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Mavroidi A, Froukala E, Tsakris A. Comparative Genomics of an Emerging Multidrug-Resistant blaNDM-Carrying ST182 Lineage in Enterobacter cloacae Complex. Antibiotics (Basel) 2024; 13:535. [PMID: 38927201 PMCID: PMC11200890 DOI: 10.3390/antibiotics13060535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/02/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Enterobacter cloacae, E. hormaechei and related subspecies remain the most clinically relevant among the Enterobacter cloacae complex (ECC). Carbapenemase-producing ECC strains are increasingly identified in hospital-acquired infections and usually belong to four main multilocus sequence types (MLST STs) named ST114, ST93, ST90 and ST78. Instead, ST182 has been sporadically reported among E. hormaechei strains, and recently, outbreaks of blaNDM-producing ST182 clonal strains have emerged. Herein, we aimed to investigate the presence of ST182 and explore its evolution and modes of blaNDM acquisition. METHODS A phylogenetic analysis of 646 MLST STs identified among 4685 E. hormaechei whole-genome sequencing (WGS) assemblies deposited in public repositories was performed, as well as an in silico comparative and phylogenomic analyses for 55 WGS assemblies of ST182. blaNDM-harboring contigs were also compared to published plasmid sequences. RESULTS ST182 E. hormaechei strains were recovered from patients on five continents during 2011-2021. They were divided into three major genomic clusters, comprising a separate clonal complex with six other STs. In 30 out of 55 ST182 WGS assemblies, blaNDM-harboring structures were identified that were similar to the plasmids predominant in Gram-negative bacteria, harboring resistance genes to multiple antibiotic classes and virulence genes. No associations between the genomic clusters and the country/continent of isolation or the presence and the plasmid types of the blaNDM-harboring contigs were observed. CONCLUSIONS Our findings show that ST182 E. hormaechei strains have been identified in the past decade worldwide; 54.5% of them carried diverse blaNDM genetic structures, suggesting recent acquisition of the blaNDM alleles. Thus, blaNDM-harboring ST182 is an emerging multidrug-resistant and virulent lineage in ECC strains that requires close monitoring.
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Affiliation(s)
- Angeliki Mavroidi
- Department of Microbiology, Faculty of Medicine, General University Hospital of Patras, 26504 Patras, Greece;
| | - Elisavet Froukala
- Department of Microbiology, Medical School, University of Athens, 11527 Athens, Greece;
| | - Athanasios Tsakris
- Department of Microbiology, Medical School, University of Athens, 11527 Athens, Greece;
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Zeng S, Huang Y, Zhang X, Fu L, Sun Z, Li X. Molecular characterization of IncFII plasmid carrying blaNDM-5 in a Salmonella enterica serovar Typhimurium ST34 clinical isolate in China. mSphere 2023; 8:e0048023. [PMID: 37909767 PMCID: PMC10732066 DOI: 10.1128/msphere.00480-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 09/26/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE In this study, an IncFII plasmid pIncFII-NDM5 carrying blaNDM-5 was found in carbapenem-resistant Salmonella enterica serovar Typhimurium (S. enterica serovar Typhimurium), which has conjugative transferability and carried blaNDM-5, bleMBL, mph(A), and blaTEM-1 four resistance genes that can mediate resistance to multiple antibiotics including cephalosporins, beta-lactamase inhibitor combinations, carbapenems, and macrolides. Phylogenetic analysis showed that 1104-65 and 1104-75 were closely related to other S. enterica serovar Typhimurium in this area. The above-mentioned S. enterica serovar Typhimurium chromosome carries blaCTX-M-55, qnrS1, and tet(A) genes, so the antibiotic resistance of isolates will be further enhanced after obtaining the pIncFII_NDM5-like plasmid. Meanwhile, we discovered a novel genetic structure of blaNDM-5 mediated by the IS26 composite transposon, which will expand our understanding of the emergence and spread of carbapenem-resistance genes. Altogether, the presence of the IncFII plasmid pIncFII-NDM5 further underscores the need for vigilant surveillance and appropriate infection control measures to mitigate the impact of carbapenem-resistant S. enterica serovar Typhimurium in clinical settings.
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Affiliation(s)
- Shihan Zeng
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Yulan Huang
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Xiwei Zhang
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Liang Fu
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Zhaohui Sun
- Department of Laboratory Medicine, General Hospital of Southern Theater Command, Guangzhou, China
| | - Xiaoyan Li
- Department of Clinical Laboratory, Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
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Boueroy P, Chopjitt P, Hatrongjit R, Morita M, Sugawara Y, Akeda Y, Iida T, Hamada S, Kerdsin A. Fluoroquinolone resistance determinants in carbapenem-resistant Escherichia coli isolated from urine clinical samples in Thailand. PeerJ 2023; 11:e16401. [PMID: 37953793 PMCID: PMC10638923 DOI: 10.7717/peerj.16401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 10/12/2023] [Indexed: 11/14/2023] Open
Abstract
Background Escherichia coli is the most common cause of urinary tract infections and has fluoroquinolone (FQ)-resistant strains, which are a worldwide concern. Objectives To characterize FQ-resistant determinants among 103 carbapenem-resistant E. coli (CREc) urinary isolates using WGS. Methods Antimicrobial susceptibility, biofilm formation, and short-read sequencing were applied to these isolates. Complete genome sequencing of five CREcs was conducted using short- and long-read platforms. Results ST410 (50.49%) was the predominant ST, followed by ST405 (12.62%) and ST361 (11.65%). Clermont phylogroup C (54.37%) was the most frequent. The genes NDM-5 (74.76%) and CTX-M-15 (71.84%) were the most identified. Most CREcs were resistant to ciprofloxacin (97.09%) and levofloxacin (94.17%), whereas their resistance rate to nitrofurantoin was 33.98%. Frequently, the gene aac(6')-Ib (57.28%) was found and the coexistence of aac(6')-Ib and blaCTX-M-15 was the most widely predominant. All isolates carried the gyrA mutants of S83L and D87N. In 12.62% of the isolates, the coexistence was detected of gyrA, gyrB, parC, and parE mutations. Furthermore, the five urinary CREc-complete genomes revealed that blaNDM-5 or blaNDM-3 were located on two plasmid Inc types, comprising IncFI (60%, 3/5) and IncFI/IncQ (40%, 2/5). In addition, both plasmid types carried other resistance genes, such as blaOXA-1, blaCTX-M-15, blaTEM-1B, and aac(6')-Ib. Notably, the IncFI plasmid in one isolate carried three copies of the blaNDM-5 gene. Conclusions This study showed FQ-resistant determinants in urinary CREc isolates that could be a warning sign to adopt efficient strategies or new control policies to prevent further spread and to help in monitoring this microorganism.
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Affiliation(s)
- Parichart Boueroy
- Faculty of Public Health, Kasetsart University, Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Peechanika Chopjitt
- Faculty of Public Health, Kasetsart University, Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Rujirat Hatrongjit
- Faculty of Science and Engineering, Kasetsart University, Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Masatomo Morita
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yo Sugawara
- Japan-Thailand Research Collaboration Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
- Japan-Thailand Research Collaboration Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tetsuya Iida
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Shigeyuki Hamada
- Japan-Thailand Research Collaboration Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University, Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
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Mr. Saddam, Khan M, Jamal M, Rahman SU, Qadeer A, Khan I, Mahmoud MH, Batiha GES, Shah SH. Nutritional analysis and characterization of carbapenemase producing-Klebsiella pneumoniae resistant genes associated with bovine mastitis infected cow's milk. PLoS One 2023; 18:e0293477. [PMID: 37889925 PMCID: PMC10610456 DOI: 10.1371/journal.pone.0293477] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
The current study was designed to analyze nutritional parameters and to characterize carbapenemase producing-Klebsiella pneumoniae isolates from bovine mastitic cow's milk. Out of 700 milk samples K. pneumoniae was identified by phenotypic and molecular techniques along with their antibiogram analysis and nutritional analysis was performed using the procedure of Association of Official Analytical Chemists. Carbapenemase-producing K. pneumoniae was detected by phenotypic CarbaNP test followed by molecular characterization of their associated resistant genes blaVIM, blaKPC, blaOXA-48, blaNDM, and blaIMP along with insertion sequence common region 1 (ISCR1) and integrons (Int1, Int2, and Int3) genes. Among nutritional parameters, fat content was observed (2.99%) followed by protein (2.78%), lactose (4.32%), and total solid (11.34%), respectively. The prevalence of K. pneumoniae among bovine mastitis was found 25.71%. Antibiogram analysis revealed that more effective antibiotics was ceftazidime (80%) followed by amikacin (72%), while highly resistant antibiotics was Fusidic acid (100%). Distribution of carbapenemase producer K. pneumoniae was found 44.4%. Among carbapenem resistant genes blaKPC was found 11.25%, blaVIM 2.75%, blaNDM 17.5%, and blaOXA-48 7.5%, while blaIMP gene was not detected. Furthermore, distribution of ISCR1 was found 40%, while integron 1 was found 61.2% followed by integron 2 (20%), and integron 3 (5%). In conclusion, the recent scenario of carbapenemase resistant K. pneumoniae isolates responsible for mastitis may affect not only the current treatment regime but also possess a serious threat to public health due to its food borne transmission and zoonotic potential.
