CC258. Of 136 diarrheic fecal samples collected from 111 residents at 26 different LTCFs, 21 (15.4%) were positive for toxigenic C. difficile; of these, 13 (62%) were MDR (resistant to 3 or more antimicrobial agents of different classes). The predominant C. difficile polymerase chain reaction ribotype was 356/607 (42.9%), followed by 018, 449, and 078 (14% each). Public health efforts are needed to contain the diffusion of CTX-M-producing Enterobacteriaceae and MDR C. difficile in LTCF settings.
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Affiliation(s)
- Maria Giufrè
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Marisa Accogli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | - Fabrizio Barbanti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | | | | | - Mario Sarti
- S. Agostino-Estense-Baggiovara Hospital, Modena, Italy
| | | | | | | | | | | | - Patrizia Spigaglia
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | - Marina Cerquetti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
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Hughes D, Andersson DI. Environmental and genetic modulation of the phenotypic expression of antibiotic resistance. FEMS Microbiol Rev 2018; 41:374-391. [PMID: 28333270 PMCID: PMC5435765 DOI: 10.1093/femsre/fux004] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 02/01/2017] [Indexed: 12/22/2022] Open
Abstract
Antibiotic resistance can be acquired by mutation or horizontal transfer of a resistance gene, and generally an acquired mechanism results in a predictable increase in phenotypic resistance. However, recent findings suggest that the environment and/or the genetic context can modify the phenotypic expression of specific resistance genes/mutations. An important implication from these findings is that a given genotype does not always result in the expected phenotype. This dissociation of genotype and phenotype has important consequences for clinical bacteriology and for our ability to predict resistance phenotypes from genetics and DNA sequences. A related problem concerns the degree to which the genes/mutations currently identified in vitro can fully explain the in vivo resistance phenotype, or whether there is a significant additional amount of presently unknown mutations/genes (genetic ‘dark matter’) that could contribute to resistance in clinical isolates. Finally, a very important question is whether/how we can identify the genetic features that contribute to making a successful pathogen, and predict why some resistant clones are very successful and spread globally? In this review, we describe different environmental and genetic factors that influence phenotypic expression of antibiotic resistance genes/mutations and how this information is needed to understand why particular resistant clones spread worldwide and to what extent we can use DNA sequences to predict evolutionary success.
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Affiliation(s)
- Diarmaid Hughes
- Corresponding author: Department of Medical Biochemistry and Microbiology, Biomedical Center (Box 582), Uppsala University, S-751 23 Uppsala, Sweden. Tel: +46 18 4714507; E-mail:
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24
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Paitan Y. Current Trends in Antimicrobial Resistance of Escherichia coli. Curr Top Microbiol Immunol 2018; 416:181-211. [PMID: 30088148 DOI: 10.1007/82_2018_110] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Escherichia coli is the most common Gram-negative bacterial pathogen, presenting both a clinical and an epidemiological challenge. In the last decade, several successful multidrug-resistant high-risk strains, such as strain E. coli ST131 have evolved, mainly due to the growing selective pressure of antimicrobial use. These strains present enhanced fitness and pathogenicity, effective transmission and colonization abilities, global distribution due to efficient dissemination, and resistance to various antimicrobial resistances. Here, we describe the emerging trends and epidemiology of resistant E. coli, including carbapenemase-producing E. coli, E. coli ST131 and colistin resistant E. coli.
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Affiliation(s)
- Yossi Paitan
- Clinical Microbiology Laboratory, Meir Medical Center, 44282, Kfar Saba, Israel. .,Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, 39978, Tel Aviv, Israel.