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Affiliation(s)
- Mr. Saddam
- Department of Microbiology, Abdul Wali Khan University, Marden, Pakistan
| | - Muddasir Khan
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Muhsin Jamal
- Department of Microbiology, Abdul Wali Khan University, Marden, Pakistan
| | - Sadeeq Ur Rahman
- College of Veterinary Sciences and Animal Husbandry, Abdul Wali Khan University, Mardan, Pakistan
| | - Abdul Qadeer
- Shanghai Tenth People’s Hospital, Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Imad Khan
- College of Veterinary Sciences and Animal Husbandry, Abdul Wali Khan University, Mardan, Pakistan
| | - Mohamed H. Mahmoud
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Gaber El-Saber Batiha
- Department of Pharmacology, Faculty of Veterinary Medicine, Damanhour University, Damanhour, AlBeheira, Egypt
| | - Syed Hussain Shah
- Department of Health and Biological Sciences, Abasyn University Peshawar, Peshawar, Pakistan
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BABINES-OROZCO L, BALBUENA-ALONSO MG, BARRIOS-VILLA E, LOZANO-ZARAIN P, MARTÍNEZ-LAGUNA Y, DEL CARMEN ROCHA-GRACIA R, CORTÉS-CORTÉS G. Antimicrobial resistance in food-associated Escherichia coli in Mexico and Latin America. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2023; 43:4-12. [PMID: 38188662 PMCID: PMC10767319 DOI: 10.12938/bmfh.2023-022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/11/2023] [Indexed: 01/09/2024]
Abstract
The World Health Organization (WHO) considers antimicrobial resistance to be one of the critical global public health priorities to address. Escherichia coli is a commensal bacterium of the gut microbiota in humans and animals; however, some strains cause infections and are resistant to antibiotics. One of the most common ways of acquiring pathogenic E. coli strains is through food. This review analyzes multidrug-resistant E. coli isolated from food, emphasizing Latin America and Mexico, and the mobile genetic elements (MGEs) responsible for spreading antibiotic resistance determinants among bacteria in different environments and hosts. We conducted a systematic search of the literature published from 2015 to 2022 in open access databases and electronic repositories. The prevalence of 11 E. coli pathotypes was described, with diarrheagenic E. coli pathotypes being the most frequently associated with foodborne illness in different Latin American countries, highlighting the presence of different antibiotic resistance genes mostly carried by IncF-type plasmids or class 1 integrons. Although the global incidence of foodborne illness is high, there have been few studies in Mexico and Latin America, which highlights the need to generate updated epidemiological data from the "One Health" approach, which allows monitoring of the multidrug-resistance phenomenon in E. coli from a common perspective in the interaction of human, veterinary, and environmental health.
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Affiliation(s)
- Lorena BABINES-OROZCO
- Posgrado en Microbiología, Centro de Investigaciones en
Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de
Puebla. Instituto de Ciencias, Ciudad Universitaria, San Manuel C.P. 72570 Puebla,
México
| | - María Guadalupe BALBUENA-ALONSO
- Posgrado en Microbiología, Centro de Investigaciones en
Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de
Puebla. Instituto de Ciencias, Ciudad Universitaria, San Manuel C.P. 72570 Puebla,
México
| | - Edwin BARRIOS-VILLA
- Departamento de Ciencias Químico Biológicas y Agropecuarias,
Unidad Regional Norte, Campus Caborca, Universidad de Sonora, Col. Eleazar Ortiz C.P.
83621 H. Caborca, Sonora, México
| | - Patricia LOZANO-ZARAIN
- Posgrado en Microbiología, Centro de Investigaciones en
Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de
Puebla. Instituto de Ciencias, Ciudad Universitaria, San Manuel C.P. 72570 Puebla,
México
| | - Ygnacio MARTÍNEZ-LAGUNA
- Posgrado en Microbiología, Centro de Investigaciones en
Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de
Puebla. Instituto de Ciencias, Ciudad Universitaria, San Manuel C.P. 72570 Puebla,
México
| | - Rosa DEL CARMEN ROCHA-GRACIA
- Posgrado en Microbiología, Centro de Investigaciones en
Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de
Puebla. Instituto de Ciencias, Ciudad Universitaria, San Manuel C.P. 72570 Puebla,
México
| | - Gerardo CORTÉS-CORTÉS
- Posgrado en Microbiología, Centro de Investigaciones en
Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de
Puebla. Instituto de Ciencias, Ciudad Universitaria, San Manuel C.P. 72570 Puebla,
México
- Department of Microbiology and Environmental Toxicology,
University of California at Santa Cruz, Santa Cruz, CA 95064, USA
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Nguyen QH, Le TTH, Nguyen ST, Nguyen KOT, Quyen DV, Hayer J, Bañuls AL, Tran TTT. Large-scale analysis of putative plasmids in clinical multidrug-resistant Escherichia coli isolates from Vietnamese patients. Front Microbiol 2023; 14:1094119. [PMID: 37323902 PMCID: PMC10265513 DOI: 10.3389/fmicb.2023.1094119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction In the past decades, extended-spectrum beta-lactamase (ESBL)-producing and carbapenem-resistant (CR) Escherichia coli isolates have been detected in Vietnamese hospitals. The transfer of antimicrobial resistance (AMR) genes carried on plasmids is mainly responsible for the emergence of multidrug-resistant E. coli strains and the spread of AMR genes through horizontal gene transfer. Therefore, it is important to thoroughly study the characteristics of AMR gene-harboring plasmids in clinical multidrug-resistant bacterial isolates. Methods The profiles of plasmid assemblies were determined by analyzing previously published whole-genome sequencing data of 751 multidrug-resistant E. coli isolates from Vietnamese hospitals in order to identify the risk of AMR gene horizontal transfer and dissemination. Results The number of putative plasmids in isolates was independent of the sequencing coverage. These putative plasmids originated from various bacterial species, but mostly from the Escherichia genus, particularly E. coli species. Many different AMR genes were detected in plasmid contigs of the studied isolates, and their number was higher in CR isolates than in ESBL-producing isolates. Similarly, the blaKPC-2, blaNDM-5, blaOXA-1, blaOXA-48, and blaOXA-181 β-lactamase genes, associated with resistance to carbapenems, were more frequent in CR strains. Sequence similarity network and genome annotation analyses revealed high conservation of the β-lactamase gene clusters in plasmid contigs that carried the same AMR genes. Discussion Our study provides evidence of horizontal gene transfer in multidrug-resistant E. coli isolates via conjugative plasmids, thus rapidly accelerating the emergence of resistant bacteria. Besides reducing antibiotic misuse, prevention of plasmid transmission also is essential to limit antibiotic resistance.
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Affiliation(s)
- Quang Huy Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- LMI DRISA, IRD-USTH, Hanoi, Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thi Thu Hang Le
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- LMI DRISA, IRD-USTH, Hanoi, Vietnam
| | - Son Thai Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- LMI DRISA, IRD-USTH, Hanoi, Vietnam
| | - Kieu-Oanh Thi Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- LMI DRISA, IRD-USTH, Hanoi, Vietnam
| | - Dong Van Quyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Juliette Hayer
- LMI DRISA, IRD-USTH, Hanoi, Vietnam
- UMR MIVEGEC, University of Montpellier-IRD-CNRS, Montpellier, France
| | - Anne-Laure Bañuls
- LMI DRISA, IRD-USTH, Hanoi, Vietnam
- UMR MIVEGEC, University of Montpellier-IRD-CNRS, Montpellier, France
| | - Tam Thi Thanh Tran
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- LMI DRISA, IRD-USTH, Hanoi, Vietnam
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Hans JB, Pfennigwerth N, Neumann B, Pfeifer Y, Fischer MA, Eisfeld J, Schauer J, Haller S, Eckmanns T, Gatermann S, Werner G. Molecular surveillance reveals the emergence and dissemination of NDM-5-producing Escherichia coli high-risk clones in Germany, 2013 to 2019. Euro Surveill 2023; 28:2200509. [PMID: 36892470 PMCID: PMC9999457 DOI: 10.2807/1560-7917.es.2023.28.10.2200509] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
BackgroundCarbapenemase-producing Enterobacterales (CPE) are rapidly increasing worldwide, also in Europe. Although prevalence of CPE in Germany is comparatively low, the National Reference Centre for Multidrug-resistant Gram-negative Bacteria noted annually increasing numbers of NDM-5-producing Escherichia coli isolates.AimAs part of our ongoing surveillance programme, we characterised NDM-5-producing E. coli isolates received between 2013 and 2019 using whole genome sequencing (WGS).MethodsFrom 329 identified NDM-5-producing E. coli, 224 isolates from known geographical locations were subjected to Illumina WGS. Analyses of 222 sequenced isolates included multilocus sequence typing (MLST), core genome (cg)MLST and single-nucleotide polymorphism (SNP)-based analyses.ResultsResults of cgMLST revealed genetically distinct clusters for many of the 43 detected sequence types (ST), of which ST167, ST410, ST405 and ST361 predominated. The SNP-based phylogenetic analyses combined with geographical information identified sporadic cases of nosocomial transmission on a small spatial scale. However, we identified large clusters corresponding to clonal dissemination of ST167, ST410, ST405 and ST361 strains in consecutive years in different regions in Germany.ConclusionOccurrence of NDM-5-producing E. coli rose in Germany, which was to a large extent due to the increased prevalence of isolates belonging to the international high-risk clones ST167, ST410, ST405 and ST361. Of particular concern is the supra-regional dissemination of these epidemic clones. Available information suggest community spread of NDM-5-producing E. coli in Germany, highlighting the importance of epidemiological investigation and an integrated surveillance system in the One Health framework.
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Affiliation(s)
- Jörg B Hans
- National Reference Centre for Multidrug-resistant Gram-negative Bacteria, Department for Medical Microbiology, Ruhr University Bochum, Bochum, Germany
| | - Niels Pfennigwerth
- National Reference Centre for Multidrug-resistant Gram-negative Bacteria, Department for Medical Microbiology, Ruhr University Bochum, Bochum, Germany
| | - Bernd Neumann
- Institute for Hospital Hygiene, Medical Microbiology and Clinical Infectiology, Paracelsus Medical University, Nuremberg General Hospital, Nuremberg, Germany.,Division of Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch-Institute, Wernigerode Branch, Wernigerode, Germany
| | - Yvonne Pfeifer
- Division of Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch-Institute, Wernigerode Branch, Wernigerode, Germany
| | - Martin A Fischer
- Division of Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch-Institute, Wernigerode Branch, Wernigerode, Germany
| | - Jessica Eisfeld
- National Reference Centre for Multidrug-resistant Gram-negative Bacteria, Department for Medical Microbiology, Ruhr University Bochum, Bochum, Germany
| | - Jennifer Schauer
- Landeszentrum Gesundheit Nordrhein-Westfalen, Fachgruppe Infektionsepidemiologie, Bochum, Germany.,National Reference Centre for Multidrug-resistant Gram-negative Bacteria, Department for Medical Microbiology, Ruhr University Bochum, Bochum, Germany
| | - Sebastian Haller
- Department for Infectious Disease Epidemiology, Robert Koch-Institute, Berlin, Germany
| | - Tim Eckmanns
- Department for Infectious Disease Epidemiology, Robert Koch-Institute, Berlin, Germany
| | - Sören Gatermann
- National Reference Centre for Multidrug-resistant Gram-negative Bacteria, Department for Medical Microbiology, Ruhr University Bochum, Bochum, Germany
| | - Guido Werner
- Division of Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch-Institute, Wernigerode Branch, Wernigerode, Germany
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Pomwised R, Naknaen A, Surachat K, Issuriya A, Prochantasene S, Wiriyaprom R, Ngasaman R. Antibiotic-resistant Escherichia coli from goat farms and the potential treatment by Acalypha indica L. extract. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Turton JF, Pike R, Perry C, Jenkins C, Turton JA, Meunier D, Hopkins KL. Wide distribution of Escherichia coli carrying IncF plasmids containing bla NDM-5 and rmtB resistance genes from hospitalized patients in England. J Med Microbiol 2022; 71. [PMID: 35925786 DOI: 10.1099/jmm.0.001569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. The New Delhi metallo-β-lactamase (NDM) variant NDM-5 was first described in 2011 in an isolate of Escherichia coli. We noted that a high proportion of isolates of E. coli positive for bla NDM carbapenemase genes submitted to the UK Health Security Agency (formerly Public Health England) between 2019 and mid-2021 carried the bla NDM-5 allele, with many co-harbouring rmtB, rendering them highly resistant to aminoglycosides as well as to most β-lactams.Hypothesis/Gap Statement. This observation suggested that a common plasmid may be circulating.Aim. To compare these isolates and describe the plasmids carrying these resistance elements.Methodology. All isolates were sequenced on an Illumina platform, with five also subjected to long-read nanopore sequencing to provide complete assemblies. The locations of bla NDM-5, rmtB and other associated genetic elements were identified. Susceptibility testing to a wide range of antibiotics was carried out on representative isolates.Results. The 34 isolates co-harbouring bla NDM-5 and rmtB were from 14 hospital groups and six different regions across England and consisted of 11 distinct sequence types. All carried IncF plasmids. Assembly of the NDM plasmids in five isolates revealed that they carried rmtB and bla NDM-5 in an IncF conjugative plasmid ranging in size from 85.5 to 161 kb. All carried a highly conserved region, previously described in E. coli plasmid pHC105-NDM, that included bla TEM-1B and rmtB followed by sequence bounded by two IS26 elements containing ΔISAba125, bla NDM-5, ble, trpF and tat followed by ISCR1 and an integron with sul1, aadA2 and dfrA12 cassettes. This arrangement has been described in isolates from other countries and continents, suggesting that such plasmids are widely distributed, at least in E. coli, with similar plasmids also found in Klebsiella pneumoniae. Tested isolates were resistant to most antibiotics except colistin, fosfomycin and tigecycline.Conclusion. These observations suggest that conjugative plasmids carrying a highly conserved resistance gene segment have become widespread in England and elsewhere. This study highlights the value of routine whole-genome sequencing in identifying genetic elements responsible for resistance dissemination.
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Affiliation(s)
- Jane F Turton
- Healthcare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Usage and Sepsis Division, UK Health Security Agency, London, UK
| | - Rachel Pike
- Reference Services Division, UK Health Security Agency, 61 Colindale Avenue, London NW9 5HT, UK
| | - Claire Perry
- Reference Services Division, UK Health Security Agency, 61 Colindale Avenue, London NW9 5HT, UK
| | - Claire Jenkins
- Reference Services Division, UK Health Security Agency, 61 Colindale Avenue, London NW9 5HT, UK
| | | | - Danièle Meunier
- Healthcare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Usage and Sepsis Division, UK Health Security Agency, London, UK
| | - Katie L Hopkins
- Healthcare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Usage and Sepsis Division, UK Health Security Agency, London, UK
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Chowdhury G, Ramamurthy T, Das B, Ghosh D, Okamoto K, Miyoshi SI, Dutta S, Mukhopadhyay AK. Characterization of NDM-5 Carbapenemase-Encoding Gene ( bla NDM-5) - Positive Multidrug Resistant Commensal Escherichia coli from Diarrheal Patients. Infect Drug Resist 2022; 15:3631-3642. [PMID: 35837541 PMCID: PMC9275505 DOI: 10.2147/idr.s364526] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/21/2022] [Indexed: 12/12/2022] Open
Abstract
Purpose The multidrug resistance Enterobacteriaceae cause many serious infections resulting in prolonged hospitalization, increased treatment charges and mortality rate. In this study, we characterized bla NDM-5-positive multidrug resistance commensal Escherichia coli (CE) isolated from diarrheal patients in Kolkata, India. Methods Three CE strains were isolated from diarrheal stools, which were negative for different pathogroups of diarrheagenic E. coli (DEC). The presence of carbapenemases encoding genes and other antimicrobial resistance genes (ARGs) was detected using PCR. The genetic arrangement adjoining bla NDM-5 was investigated by plasmid genome sequencing. The genetic relatedness of the strains was determined by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) methods. Results In addition to colistin, the bla NDM-5-positive CE strains showed resistance to most of the antibiotics. Higher MICs were detected for ciprofloxacin (>32 mg/L) and imipenem (8 mg/L). Molecular typing revealed that three CE strains belonged to two different STs (ST 101 and ST 648) but they were 95% similar in the PFGE analysis. Screening for ARGs revealed that CE strains harbored Int-1, bla TEM, blaC TX-M3, bla OXA-1, bla OXA-7, bla OXA-9, tetA, strA, aadA1, aadB, sul2, floR, mph(A), and aac(6´)-Ib-cr. In conjugation experiment, transfer frequencies ranged from 2.5×10-3 to 8.4x10-5. The bla NDM-5 gene was located on a 94-kb pNDM-TC-CE-89 type plasmid, which is highly similar to the IncFII plasmid harboring an IS26-IS30-bla NDM-5-ble MBL-trpF-dsbd-IS91-dhps structure. Conclusion To the best of our knowledge, this is the first report on carbapenem resistance involving the bla NDM-5 gene in CE from diarrheal patients. The circulation of bla NDM-5 gene in CE is worrisome, since it has the potential to transfer bla NDM-5 gene to other enteric pathogens.
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Affiliation(s)
- Goutam Chowdhury
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India.,Collaborative Research Centre of Okayama University for Infectious Diseases, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Thandavarayan Ramamurthy
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Bhabatosh Das
- Department of Infection and Immunology, Translational Health Science and Technology Institute, Faridabad, India
| | - Debjani Ghosh
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Keinosuke Okamoto
- Collaborative Research Centre of Okayama University for Infectious Diseases, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shin-Ichi Miyoshi
- Collaborative Research Centre of Okayama University for Infectious Diseases, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Asish K Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
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Chukamnerd A, Pomwised R, Jeenkeawpiam K, Sakunrang C, Chusri S, Surachat K. Genomic insights into bla NDM-carrying carbapenem-resistant Klebsiella pneumoniae clinical isolates from a university hospital in Thailand. Microbiol Res 2022; 263:127136. [PMID: 35870342 DOI: 10.1016/j.micres.2022.127136] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/04/2022] [Accepted: 07/13/2022] [Indexed: 11/18/2022]
Abstract
The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates is a serious threat to global health. Here, we elucidate the genetic features of blaNDM-carrying CRKP clinical isolates from a university hospital in Thailand. The entire genomes of 19 CRKP isolates were extracted and then sequenced using the MGISEQ200 platform. Using various bioinformatics tools, we analyzed the antimicrobial resistance (AMR), virulence factors, gene transfer, bacterial defense mechanisms, and genomic diversity of the CRKP isolates. The sequence type (ST) 16 was found in most of the isolates, along with carriages of the blaNDM-1, blaOXA-232, and blaCTX-M-15 genes. The IncFIB(pQil), Col440II, and ColKP3 plasmids were identified with high frequency. The CRKP isolates harbored genes encoding for virulence factors such as adherence, biofilm formation, immune evasion, and iron uptake. The CRISPR-Cas region in the CRKP9 isolate consisted of 28 distinct spacer sequences. The genomes of the CRKP isolates presented restriction-modification (R-M) sites (M.Kpn34618Dcm and M.Kpn928I) and integrated bacteriophage genomes (Klebsiella phage ST16-OXA48phi5.4 and Enterobacteria phage mEp390). Bottromycin and sactipeptides were also identified. The isolates could be separated into three clades according to STs and pairwise single nucleotide polymorphism (SNP) distance. Pairwise average nucleotide identity (ANI) values revealed intra-species. These findings support the importance of whole-genome sequencing (WGS) to the rapid and accurate genomic analysis of clinical isolates of CRKP.