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Emergence of Escherichia coli Sequence Type 131 (ST131) and ST3948 with KPC-2, KPC-3 and KPC-8 carbapenemases from a Long-Term Care and Rehabilitation Facility (LTCRF) in Northern Italy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017. [PMID: 26810233 DOI: 10.1007/5584_2015_5017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Aim of the study was to characterize KPC-producing Escherichia coli (KPC-Ec) clinical isolates among a Northern Italy Long-Term Care and Rehabilitation Facility (LTCRF) residents. Thirteen consecutive non repeated MDR E. coli isolates showing ertapenem Minimum Inhibitory Concentrations (MICs) >0.5 mg/L, collected during the period March 2011 - May 2013 from ASP "Redaelli" inpatients, were investigated. The bla KPC/CTX-M/SHV/TEM/OXA genes were identified by PCR and sequencing. KPC-Ec isolates underwent phylotyping, Pulsed-Field Gel Electrophoresis (PFGE), multilocus sequence typing (MLST) and repetitive sequence-based PCR (rep-PCR) profiling. Incompatibility groups analysis and conjugation were also performed. Eleven out of 13 isolates, resulted bla KPC-type positive, were consistently resistant to third generation cephalosporins, fluoroquinolones and trimethoprim-sulphametoxazole (84.6 %), retaining susceptibility to colistin (EUCAST guidelines). At least n = 4/11 of KPC-Ec patients received ≥48 h of meropenem therapy. Sequencing identified 9 bla KPC-2, 1 bla KPC-3 and 1 bla KPC-8 determinants. KPC-Ec plasmids belonged to IncF group (FIIk replicon); conjugation confirmed bla KPC/TEM-1/OXA-9 genes transferability for 10 KPC-Ec. Although three pulsotypes (A, B, C) were identified, all KPC-Ec belonged to phylogenetic group B2. Clone B (B-B5) caused an outbreak of infection involving nine inpatients at five wards. Rep-PCR showed relatedness for seven representative KPC-Ec isolates. Here we report a LTCRF outbreak caused by a ST131-B2 E. coli associated with bla KPC-2 and bla KPC-8 genes, and the emergence of the new ST3948. Elderly people with co-morbidities are at risk for ST131 colonization. KPC-Ec clones local monitoring appears essential both to avoid their spreading among healthcare settings, and to improve therapeutic choices for LTCRF residents.
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Nübel U. Emergence and Spread of Antimicrobial Resistance: Recent Insights from Bacterial Population Genomics. Curr Top Microbiol Immunol 2017; 398:35-53. [PMID: 27738914 DOI: 10.1007/82_2016_505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Driven by progress of DNA sequencing technologies, recent population genomics studies have revealed that several bacterial pathogens constitute 'measurably evolving populations'. As a consequence, it was possible to reconstruct the emergence and spatial spread of drug-resistant bacteria on the basis of temporally structured samples of bacterial genome sequences. Based on currently available data, some general inferences can be drawn across different bacterial species as follows: (1) Resistance to various antibiotics evolved years to decades earlier than had been anticipated on the basis of epidemiological surveillance data alone. (2) Resistance traits are more rapidly acquired than lost and commonly persist in bacterial populations for decades. (3) Global populations of drug-resistant pathogens are dominated by very few clones, yet the features enabling such spreading success have not been revealed, aside from antibiotic resistance. (4) Whole-genome sequencing proved very effective at identifying bacterial isolates as parts of the same transmission networks.
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Affiliation(s)
- Ulrich Nübel
- DZIF Group on Microbial Genome Research, Leibniz Institute DSMZ, Braunschweig, Germany. .,Technical University Braunschweig, Braunschweig, Germany. .,German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany.