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Affiliation(s)
- Arnon Chukamnerd
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
| | - Rattanaruji Pomwised
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
| | - Kongpop Jeenkeawpiam
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
| | - Chanida Sakunrang
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
| | - Sarunyou Chusri
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand; Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand; Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
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12
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Aghamohammad S, Nikbin VS, Badmasti F, Shahcheraghi F. High heterogeneity of fecal carriage extended-spectrum beta-lactamase-producing E. coli isolated from iranian community and clinical settings. BMC Infect Dis 2022; 22:318. [PMID: 35361158 PMCID: PMC8973555 DOI: 10.1186/s12879-022-07304-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/23/2022] [Indexed: 11/21/2022] Open
Abstract
Background Extended-spectrum beta-lactamase-producing enterobacteria (ESBL-PE) in carriers have become a global health problem. Using molecular typing techniques, including PFGE, could be useful to determine the source of bacterial dissemination. The current study aimed to investigate the intestinal carriage of ESBL-producing E. coli (ESBL-EC) and clonal relatedness among ESBL-EC isolated from hospitalized and outpatient fecal carriers in Iran. Methods A total of 120 rectal swabs were collected; 50.8% (61/120) from intensive care unit (ICU) inpatients and 49.2% (59/120) from outpatients. MacConkey agar enriched with cefotaxime was used to screen the ESBL-EC. PCR assays were performed to detect ESBL and carbapenemase genes. Pulse-fields gel electrophoresis (PFGE) was performed to assess clonal relatedness. Results Totally, 60.0% (72/120) were carrier for ESBL-EC. The rates of resistance against ceftazidime and cefepime were 90.2% (65/72) and 93.0% (67/72), respectively. The rates of blaCTX-M-15, blaTEM, blaSHV, blaNDM-1, blaOXA-48 and blaIMP was 90.2% (65/72), 50.0% (36/72), 5.5% (4/72), 4.1% (3/72), 4.1% (3/72) and 1.3% (1/72), respectively. Based on a cut-off 80%, 69 ESBL-EC isolates could be categorized in 10 mini-cluster and 47 isolates were considered as singletons. Discussion High heterogeneity among isolates from ESBL-EC suggests that this bacterium probably has a different source of dissemination. Screening of carriers in hospitals and communities could help the infection control program in public health. Supplementary information The online version contains supplementary material available at 10.1186/s12879-022-07304-7.
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Affiliation(s)
| | | | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
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13
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Molecular characterization of an outbreak of NDM-7-producing Klebsiella pneumoniae reveals ST11 clone expansion combined with interclonal plasmid dissemination. Int J Antimicrob Agents 2022; 59:106551. [PMID: 35176478 DOI: 10.1016/j.ijantimicag.2022.106551] [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: 07/26/2021] [Revised: 01/29/2022] [Accepted: 02/07/2022] [Indexed: 11/21/2022]
Abstract
The aim of this study was to characterize a hospital outbreak of NDM-7-producing K. pneumoniae associated with the successful multidrug-resistant high-risk clone ST11 between 2017 and 2019 in southern Spain. Forty-six NDM-7 producers were recovered during the outbreak: 16 from clinical samples, 27 from surveillance samples and three from environmental samples. All isolates were multidrug-resistant, including carbapenem-resistant. XbaI PFGE showed three pulsotypes belonging to 3 different clones by MLST: ST307 (one isolate), ST152 (one isolate) and ST11 (44 isolates). Representative isolates were selected for characterization of blaNDM-7-carrying plasmids using PCR-based replicon typing and whole-genome sequencing (WGS) analysis. IncX3 plasmids containing NDM-7 were identified in the 3 clones. The blaNDM-7-carrying plasmids from the ST307 and ST11 clones were identical, and very similar to the IncX3 NDM-7 plasmid previously described. The carbapenemase NDM-7 was introduced into the hospital by means of the ST307 clone, while the ST11 high-risk clone was responsible for NDM-7 dissemination. It is essential to develop and implement strategies to control the introduction and spread of successful multidrug-resistant clones in hospitals that include active surveillance programmes to detect colonised patients.
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14
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Dewi DAR, Thomas T, Ahmad Mokhtar AM, Mat Nanyan NS, Zulfigar SB, Salikin NH. Carbapenem Resistance among Marine Bacteria-An Emerging Threat to the Global Health Sector. Microorganisms 2021; 9:microorganisms9102147. [PMID: 34683467 PMCID: PMC8537846 DOI: 10.3390/microorganisms9102147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/08/2021] [Accepted: 10/10/2021] [Indexed: 01/24/2023] Open
Abstract
The emergence of antibiotic resistance among pathogenic microorganisms is a major issue for global public health, as it results in acute or chronic infections, debilitating diseases, and mortality. Of particular concern is the rapid and common spread of carbapenem resistance in healthcare settings. Carbapenems are a class of critical antibiotics reserved for treatment against multidrug-resistant microorganisms, and resistance to this antibiotic may result in limited treatment against infections. In addition to in clinical facilities, carbapenem resistance has also been identified in aquatic niches, including marine environments. Various carbapenem-resistant genes (CRGs) have been detected in different marine settings, with the majority of the genes incorporated in mobile genetic elements, i.e., transposons or plasmids, which may contribute to efficient genetic transfer. This review highlights the potential of the marine environment as a reservoir for carbapenem resistance and provides a general overview of CRG transmission among marine microbes.
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Affiliation(s)
- Dewa A.P. Rasmika Dewi
- School of Medicine, International University of Health and Welfare, Narita 286-8686, Japan;
- Faculty of Medicine and Health Sciences, Udayana University, Bali 80232, Indonesia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney 2052, Australia;
| | - Ana Masara Ahmad Mokhtar
- School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (A.M.A.M.); (N.S.M.N.); (S.B.Z.)
| | - Noreen Suliani Mat Nanyan
- School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (A.M.A.M.); (N.S.M.N.); (S.B.Z.)
| | - Siti Balqis Zulfigar
- School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (A.M.A.M.); (N.S.M.N.); (S.B.Z.)
| | - Nor Hawani Salikin
- School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (A.M.A.M.); (N.S.M.N.); (S.B.Z.)
- Correspondence: ; Tel.: +60-4-653-2241
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15
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Occurrence of Aztreonam-Avibactam-Resistant NDM-5-Producing Escherichia coli in the Food Chain. Antimicrob Agents Chemother 2021; 65:e0088221. [PMID: 34125588 DOI: 10.1128/aac.00882-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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16
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Huang J, Zhang S, Zhao Z, Chen M, Cao Y, Li B. Acquisition of a Stable and Transferable bla NDM-5-Positive Plasmid With Low Fitness Cost Leading to Ceftazidime/Avibactam Resistance in KPC-2-Producing Klebsiella pneumoniae During Treatment. Front Cell Infect Microbiol 2021; 11:658070. [PMID: 34354959 PMCID: PMC8329419 DOI: 10.3389/fcimb.2021.658070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/29/2021] [Indexed: 12/12/2022] Open
Abstract
The emergence and prevalence of carbapenem-resistant Enterobacteriaceae (CRE) have drawn worldwide attention. Ceftazidime/avibactam (CAZ/AVI) gives us a valuable alternative strategy to treat CRE infections. Unfortunately, CAZ/AVI resistance could occur during CAZ/AVI treatment. The CAZ/AVI-resistant Carbapenem-resistant Klebsiella pneumoniae (CR-KP) (KP137060) and earlier CAZ/AVI-susceptible isolate (KP135194) from the same hospitalized patient were collected at Fujian Medical University Union Hospital between October and November 2019. In this study, CAZ/AVI MICs of CAZ/AVI-susceptible and -resistant isolates (KP135194 and KP137060) were 4 mg/L and 128 mg/L, respectively; and the two isolates had the same antibiotic resistance pattern to other carbapenems. Two strains were then submitted for whole-genome sequencing and bioinformatic analysis. ompK36 was not detected in two isolates. No mutation was observed in bla KPC-2, ompK35 and ompK37 in this study and there was no significant difference of the expression in bla KPC-2, ompK35 and ompK37 between the two isolates (p>0.05). Two isolates were sequence type 11 and harbored bla KPC-2, bla SHV-182 and bla TEM-1B. Compared with KP135194, KP137060 harbored an additional bla NDM-5 positive plasmid. bla NDM-5 gene could be successfully transferred into E. coli J53 at a conjugation frequency of 1.14×10-4. Plasmid stability testing showed that bla KPC-2- and bla NDM-5-harboring plasmids were still stably maintained in the hosts. Growth assay and growth competition experiments showed there was no significant difference in fitness cost between two CR-KP isolates. Our study described the acquisition of a bla NDM-5-harboring plasmid leading to resistance to ceftazidime/avibactam in KPC-2-producing Klebsiella pneumoniae during treatment. This phenomenon deserves further exploration.
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Affiliation(s)
- Jiangqing Huang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Shengcen Zhang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Zhichang Zhao
- Department of Pharmacy, Fujian Medical University Union Hospital, Fuzhou, China
| | - Min Chen
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Yingping Cao
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Bin Li
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
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17
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Marí-Almirall M, Cosgaya C, Pitart C, Viñes J, Muñoz L, Campo I, Cuscó A, Rodríguez-Serna L, Santana G, Del Río A, Francino O, Ciruela P, Pujol I, Ballester F, Marco F, Martínez JA, Soriano Á, Vila J, Roca I. Dissemination of NDM-producing Klebsiella pneumoniae and Escherichia coli high-risk clones in Catalan healthcare institutions. J Antimicrob Chemother 2021; 76:345-354. [PMID: 33200193 DOI: 10.1093/jac/dkaa459] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 10/12/2020] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES To characterize the clonal spread of carbapenem-resistant Klebsiella pneumoniae and Escherichia coli isolates between different healthcare institutions in Catalonia, Spain. METHODS Antimicrobial susceptibility was tested by disc diffusion. MICs were determined by gradient diffusion or broth microdilution. Carbapenemase production was confirmed by lateral flow. PCR and Sanger sequencing were used to identify the allelic variants of resistance genes. Clonality studies were performed by PFGE and MLST. Plasmid typing, conjugation assays, S1-PFGE plus Southern blotting and MinION Oxford Nanopore sequencing were used to characterize resistance plasmids. RESULTS Twenty-nine carbapenem-resistant isolates recovered from three healthcare institutions between January and November 2016 were included: 14 K. pneumoniae isolates from a tertiary hospital in the south of Catalonia (hospital A); 2 K. pneumoniae isolates from a nearby healthcare centre; and 12 K. pneumoniae isolates and 1 E. coli isolate from a tertiary hospital in Barcelona (hospital B). The majority of isolates were resistant to all antimicrobial agents, except colistin, and all were NDM producers. PFGE identified a major K. pneumoniae clone (n = 27) belonging to ST147 and co-producing NDM-1 and CTX-M-15, with a few isolates also harbouring blaOXA-48. Two sporadic isolates of K. pneumoniae ST307 and E. coli ST167 producing NDM-7 were also identified. blaNDM-1 was carried in two related IncR plasmid populations and blaNDM-7 in a conjugative 50 kb IncX3 plasmid. CONCLUSIONS We report the inter-hospital dissemination of XDR high-risk clones of K. pneumoniae and E. coli associated with the carriage of small, transferable plasmids harbouring blaNDM genes.
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Affiliation(s)
- Marta Marí-Almirall
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Clara Cosgaya
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Cristina Pitart
- Department of Clinical Microbiology, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Joaquim Viñes
- SVGM, Molecular Genetics Veterinary Service, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.,Vetgenomics, PRUAB, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Laura Muñoz
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Irene Campo
- Department of Clinical Microbiology, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Anna Cuscó
- Vetgenomics, PRUAB, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Laura Rodríguez-Serna
- Department of Epidemiology and Preventive Medicine, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Gemina Santana
- Department of Epidemiology and Preventive Medicine, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Ana Del Río
- Department of Infectious Diseases, Hospital Clínic - Institut d'investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Olga Francino
- SVGM, Molecular Genetics Veterinary Service, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Pilar Ciruela
- Public Health Agency of Catalonia (ASPCAT), Generalitat de Catalunya, Barcelona, Spain.,CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Isabel Pujol
- Laboratori de Microbiologia, Hospital Universitari Sant Joan de Reus, Reus, Spain.,Unitat de Microbiologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Frederic Ballester
- Hospital Universitari Sant Joan de Reus-Laboratori de Referència del Camp de Tarragona i de les Terres de l'Ebre, Reus, Spain
| | - Francesc Marco
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Department of Clinical Microbiology, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - José Antonio Martínez
- Department of Infectious Diseases, Hospital Clínic - Institut d'investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Álex Soriano
- Department of Infectious Diseases, Hospital Clínic - Institut d'investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain
| | - Jordi Vila
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Department of Clinical Microbiology, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Ignasi Roca
- Laboratory of Antimicrobial Resistance, ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
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18
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Reynolds ME, Phan HTT, George S, Hubbard ATM, Stoesser N, Maciuca IE, Crook DW, Timofte D. Occurrence and characterization of Escherichia coli ST410 co-harbouring blaNDM-5, blaCMY-42 and blaTEM-190 in a dog from the UK. J Antimicrob Chemother 2021; 74:1207-1211. [PMID: 30753576 DOI: 10.1093/jac/dkz017] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 01/02/2019] [Accepted: 01/07/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND/OBJECTIVES Carbapenemase-producing Enterobacteriaceae (CPE) are a public health threat, and have been found in humans, animals and the environment. Carbapenems are not authorized for use in EU or UK companion animals, and the prevalence of carbapenem-resistant Gram-negative bacilli (CRGNB) in this population is unknown. METHODS We investigated CRGNB isolated from animal specimens received by one diagnostic laboratory from 34 UK veterinary practices (September 2015-December 2016). Any Gram-negative isolates from clinical specimens showing reduced susceptibility to fluoroquinolones and/or aminoglycosides and/or cephalosporins were investigated phenotypically and genotypically for carbapenemases. A complete genome assembly (Illumina/Nanopore) was generated for the single isolate identified to investigate the genetic context for carbapenem resistance. RESULTS One ST410 Escherichia coli isolate [(CARB35); 1/191, 0.5%], cultured from a wound in a springer spaniel, harboured a known carbapenem resistance gene (blaNDM-5). The gene was located in the chromosome on an integrated 100 kb IncF plasmid, also harbouring other drug resistance genes (mrx, sul1, ant1 and dfrA). The isolate also contained blaCMY-42 and blaTEM-190 on two separate plasmids (IncI1 and IncFII, respectively) that showed homology with other publicly available plasmid sequences from Italy and Myanmar. CONCLUSIONS Even though the use of carbapenems in companion animals is restricted, the concurrent presence of blaCMY-42 and other antimicrobial resistance genes could lead to co-selection of carbapenemase genes in this population. Further studies investigating the selection and flow of plasmids carrying important resistance genes amongst humans and companion animals are needed.
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Affiliation(s)
- M E Reynolds
- Axiom Veterinary Laboratories Ltd, The Manor House, Brunel Road, Newton Abbot, UK
| | - H T T Phan
- Modernising Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - S George
- Modernising Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - A T M Hubbard
- Modernising Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - N Stoesser
- Modernising Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - I E Maciuca
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Cheshire, UK
| | - D W Crook
- Modernising Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - D Timofte
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Cheshire, UK
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
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19
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Cross-Border Emergence of Escherichia coli Producing the Carbapenemase NDM-5 in Switzerland and Germany. J Clin Microbiol 2021; 59:JCM.02238-20. [PMID: 33361340 DOI: 10.1128/jcm.02238-20] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/04/2020] [Indexed: 01/05/2023] Open
Abstract
A series of clinical NDM-5-producing Escherichia coli isolates obtained from two surveillance networks for carbapenem-producing Enterobacterales from 2018 to 2019, namely, Switzerland (NARA) and Germany (SurvCARE), were analyzed. The 33 NDM-5-producing E. coli isolates were highly resistant to β-lactams, including novel β-lactam/β-lactamase inhibitor combinations (ceftazidime-avibactam, imipenem-relebactam, and meropenem-vaborbactam), and remained susceptible to fosfomycin, colistin, and tigecycline. These isolates were assigned to different sequence types (STs) and indicated a predominance of isolates exhibiting ST167 in Switzerland and Germany (n = 10) (phylogenetic group C), followed by ST405 (n = 4) (phylogenetic group E), ST1284 (n = 4) (phylogenetic group C), and ST361 (n = 4) (phylogenetic group C). The bla NDM-5 gene was predominantly present on an IncF-type plasmid (n = 29) and, to a lesser extent, on the narrow-host-range IncX3 plasmid (n = 4). Sequence analyses of eight NDM-5 plasmids indicated that NDM-5-encoding F-type plasmids varied in size between 86 and 132 kb. The two IncX3 plasmids pCH8NDM5 and pD12NDM5 were 46 and 45 kb in size, respectively. The highly conserved bla NDM-5 genetic surrounding structures (ΔISAba125-bla NDM-5-ble MBL-trpT-dsbD-IS26) of both the F-type and IncX3 plasmids suggested a common genetic origin. The emergence of the NDM-5 carbapenemase was evidenced in particular for the E. coli ST167 clone, which is a successful epidemic clone known to be associated with both multiresistance and virulence traits and is therefore of high public health concern. The occurrence of clonally related NDM-5-producing E. coli isolates in Switzerland and Germany further indicates the international spread of this multidrug-resistant superbug at least throughout Europe.
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OXA-181-Like Carbapenemases in Klebsiella pneumoniae ST14, ST15, ST23, ST48, and ST231 from Septicemic Neonates: Coexistence with NDM-5, Resistome, Transmissibility, and Genome Diversity. mSphere 2021; 6:6/1/e01156-20. [PMID: 33441403 PMCID: PMC7845606 DOI: 10.1128/msphere.01156-20] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Neonatal sepsis is a leading cause of neonatal mortality in low- and middle-income countries (LMICs). Treatment of sepsis in this vulnerable population is dependent on antimicrobials, and resistance to these life-saving antimicrobials is worrisome. Studies on the epidemiology and genomes of isolates harboring OXA-48-like genes in septicemic neonates are rare. Here, isolates producing these carbapenemases which emerged and persisted in an Indian neonatal unit were characterized in terms of their resistome, transmissibility, and genome diversity. Antibiotic susceptibility and whole-genome sequencing were carried out. The sequence types, resistome, virulome, mobile genetic elements, and transmissibility of carbapenem-resistant plasmids were evaluated. Core genome analysis of isolates was shown in a global context with other OXA-48-like carbapenemase-harboring genomes, including those from neonatal studies. Eleven OXA-48-like carbapenemase-producing Klebsiella pneumoniae (blaOXA-181, n = 7 and blaOXA-232, n = 4) isolates belonging to diverse sequence types (ST14, ST15, ST23, ST48, and ST231) were identified. blaOXA-181/OXA-232 and blaNDM-5 were found in a high-risk clone, ST14 (n = 4). blaOXA-181/OXA-232 were in small, nonconjugative ColKP3 plasmids located on truncated Tn2013, whereas blaNDM-5 was in self-transmissible, conjugative IncFII plasmids, within truncated Tn125. Conjugal transfer of blaOXA-181/OXA-232 was observed in the presence of blaNDM-5. The study strains were diverse among themselves and showed various levels of relatedness with non-neonatal strains from different parts of the world and similarity with neonatal strains from Tanzania and Ghana when compared with a representative collection of carbapenemase-positive K. pneumoniae strains. We found that blaOXA-181/OXA-232-harboring isolates from a single neonatal unit had remarkably diverse genomes, ruling out clonal spread and emphasizing the extent of plasmid spreading across different STs. This study is probably the first to report the coexistence of blaOXA-181/232 and blaNDM-5 in neonatal isolates. IMPORTANCE Neonatal sepsis is a leading cause of neonatal mortality in low- and middle-income countries (LMICs). Treatment of sepsis in this vulnerable population is dependent on antimicrobials, and resistance to these life-saving antimicrobials is worrisome. Carbapenemases, enzymes produced by bacteria, can make these antimicrobials useless. Our study describes how OXA-48-like carbapenemases in neonatal septicemic Klebsiella pneumoniae shows remarkable diversity in the genomes of the strains and relatedness with strains from other parts of world and also to some neonatal outbreak strains. It is also the first to describe such resistance due to coproduction of dual carbapenemases, (OXA)-48 and New Delhi metallo-β-lactamase-5, in Klebsiella pneumoniae from neonatal settings. Carbapenemase genes situated on plasmids within high-risk international clones, as seen here, increase the ease and transfer of resistant genetic material. With the WHO treatment protocols not adequately poised to handle such infections, prompt attention to neonatal health care is required.