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27
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Giufrè M, Ricchizzi E, Accogli M, Barbanti F, Monaco M, Pimentel de Araujo F, Farina C, Fazii P, Mattei R, Sarti M, Barozzi A, Buttazzi R, Cosentino M, Nardone M, Savini V, Spigaglia P, Pantosti A, Moro ML, Cerquetti M. Colonization by multidrug-resistant organisms in long-term care facilities in Italy: a point-prevalence study. Clin Microbiol Infect 2017; 23:961-967. [PMID: 28412380 DOI: 10.1016/j.cmi.2017.04.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/30/2017] [Accepted: 04/06/2017] [Indexed: 11/24/2022]
Abstract
OBJECTIVES To determine prevalence and risk factors for colonization by multidrug-resistant organisms (MDROs) in long-term care facility (LTCF) residents in Italy. Genotypes of MDRO isolates were investigated. METHODS A point-prevalence study was conducted at 12 LTCFs located in four Italian cities (2 February to 14 March 2015). Rectal swabs, faeces and nasal/auxiliary swabs were cultured for extended-spectrum β-lactamase (ESBL)- and/or carbapenemase-producing Enterobacteriaceae, Clostridium difficile and methicillin-resistant Staphylococcus aureus (MRSA) respectively. Antimicrobial susceptibility testing, detection of ESBL and/or carbapenemase genes and molecular typing of MDROs were performed. Risk factors for colonization were determined by univariate and multivariate analysis. RESULTS A total of 489 LTCF residents aged ≥65 years were enrolled. The prevalence of colonization by ESBL-producing Enterobacteriaceae, MRSA and C. difficile was 57.3% (279/487), 17.2% (84/487) and 5.1% (21/409) respectively. Carriage rate of carbapenemase-producing Enterobacteriaceae was 1% (5/487). Being bedridden was a common independent risk factor for colonization by all MDROs, although risk factors specific for each MDRO were identified. ESBL-producing Escherichia coli carriage was associated with the sequence type (ST) 131-H30 subclone, but other minor STs predominated in individual LTCF or in LTCFs located in the same city, suggesting a role for intrafacility or local transmission. Similarly, MRSA from LTCF residents belonged to the same spa types/ST clones (t008/ST8 and t032/ST22) commonly found in Italian acute-care hospitals, but infrequent spa types were recovered in individual LTCFs. The prevalent C. difficile PCR ribotypes were 356/607 and 018, both common in Italian acute-care hospitals. CONCLUSIONS MDRO colonization is common among residents in Italian LTCFs.
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Affiliation(s)
- M Giufrè
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - E Ricchizzi
- Health and Social Agency, Emilia-Romagna Region, Bologna, Italy
| | - M Accogli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - F Barbanti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - M Monaco
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | - C Farina
- Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - P Fazii
- Spirito Santo Hospital, Pescara, Italy
| | - R Mattei
- Campo di Marte Hospital, Lucca, Italy
| | - M Sarti
- S. Agostino-Estense-Baggiovara Hospital, Modena, Italy
| | - A Barozzi
- S. Agostino-Estense-Baggiovara Hospital, Modena, Italy
| | - R Buttazzi
- Health and Social Agency, Emilia-Romagna Region, Bologna, Italy
| | - M Cosentino
- Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - M Nardone
- Campo di Marte Hospital, Lucca, Italy
| | - V Savini
- Spirito Santo Hospital, Pescara, Italy
| | - P Spigaglia
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - A Pantosti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - M L Moro
- Health and Social Agency, Emilia-Romagna Region, Bologna, Italy
| | - M Cerquetti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
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Cunha MPV, Lincopan N, Cerdeira L, Esposito F, Dropa M, Franco LS, Moreno AM, Knöbl T. Coexistence of CTX-M-2, CTX-M-55, CMY-2, FosA3, and QnrB19 in Extraintestinal Pathogenic Escherichia coli from Poultry in Brazil. Antimicrob Agents Chemother 2017; 61:e02474-16. [PMID: 28167554 PMCID: PMC5365709 DOI: 10.1128/aac.02474-16] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Marcos P V Cunha