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21
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Yin D, Lin Y, Li Z, Ma H, Lu L, Wang K, Yang L, Du X, Li P, Qi K, Song H. Characterization of a Novel NDM-5-Harboring Plasmid from a Carbapenem-Resistant Escherichia coli Isolate from China. Infect Drug Resist 2020; 13:3929-3935. [PMID: 33173318 PMCID: PMC7646509 DOI: 10.2147/idr.s277997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/15/2020] [Indexed: 11/23/2022] Open
Abstract
Background A carbapenem-resistant Escherichia coli (sequence type 5415) strain was isolated from a male patient through routine surveillance in 2018 in Guangzhou, China. Materials and Methods Bacteria were isolated from a sputum culture and identified by using the Vitek 2 compact system. The blaNDM-5 gene was amplified and confirmed by sequencing. Antimicrobial susceptibility testing was determined by a Vitek 2 compact system. The blaNDM-5 gene was located by Southern blotting. Whole-genome sequencing was carried out using both Illumina MiSeq and Oxford Nanopore MinION. Results S1-PFGE and Southern blotting showed that the bla NDM-5 gene was located on a novel 66-kb IncFII [F2:A-:B-] plasmid. Conjugation assays revealed that the bla NDM-5-bearing plasmid was self-transferrable. Genomic sequencing and comparative analysis suggested that plasmid p2947-NDM5 likely originated from a combination of an IncFII-type backbone and the bla NDM-5 flanking genetic elements. Conclusion This is the first report of an ST5414 E. coli strain expressing an NDM-5 β-lactamase. This study highlights the genetic complexity of bla NDM-5 carrying plasmids and the urgent need for continuous active monitoring.
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Affiliation(s)
- Dongdong Yin
- Center for Disease Control and Prevention of PLA, Beijing, People's Republic of China.,Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control College of Animal Science and Technology, Anhui Agricultural University, Hefei, People's Republic of China
| | - Yanfeng Lin
- Center for Disease Control and Prevention of PLA, Beijing, People's Republic of China.,Institute for Disease Control and Prevention, AMMS, Beijing, People's Republic of China
| | - Zhonghong Li
- Center for Disease Control and Prevention of PLA, Beijing, People's Republic of China.,College of Environmental and Chemical Engineering, Nanchang Hangkong University, Nanchang, People's Republic of China
| | - Hui Ma
- The Sixth Medical Center of PLA General Hospital, Beijing, People's Republic of China
| | - Lanfen Lu
- Department of Laboratory Diagnosis, Sun Yat-Sen University Affiliated Zhongshan Hospital, Zhongshan, People's Republic of China
| | - Kaiying Wang
- Center for Disease Control and Prevention of PLA, Beijing, People's Republic of China.,Institute for Disease Control and Prevention, AMMS, Beijing, People's Republic of China
| | - Lang Yang
- Center for Disease Control and Prevention of PLA, Beijing, People's Republic of China.,Institute for Disease Control and Prevention, AMMS, Beijing, People's Republic of China
| | - Xinying Du
- Center for Disease Control and Prevention of PLA, Beijing, People's Republic of China
| | - Peng Li
- Center for Disease Control and Prevention of PLA, Beijing, People's Republic of China
| | - Kezong Qi
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control College of Animal Science and Technology, Anhui Agricultural University, Hefei, People's Republic of China
| | - Hongbin Song
- Center for Disease Control and Prevention of PLA, Beijing, People's Republic of China
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22
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Merida-Vieyra J, De Colsa-Ranero A, Calderón-Castañeda Y, Aquino-Andrade A. Detection of CMY-type beta-lactamases in Escherichia coli isolates from paediatric patients in a tertiary care hospital in Mexico. Antimicrob Resist Infect Control 2020; 9:168. [PMID: 33121527 PMCID: PMC7596940 DOI: 10.1186/s13756-020-00840-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/22/2020] [Indexed: 12/29/2022] Open
Abstract
Background The aim of this study was to detect CMY-type beta-lactamases in E. coli isolates obtained from paediatric patients.
Methods In total, 404 infection-causing E. coli isolates resistant to third and fourth generation cephalosporins (3GC, 4GC) were collected from paediatric patients over a 2 years period. The identification and susceptibility profiles were determined with an automated microbiology system. Typing of blaCMY and other beta-lactamase genes (blaTEM, blaSHV, blaCTX-M, blaVIM, blaIMP, blaKPC, blaNDM, blaOXA and blaGES) was realized by PCR and sequencing. Phenotypic detection of AmpC-type enzymes was performed using boronic acid (20 mg/mL) and cloxacillin (20 mg/mL) as inhibitors, and the production of extended-spectrum beta-lactamases was determined with the double-disk diffusion test with cefotaxime (CTX) and ceftazidime (CAZ) discs alone and in combination with clavulanic acid. The CarbaNP test and modified carbapenem inhibition method (mCIM) were used for isolates with decreased susceptibility to carbapenems. The clonal origin of the isolates was established by pulsed-field gel electrophoresis (PFGE), phylotyping method and multilocus sequence typing.
Results CMY-type beta-lactamases were detected in 18 isolates (4.5%). The allelic variants found were CMY-2 (n = 14) and CMY-42 (n = 4). Of the E. coli strains with CMY, the AmpC phenotypic production test was positive in 11 isolates with cloxacillin and in 15 with boronic acid. ESBL production was detected in 13 isolates. Coexistence with other beta-lactamases was observed such as CTX-M-15 ESBL and original spectrum beta-lactamases TEM-1 and TEM-190. In one isolate, the CarbaNP test was negative, the mCIM was positive, and OXA-48 carbapenemase was detected. Phylogroup A was the most frequent (n = 9) followed by B2, E and F (n = 2, respectively), and through PFGE, no clonal relationship was observed. Eleven different sequence types (ST) were found, with ST10 high-risk clone being the most frequent (n = 4). Seventy-two percent of the isolates were from health care-associated infections; the mortality rate was 11.1%.
Conclusions This is the first report in Mexico of E. coli producing CMY isolated from paediatric patients, demonstrating a frequency of 4.5%. In addition, this is the first finding of E. coli ST10 with CMY-2 and OXA-48.
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Affiliation(s)
- Jocelin Merida-Vieyra
- Molecular Microbiology Laboratory, Instituto Nacional de Pediatria, Insurgentes Sur 3700C, Insurgentes Cuicuilco, Coyoacan, 04530, Mexico City, Mexico
| | - Agustín De Colsa-Ranero
- Molecular Microbiology Laboratory, Instituto Nacional de Pediatria, Insurgentes Sur 3700C, Insurgentes Cuicuilco, Coyoacan, 04530, Mexico City, Mexico.,Department of Paediatric Infectious Diseases, Instituto Nacional de Pediatria, Mexico City, Mexico
| | | | - Alejandra Aquino-Andrade
- Molecular Microbiology Laboratory, Instituto Nacional de Pediatria, Insurgentes Sur 3700C, Insurgentes Cuicuilco, Coyoacan, 04530, Mexico City, Mexico.
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23
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Ultrasensitive Label-Free Detection of Unamplified Multidrug-Resistance Bacteria Genes with a Bimodal Waveguide Interferometric Biosensor. Diagnostics (Basel) 2020; 10:diagnostics10100845. [PMID: 33086716 PMCID: PMC7589074 DOI: 10.3390/diagnostics10100845] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 11/18/2022] Open
Abstract
Infections by multidrug-resistant bacteria are becoming a major healthcare emergence with millions of reported cases every year and an increasing incidence of deaths. An advanced diagnostic platform able to directly detect and identify antimicrobial resistance in a faster way than conventional techniques could help in the adoption of early and accurate therapeutic interventions, limiting the actual negative impact on patient outcomes. With this objective, we have developed a new biosensor methodology using an ultrasensitive nanophotonic bimodal waveguide interferometer (BiMW), which allows a rapid and direct detection, without amplification, of two prevalent and clinically relevant Gram-negative antimicrobial resistance encoding sequences: the extended-spectrum betalactamase-encoding gene blaCTX-M-15 and the carbapenemase-encoding gene blaNDM-5 We demonstrate the extreme sensitivity and specificity of our biosensor methodology for the detection of both gene sequences. Our results show that the BiMW biosensor can be employed as an ultrasensitive (attomolar level) and specific diagnostic tool for rapidly (less than 30 min) identifying drug resistance. The BiMW nanobiosensor holds great promise as a powerful tool for the control and management of healthcare-associated infections by multidrug-resistant bacteria.