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Louise Cerdeira
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Fernanda Esposito
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Milena Dropa
- School of Public Health, University of São Paulo, São Paulo, Brazil
| | - Leticia S Franco
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Andrea M Moreno
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Terezinha Knöbl
- School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
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29
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Aschbacher R, Pagani E, Confalonieri M, Farina C, Fazii P, Luzzaro F, Montanera PG, Piazza A, Pagani L. Review on colonization of residents and staff in Italian long-term care facilities by multidrug-resistant bacteria compared with other European countries. Antimicrob Resist Infect Control 2016; 5:33. [PMID: 27766146 PMCID: PMC5057254 DOI: 10.1186/s13756-016-0136-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 09/27/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Rates of colonization and infection with multidrug-resistant (MDR) bacteria are increasing worldwide, in both acute care hospitals and long-term care facilities (LTCFs). Italy has one of the highest prevalence of MDR bacteria in European countries, especially with regard to methicillin-resistant Staphylococcus aureus (MRSA) and extended-spectrum β-lactamase (ESBL) or carbapenemase producing Enterobacteriaceae (CPE). METHOD Review of studies on colonization by MDR bacteria from Italian LTCFs, risk factors for colonization and molecular characteristics of surveillance and clinical isolates, compared with other European countries. RESULTS High variability of MDR colonization has been reported within and especially between European countries. Only a few surveillance studies have been performed in Italian LTCFs; these show MRSA colonization prevalence of 7.8-38.7 % for residents and 5.2-7.0 % for staff members, ESBL prevalence of 49.0-64.0 % for residents and 5.2-14.5 % for staff and prevalence of CPE of 1.0-6.3 % for residents and 0.0-1.5 % for staff. In Italian LTCFs, as well as in other European countries, the most prevalent ESBLs from surveillance or clinical Escherichia coli isolates were found to be CTX-M-type enzymes, particularly CTX-M-15, expressed by the pandemic ST131 clonal group; this lineage also expresses carbapenemase genes of the blaVIM and blaKPC types. Various risk factors for colonization of residents by MDR bacteria were identified. CONCLUSIONS The limited data from Italian LTCFs confirms these settings as important reservoirs for MDR organisms, allowing important considerations regarding the infection risk by these organisms. Nevertheless, more extended and countrywide screening studies for MDR colonization in Italian LTCFs are required. To promote further studies of various microbiological aspects related to LTCFs, the Association of Italian Clinical Microbiologists (Associazione Microbiologi Clinici Italiani; AMCLI) in 2016 has set up a new Working Group for the Study of Infections in LTCFs (Gruppo di Lavoro per lo Studio delle Infezioni nelle Residenze Sanitarie Assistite e Strutture Territoriali assimilabili; GLISTer), consisting of Clinical Microbiologists represented by the authors of this review article.
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Affiliation(s)
- Richard Aschbacher
- Laboratorio Aziendale di Microbiologia e Virologia, Comprensorio Sanitario di Bolzano, Bolzano, Italy
| | - Elisabetta Pagani
- Laboratorio Aziendale di Microbiologia e Virologia, Comprensorio Sanitario di Bolzano, Bolzano, Italy
| | | | - Claudio Farina
- Azienda Socio-Sanitaria Territoriale Papa Giovanni XXIII, USC Microbiologia e Virologia, Bergamo, Italy
| | - Paolo Fazii
- P.O. Spirito Santo Laboratorio Analisi, Pescara, Italy
| | - Francesco Luzzaro
- Ospedale A. Manzoni, Laboratorio Microbiologia e Virologia, Lecco, Italy
| | | | - Aurora Piazza
- Dipartimento SCCDP, Unità di Microbiologia e Microbiologia clinica, Pavia, Italy
| | - Laura Pagani
- Dipartimento SCCDP, Unità di Microbiologia e Microbiologia clinica, Pavia, Italy
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Escherichia coli Harboring mcr-1 and blaCTX-M on a Novel IncF Plasmid: First Report of mcr-1 in the United States. Antimicrob Agents Chemother 2016; 60:4420-1. [PMID: 27230792 PMCID: PMC4914657 DOI: 10.1128/aac.01103-16] [Citation(s) in RCA: 281] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Arshad M, Goller CC, Pilla D, Schoenen FJ, Seed PC. Threading the Needle: Small-Molecule Targeting of a Xenobiotic Receptor to Ablate Escherichia coli Polysaccharide Capsule Expression Without Altering Antibiotic Resistance. J Infect Dis 2015; 213:1330-9. [PMID: 26671885 DOI: 10.1093/infdis/jiv584] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/19/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Uropathogenic Escherichia coli (UPEC), a leading cause of urinary tract and invasive infections worldwide, is rapidly acquiring multidrug resistance, hastening the need for selective new anti-infective agents. Here we demonstrate the molecular target of DU011, our previously discovered potent, nontoxic, small-molecule inhibitor of UPEC polysaccharide capsule biogenesis and virulence. METHODS Real-time polymerase chain reaction analysis and a target-overexpression drug-suppressor screen were used to localize the putative inhibitor target. A thermal shift assay quantified interactions between the target protein and the inhibitor, and a novel DNase protection assay measured chemical inhibition of protein-DNA interactions. Virulence of a regulatory target mutant was assessed in a murine sepsis model. RESULTS MprA, a MarR family transcriptional repressor, was identified as the putative target of the DU011 inhibitor. Thermal shift measurements indicated the formation of a stable DU011-MprA complex, and DU011 abrogated MprA binding to its DNA promoter site. Knockout of mprA had effects similar to that of DU011 treatment of wild-type bacteria: a loss of encapsulation and complete attenuation in a murine sepsis model, without any negative change in antibiotic resistance. CONCLUSIONS MprA regulates UPEC polysaccharide encapsulation, is essential for UPEC virulence, and can be targeted without inducing antibiotic resistance.
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Affiliation(s)
| | | | | | | | - Patrick C Seed
- Department of Pediatrics Department of Molecular Genetics and Microbiology Center for Microbial Pathogenesis, Duke University School of Medicine, Durham, North Carolina
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The role of epidemic resistance plasmids and international high-risk clones in the spread of multidrug-resistant Enterobacteriaceae. Clin Microbiol Rev 2015; 28:565-91. [PMID: 25926236 DOI: 10.1128/cmr.00116-14] [Citation(s) in RCA: 540] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Escherichia coli sequence type 131 (ST131) and Klebsiella pneumoniae ST258 emerged in the 2000s as important human pathogens, have spread extensively throughout the world, and are responsible for the rapid increase in antimicrobial resistance among E. coli and K. pneumoniae strains, respectively. E. coli ST131 causes extraintestinal infections and is often fluoroquinolone resistant and associated with extended-spectrum β-lactamase production, especially CTX-M-15. K. pneumoniae ST258 causes urinary and respiratory tract infections and is associated with carbapenemases, most often KPC-2 and KPC-3. The most prevalent lineage within ST131 is named fimH30 because it contains the H30 variant of the type 1 fimbrial adhesin gene, and recent molecular studies have demonstrated that this lineage emerged in the early 2000s and was then followed by the rapid expansion of its sublineages H30-R and H30-Rx. K. pneumoniae ST258 comprises 2 distinct lineages, namely clade I and clade II. Moreover, it seems that ST258 is a hybrid clone that was created by a large recombination event between ST11 and ST442. Epidemic plasmids with blaCTX-M and blaKPC belonging to incompatibility group F have contributed significantly to the success of these clones. E. coli ST131 and K. pneumoniae ST258 are the quintessential examples of international multidrug-resistant high-risk clones.