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24
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Pérez-Vázquez M, Sola Campoy PJ, Ortega A, Bautista V, Monzón S, Ruiz-Carrascoso G, Mingorance J, González-Barberá EM, Gimeno C, Aracil B, Sáez D, Lara N, Fernández S, González-López JJ, Campos J, Kingsley RA, Dougan G, Oteo-Iglesias J. Emergence of NDM-producing Klebsiella pneumoniae and Escherichia coli in Spain: phylogeny, resistome, virulence and plasmids encoding blaNDM-like genes as determined by WGS. J Antimicrob Chemother 2020; 74:3489-3496. [PMID: 31504589 DOI: 10.1093/jac/dkz366] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/18/2019] [Accepted: 07/24/2019] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES NDM carbapenemases have spread worldwide. However, little information exists about the impact of NDM-producing Enterobacteriaceae in Spain. By WGS, we sought to elucidate the population structure of NDM-like-producing Klebsiella pneumoniae and Escherichia coli in Spain and to determine the plasmids harbouring blaNDM-like genes. METHODS High-resolution SNP typing, core-genome MLST and plasmid reconstruction (PlasmidID) were performed on 59 NDM-like-producing K. pneumoniae and 8 NDM-like-producing E. coli isolated over an 8 year period in Spain. RESULTS Five major epidemic clones of NDM-producing K. pneumoniae caused five important nationwide outbreaks: ST437/NDM-7, ST437/NDM-1, ST147/NDM-1, ST11/NDM-1 and ST101/NDM-1; in contrast, the spread of NDM-producing E. coli was polyclonal. Three blaNDM types were identified: blaNDM-1, 61.2%; blaNDM-7, 32.8%; and blaNDM-5, 6%. Five K. pneumoniae isolates co-produced other carbapenemases (three blaOXA-48 and two blaVIM-1). The average number of acquired resistance genes was higher in K. pneumoniae than in E. coli. The plasmids encoding blaNDM-like genes belonged to IncFII, IncFIB, IncX3, IncR, IncN and IncC types, of which IncF, IncR and IncC were associated with MDR. The genetic surroundings of blaNDM-like genes showed a highly variable region upstream of ISAba125. CONCLUSIONS In recent years NDM-producing K. pneumoniae and E. coli have emerged in Spain; the spread of a few high-risk K. pneumoniae clones such as ST437/NDM-7, ST437/NDM-1, ST147/NDM-1, ST11/NDM-1 and ST101/NDM-1 have caused several interregional outbreaks. In contrast, the spread of NDM-producing E. coli has been polyclonal. Plasmid types IncFII, IncFIB, IncX3, IncR, IncN and IncC carried blaNDM, and the same IncX3 plasmid was detected in K. pneumoniae and E. coli.
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Affiliation(s)
- María Pérez-Vázquez
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Pedro J Sola Campoy
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Adriana Ortega
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Verónica Bautista
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Sara Monzón
- Unidad de Bioinformátia (BU-ISCIII), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Guillermo Ruiz-Carrascoso
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain.,Servicio de Microbiología, Hospital Universitario La Paz-idiPAZ, Madrid, Spain
| | - Jesus Mingorance
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain.,Servicio de Microbiología, Hospital Universitario La Paz-idiPAZ, Madrid, Spain
| | | | - Concepción Gimeno
- Servicio de Microbiología, Hospital General Universitario de Valencia, Valencia, Spain
| | - Belén Aracil
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - David Sáez
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Noelia Lara
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Sara Fernández
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan José González-López
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain.,Clinical Microbiology Department, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - José Campos
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Robert A Kingsley
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,Quadram Institute Bioscience, Colney, Norwich, UK
| | - Gordon Dougan
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Jesús Oteo-Iglesias
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
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25
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Rehman MU, Yang H, Zhang S, Huang Y, Zhou R, Gong S, Feng Q, Chen S, Yang J, Yang Z, Abbas M, Cui M, Wang M, Jia R, Chen S, Liu M, Zhu D, Zhao X, Wu Y, Yang Q, Huang J, Zhang L, Liu Y, Yu Y, Tian B, Cheng A. Emergence of Escherichia coli isolates producing NDM-1 carbapenemase from waterfowls in Hainan island, China. Acta Trop 2020; 207:105485. [PMID: 32277927 DOI: 10.1016/j.actatropica.2020.105485] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 11/16/2022]
Abstract
Carbapenems are traditionally recognized to be the last resort drugs to treat infections due to MDR organisms such as E. coli. As such, the emergence of New Delhi metallo-β-lactamase-producing E. coli strains have become a challenging threat to the public health. In this regard, we examined the molecular characteristics of carbapenem-resistant E. coli (CRE) isolated from waterfowls in China's tropical island, Hainan. A total of 311 single E. coli strains were obtained from 20 various farms of healthy ducks and geese in 2 districts of Hainan island. The CRE strains were initially identified via phenotypic resistance and modified Hodge test. PCR assay and subsequent nucleotide sequencing were used to detect different types of carbapenemase encoding genes (blaNDM, blaVIM, blaIMP, blaOXA and blaKPC). In addition, MLST and PFGE analyses were also performed. Among the 311 E. coli strains, 8 strains were detected to produce a single type of carbapenemase i.e. NDM-1 (2.6%). A total of 5 sequence types (STs) were observed, of which ST10 was the most prevalent accounting for 37.5% (3/8). Moreover, these 8 isolates yielded 6 different PFGE clusters but showed approximately related PFGE types, suggesting the propagation of similar clone between the farms. This is the first report on the identification of NDM-1-producing E. coli from waterfowls in Hainan island, China. Our results emphasize the need for better efforts to control the further spread of NDM-1-producing E. coli strains in this tropical island.
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Affiliation(s)
- Mujeeb Ur Rehman
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Hong Yang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Shaqiu Zhang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China.
| | - Yahui Huang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Rui Zhou
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Siyue Gong
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Qi Feng
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Shuling Chen
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Jing Yang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Zhishuang Yang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Muhammad Abbas
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Min Cui
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Mingshu Wang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Renyong Jia
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Shun Chen
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Mafeng Liu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Dekang Zhu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Xinxin Zhao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Ying Wu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Qiao Yang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Juan Huang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Ling Zhang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Yunya Liu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Yanling Yu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Bin Tian
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China
| | - Anchun Cheng
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, 611130, Chengdu, P. R. China.
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Aghamohammad S, Badmasti F, Solgi H, Aminzadeh Z, Khodabandelo Z, Shahcheraghi F. First Report of Extended-Spectrum Betalactamase-Producing Klebsiella pneumoniae Among Fecal Carriage in Iran: High Diversity of Clonal Relatedness and Virulence Factor Profiles. Microb Drug Resist 2020; 26:261-269. [PMID: 30277830 DOI: 10.1089/mdr.2018.0181] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Increasing rate of silent intestinal carriers with extended-spectrum betalactamase (ESBL)-producing Klebsiella pneumonia (ESBL-KP) has given rise to a serious healthcare problem in clinical settings. Various epidemiological studies are being conducted to determine clonal relatedness among carriers. In this study, we investigated the intestinal carriage of ESBL-KP and clonal relatedness among ESBL-KP isolated from fecal carriage in Iran for the first time. A total of 120 rectal swabs (RSs) were collected including 61 from inpatients of intensive care unit and 59 from outpatients. ESBL-KP screening was performed using MacConkey agar supplemented with cefotaxime. PCR was done for detection of ESBL, carbapenemase, and virulence factor genes. Conjugation experiments and PCR-based replicon typing were performed. Clonal relatedness was investigated by multilocus sequence typing (MLST) and multiple locus variable number tandem repeat analysis (MLVA). Out of a total of 120 RSs, 18.3% (22/120) ESBL-KP were isolated. The rate of blaCTXM-15 was 81%. ompk35 was the most prevalent virulence gene detected in 86.3% of the isolates. In conjugation experiments, three out of five tested isolates had conjugative plasmids. The most prevalent plasmid types belonged to IncL/M, IncA/C, and Inc FII. The MLST analysis showed that the main sequence types (STs) identified among ESBL-KP isolates were ST147, ST15, and ST16. The isolates were characterized into 4 miniclusters and 11 singletons using MLVA. High heterogeneity among ESBL-KP isolates indicated that this bacterium could be colonized in different sites and easily transferred. Screening of carriers in hospitals and community could help in controlling of infection in the healthcare and community settings.
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Affiliation(s)
| | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Hamid Solgi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Zohreh Aminzadeh
- Infectious Disease and Tropical Medicine Research Centre, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Li J, Yu T, Tao XY, Hu YM, Wang HC, Liu JL, Zhou HJ, Zou MX. Emergence of an NDM-5-Producing Escherichia coli Sequence Type 410 Clone in Infants in a Children's Hospital in China. Infect Drug Resist 2020; 13:703-710. [PMID: 32184632 PMCID: PMC7054006 DOI: 10.2147/idr.s244874] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/15/2020] [Indexed: 12/14/2022] Open
Abstract
Purpose Outbreaks of infection due to carbapenem-resistant Enterobacterales (CRE), including New Delhi metallo-β-lactamase (NDM)-producing Escherichia coli, have been increasingly reported worldwide, primarily in adults and rarely in children. The goal of this study was to characterize an outbreak of infection caused by NDM-5-producing E. coli in a children’s hospital in China. Methods A total of 86 CRE isolates were collected from 85 hospitalized children between June 2017 and May 2018. These isolates were subjected to multiple phenotypic and molecular tests, including in vitro antimicrobial susceptibility testing, PCR, pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and whole-genome sequencing (WGS). Results Among the 86 CRE isolates, we identified 9 NDM-5-producing E. coli isolates, with 5 of them sharing the same PFGE pattern, same MLST type (ST410), same plasmid replicon type (IncFII), and nearly the same set of additional resistance genes. All 9 isolates were resistant to most antimicrobial agents, including carbapenems, cephalosporins, and levofloxacin, while being sensitive to trimethoprim/sulfamethoxazole, amikacin, tigecycline, and colistin. According to the clinical background, all 9 isolates were collected in a period of < 3 months from infants among whom there was overlap in the time of hospitalization. None of them had a travel history. Conclusion Our analysis suggests an outbreak of clonal dissemination, presumably due to nosocomial transmission. This study represents the first documented outbreak of NDM-5-producing E. coli mediated by IncFII in infants. Close monitoring is urgently needed to prevent and control the spread of this difficult-to-treat superbug.