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Schembri MA, Zakour NLB, Phan MD, Forde BM, Stanton-Cook M, Beatson SA. Molecular Characterization of the Multidrug Resistant Escherichia coli ST131 Clone. Pathogens 2015; 4:422-30. [PMID: 26131613 PMCID: PMC4584265 DOI: 10.3390/pathogens4030422] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 06/08/2015] [Accepted: 06/23/2015] [Indexed: 01/20/2023] Open
Abstract
Escherichia coli ST131 is a recently emerged and globally disseminated multidrug resistant clone associated with urinary tract and bloodstream infections in both community and clinical settings. The most common group of ST131 strains are defined by resistance to fluoroquinolones and possession of the type 1 fimbriae fimH30 allele. Here we provide an update on our recent work describing the globally epidemiology of ST131. We review the phylogeny of ST131 based on whole genome sequence data and highlight the important role of recombination in the evolution of this clonal lineage. We also summarize our findings on the virulence of the ST131 reference strain EC958, and highlight the use of transposon directed insertion-site sequencing to define genes associated with serum resistance and essential features of its large antibiotic resistance plasmid pEC958.
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Affiliation(s)
- Mark A Schembri
- School of Chemistry & Molecular Biosciences, the University of Queensland, Brisbane, Queensland 4072, Australia.
- Australian Infectious Diseases Research Centre, the University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Nouri L Ben Zakour
- School of Chemistry & Molecular Biosciences, the University of Queensland, Brisbane, Queensland 4072, Australia.
- Australian Infectious Diseases Research Centre, the University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Minh-Duy Phan
- School of Chemistry & Molecular Biosciences, the University of Queensland, Brisbane, Queensland 4072, Australia.
- Australian Infectious Diseases Research Centre, the University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Brian M Forde
- School of Chemistry & Molecular Biosciences, the University of Queensland, Brisbane, Queensland 4072, Australia.
- Australian Infectious Diseases Research Centre, the University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Mitchell Stanton-Cook
- School of Chemistry & Molecular Biosciences, the University of Queensland, Brisbane, Queensland 4072, Australia.
- Australian Infectious Diseases Research Centre, the University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Scott A Beatson
- School of Chemistry & Molecular Biosciences, the University of Queensland, Brisbane, Queensland 4072, Australia.
- Australian Infectious Diseases Research Centre, the University of Queensland, Brisbane, Queensland 4072, Australia.
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Variation in resistance traits, phylogenetic backgrounds, and virulence genotypes among Escherichia coli clinical isolates from adjacent hospital campuses serving distinct patient populations. Antimicrob Agents Chemother 2015; 59:5331-9. [PMID: 26100703 DOI: 10.1128/aac.00048-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 06/10/2015] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli sequence type 13 (ST131), an emergent cause of multidrug-resistant extraintestinal infections, has important phylogenetic subsets, notably the H30 and H30Rx subclones, with distinctive resistance profiles and, possibly, clinical associations. To clarify the local prevalence of these ST131 subclones and their associations with antimicrobial resistance, ecological source, and virulence traits, we extensively characterized 233 consecutive E. coli clinical isolates (July and August 2013) from the University of Minnesota Medical Center-Fairview Infectious Diseases and Diagnostic Laboratory, Minneapolis, MN, which serves three adjacent facilities (a children's hospital and low- and high-acuity adult facilities). ST131 accounted for 26% of the study isolates (more than any other clonal group), was distributed similarly by facility, and was closely associated with ciprofloxacin resistance and extended-spectrum β-lactamase (ESBL) production. The H30 and H30Rx subclones accounted for most ST131 isolates and for the association of ST131 with fluoroquinolone resistance and ESBL production. Unlike ST131 per se, these subclones were distributed differentially by hospital, being most prevalent at the high-acuity adult facility and were absent from the children's hospital. The virulence gene profiles of ST131 and its subclones were distinctive and more extensive than those of other fluoroquinolone-resistant or ESBL-producing isolates. Within ST131, bla CTX-M-15 was confined to H30Rx isolates and other bla CTX-M variants to non-Rx H30 isolates. Pulsed-field gel electrophoresis documented a predominance of globally distributed pulsotypes and no local outbreak pattern. These findings help clarify the epidemiology, ecology, and bacterial correlates of the H30 and H30Rx ST131 subclones by documenting a high overall prevalence but significant segregation by facility, strong associations with fluoroquinolone resistance and specific ESBL variants, and distinctive virulence gene associations that may confer fitness advantages over other resistant E. coli.
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Complete Genome Sequence of a Carbapenem-Resistant Extraintestinal Pathogenic Escherichia coli Strain Belonging to the Sequence Type 131 H30R Subclade. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00272-15. [PMID: 25858844 PMCID: PMC4392156 DOI: 10.1128/genomea.00272-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the completed genome sequence of a carbapenem-resistant extraintestinal pathogenic Escherichia coli sequence type 131 (ST131) isolate, MNCRE44. The isolate was obtained in 2012 in Minnesota, USA, from a sputum sample from a hospitalized patient with multiple comorbidities, and it belongs to the H30R sublineage.
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Giacobbe DR, Del Bono V, Coppo E, Marchese A, Viscoli C. Emergence of a KPC-3-Producing Escherichia coli ST69 as a Cause of Bloodstream Infections in Italy. Microb Drug Resist 2014; 21:342-4. [PMID: 25514440 DOI: 10.1089/mdr.2014.0230] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The spread of carbapenem-resistant gram negatives is a global emergency, and surveillance of new resistant clones is critical from both public health and clinical standpoints. Herein, we describe the emergence of a KPC-3-producing Escherichia coli ST69 as a cause of bloodstream infection in two Italian patients.
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Affiliation(s)
- Daniele Roberto Giacobbe
- 1Infectious Diseases Unit, IRCCS San Martino University Hospital-IST, University of Genoa, Genoa, Italy
| | - Valerio Del Bono
- 1Infectious Diseases Unit, IRCCS San Martino University Hospital-IST, University of Genoa, Genoa, Italy
| | - Erika Coppo
- 2Microbiology Unit DISC, IRCCS San Martino University Hospital-IST, University of Genoa, Genoa, Italy
| | - Anna Marchese
- 2Microbiology Unit DISC, IRCCS San Martino University Hospital-IST, University of Genoa, Genoa, Italy
| | - Claudio Viscoli
- 1Infectious Diseases Unit, IRCCS San Martino University Hospital-IST, University of Genoa, Genoa, Italy
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37
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Mathers AJ, Peirano G, Pitout JDD. Escherichia coli ST131: The quintessential example of an international multiresistant high-risk clone. ADVANCES IN APPLIED MICROBIOLOGY 2014; 90:109-54. [PMID: 25596031 DOI: 10.1016/bs.aambs.2014.09.002] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Escherichia coli ST131 emerged during the early to mid-2000s is an important human pathogen, has spread extensively throughout the world, and is responsible for the rapid increase in antimicrobial resistance among E. coli. ST131 is known to cause extraintestinal infections, being fluoroquinolone resistant, and is associated with ESBL production most often due to CTX-M-15. Recent molecular epidemiologic studies using whole-genome sequencing and phylogenetic analysis have demonstrated that the H30 ST131 lineage emerged in early 2000s that was followed by the rapid expansion of its sublineages H30-R and H30-Rx. Escherichia coli ST131 clearly has all of the essential characteristics that define a high-risk clone and might be the quintessential example of an international multiresistant high-risk clone. We urgently need rapid cost-effective detection methods for E. coli ST131, as well as well-designed epidemiological and molecular studies to understand the dynamics of transmission, risk factors, and reservoirs for ST131. This will provide insight into the emergence and spread of this multiresistant sequence type that will hopefully lead to information essential for preventing the spread of ST131.
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Affiliation(s)
| | - Gisele Peirano
- Division of Microbiology, Calgary Laboratory Services, University of Calgary, Calgary, AB, Canada; Departments of Pathology & Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | - Johann D D Pitout
- Division of Microbiology, Calgary Laboratory Services, University of Calgary, Calgary, AB, Canada; Departments of Pathology & Laboratory Medicine, University of Calgary, Calgary, AB, Canada; Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
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