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Affiliation(s)
- Jun Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
| | - Ting Yu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
| | - Xiao-Yan Tao
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
| | - Yong-Mei Hu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
| | - Hai-Chen Wang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
| | - Jian-Long Liu
- Department of Clinical Laboratory, Hunan Children's Hospital, Changsha, Hunan 410007, People's Republic of China
| | - Hai-Jian Zhou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Ming-Xiang Zou
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
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Marchetti VM, Bitar I, Mercato A, Nucleo E, Bonomini A, Pedroni P, Hrabak J, Migliavacca R. Complete Nucleotide Sequence of Plasmids of Two Escherichia coli Strains Carrying bla NDM- 5 and bla NDM - 5 and bla OXA - 181 From the Same Patient. Front Microbiol 2020; 10:3095. [PMID: 32038543 PMCID: PMC6985152 DOI: 10.3389/fmicb.2019.03095] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/20/2019] [Indexed: 11/13/2022] Open
Abstract
Aim of this study was to genetically characterize two carbapenemase-producing Escherichia coli strains obtained from a pediatric patient affected by diarrhea, expressing OXA-181 and/or NDM-5 type enzymes. The above microorganisms were collected in the same Desenzano hospital (Northern Italy) where the blaNDM–5 gene was detected for the first time in Italy 3 years ago. One strain (5P), belonged to sequence type ST405/ST477 (according to Pasture/Oxford schemes) and serotype O102:H6. It was characterized by a 130562 bp multi-replicon plasmid IncFII/IncFIA/IncFIB (pVSI_NDM-5) enclosing two main antibiotic resistance islands: (i) ARI-I, 10030 bp in size, carried genes coding for β-lactam- (blaOXA–1, blaCTX–M–15), fluoroquinolone/aminoglycoside- (aac(6′)-lb-cr) and phenicol- resistance (catB3), (ii) ARI-II, 15326 bp in size, carried genes coding for sulfonamide- (sul1), β-lactam- (blaNDM–5, blaTEM–1B), phenicol- (catB3), trimethoprim- (dfrA17), antiseptic- (qacEΔ1), and aminoglycoside- (aadA5, rmtB) resistance. The other isolate (5M), belonged to sequence type ST2659/ST759 and serotype O50/02:H18, and carried four plasmids: a 153866 bp multi-replicon IncFII/IncFIA/IncFIB (pISV_IncFII_NDM-5), an 89866 bp IncI1 plasmid, a 51480 bp IncX3 plasmid (pISV_IncX3_OXA181), and a 41143 bp IncI plasmid (pISV_IncI_CMY-42). pISV_IncFII_NDM-5 carried two main antibiotic resistance islands: (i) ARI-III, 12220 bp in size, carried genes coding for β-lactam- (blaOXA–1), fluoroquinolone/aminoglycoside- (aac(6′)-lb-cr), tetracycline- (tet(B)) and phenicol- resistance (catB3, catA1), and ii) ARI-IV, 26527 bp in size, carried determinants coding for macrolide- (erm(B), mph(A)), sulfonamide- (sul1), beta-lactam- (blaNDM–5, blaTEM–1B), trimethoprim- (dfrA14, dfrA12), antiseptic- (qacEΔ1), and aminoglycoside- resistance (aadA5). pISV_IncI_CMY-42 harbored the blaCMY–42 gene coding for beta-lactam resistance, pISV_IncX3_OXA181 harbored genes encoding fluoroquinolone- (qnrS1) and beta-lactams- resistance (blaOXA–181). In conclusion, the detection of two different NDM-5 E. coli strains from a pediatric patient with a history of travel to the Far East countries strongly highlight an increasing trend and risk of importation from such areas.
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Affiliation(s)
- Vittoria Mattioni Marchetti
- Department of Clinical Surgical Diagnostic and Pediatric Sciences, Unit of Microbiology and Clinical Microbiology, University of Pavia, Pavia, Italy
| | - Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine in Pilsen, University Hospital in Pilsen, Charles University, Pilsen, Czechia.,Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
| | - Alessandra Mercato
- Department of Clinical Surgical Diagnostic and Pediatric Sciences, Unit of Microbiology and Clinical Microbiology, University of Pavia, Pavia, Italy
| | - Elisabetta Nucleo
- Department of Clinical Surgical Diagnostic and Pediatric Sciences, Unit of Microbiology and Clinical Microbiology, University of Pavia, Pavia, Italy
| | - Annalisa Bonomini
- Clinical Microbiology Laboratory, "AO Desenzano del Garda," Brescia, Italy
| | - Palmino Pedroni
- Clinical Microbiology Laboratory, "AO Desenzano del Garda," Brescia, Italy
| | - Jaroslav Hrabak
- Department of Microbiology, Faculty of Medicine in Pilsen, University Hospital in Pilsen, Charles University, Pilsen, Czechia.,Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
| | - Roberta Migliavacca
- Department of Clinical Surgical Diagnostic and Pediatric Sciences, Unit of Microbiology and Clinical Microbiology, University of Pavia, Pavia, Italy
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High Prevalence of CTX-M Type Extended-Spectrum Beta-Lactamase Genes and Detection of NDM-1 Carbapenemase Gene in Extraintestinal Pathogenic Escherichia coli in Cuba. Pathogens 2020; 9:pathogens9010065. [PMID: 31963265 PMCID: PMC7168674 DOI: 10.3390/pathogens9010065] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 12/21/2022] Open
Abstract
Increase of extraintestinal pathogenic Escherichia coli (ExPEC) showing resistance to beta-lactams is a major public health concern. This study was conducted as a first molecular epidemiological study on ExPEC in Cuba, regarding prevalence of extended-spectrum beta-lactamases (ESBLs) and carbapenemase genes. A total of 306 ExPEC isolates collected in medical institutions in 16 regions in Cuba (2014–2018) were analyzed for their genotypes and presence of genes encoding ESBL, carbapenemase, plasmid-mediated quinolone resistance (PMQR) determinants by PCR and sequencing. The most common phylogenetic group of ExPEC was B2 (49%), followed by D (23%), A (21%), and B1 (7%). Among ESBL genes detected, blaCTX-M was the most common and detected in 61% of ExPEC, with blaCTX-M-15 being dominant and distributed to all the phylogenetic groups. NDM-1 type carbapenemase gene was identified in two isolates of phylogenetic group B1-ST448. Phylogenetic group B2 ExPEC belonged to mostly ST131 (or its single-locus variant) with O25b allele, harboring blaCTX-M-27, and included an isolate of emerging type ST1193. aac (6’)-Ib-cr was the most prevalent PMQR gene (40.5%), being present in 54.5% of CTX-M-positive isolates. These results indicated high prevalence of CTX-M genes and the emergence of NDM-1 gene among recent ExPEC in Cuba, depicting an alarming situation.
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Flerlage T, Brazelton de Cardenas JN, Garner CD, Hasan NA, Karathia H, Qudeimat A, Maron G, Hayden R. Multiple NDM-5-Expressing Escherichia Coli Isolates From an Immunocompromised Pediatric Host. Open Forum Infect Dis 2020; 7:ofaa018. [PMID: 32047833 PMCID: PMC7003983 DOI: 10.1093/ofid/ofaa018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 01/09/2020] [Indexed: 11/17/2022] Open
Abstract
Background Genes conferring carbapenem resistance have disseminated worldwide among Gram-negative bacteria. Here we present longitudinal changes in clinically obtained Escherichia coli isolates from 1 immunocompromised pediatric patient. This report demonstrates potential for antibiotic resistance genes and plasmids to emerge over time in clinical isolates from patients receiving intensive anticancer chemotherapy and broad-spectrum antibiotics. Methods Thirty-three isolates obtained over 7 months from 1 patient were included. Clinical data were abstracted from the medical record. For each isolate, studies included phenotypic antibacterial resistance patterns, sequence typing, bacterial isolate sequencing, plasmid identification, and antibiotic resistance gene identification. Results Sites of isolation included blood, wound culture, and culture for surveillance purposes from the perianal area. Isolates were of 5 sequence types (STs). All were resistant to multiple classes of antibiotics; 23 (69.6%) were phenotypically resistant to all carbapenems. The blaNDM-5 gene was identified in 22 (67%) isolates, all of ST-167 and ST-940, and appeared to coincide with the presence of the IncFII and IncX3 plasmid. Conclusions We present unique microbiologic data from 33 multidrug-resistant E. coli isolates obtained over the course of 7 months from an individual patient in the United States. Two E. coli sequence types causing invasive infection in the same patient and harboring the blaNDM-5 gene, encoded on the IncX3 plasmid and the IncFII plasmid, were identified. This study highlights the emergence of multidrug-resistant bacteria on antibiotic therapy and the necessity of adequate neutrophil number and function in the clearance of bacteremia.
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Affiliation(s)
- Tim Flerlage
- Division of Pediatric Critical Care Medicine, Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA.,Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Cherilyn D Garner
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Nur A Hasan
- CosmosID Incorporated, Rockville, Maryland, USA
| | | | - Amr Qudeimat
- Department of Bone Marrow Transplant and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Gabriela Maron
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Randall Hayden
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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Abstract
The emergence of CRE strains resistant to multiple antibiotics is considered a substantial threat to human health. Therefore, all the efforts to provide a detailed molecular transmission mechanism of specific drug resistance can contribute positively to prevent the further spread of multidrug-resistant bacteria. Although the new superbug harboring blaNDM-5 has been reported in many countries, it was mostly identified among E. coli strains, and the gene transfer mechanism has not been fully recognized and studied. In this work, we identified 22 blaNDM-5-positive strains in different species of Enterobacteriaceae, including 16 Klebsiella pneumoniae strains, four Klebsiella aerogenes strains, and two Escherichia coli strains, which indicated the horizontal gene transfer of blaNDM-5 among Enterobacteriaceae strains in pediatric patients. Moreover, blaNDM-5 was located on a 46-kb IncX3 plasmid, which is possibly responsible for this widespread horizontal gene transfer. The different genetic contexts of the blaNDM-5 gene indicated some minor evolutions of the plasmid, based on the complete sequences of the blaNDM-5 plasmids. These findings are of great significance to understand the transmission mechanism of drug resistance genes, develop anti-infection treatment, and take effective infection control measures. The continuous emergence of novel New Delhi metallo-β-lactamase-5 (NDM-5)-producing Enterobacteriaceae isolates is receiving more and more public attention. Twenty-two NDM-5-producing strains were identified from 146 carbapenemase-producing Enterobacteriaceae (CRE) strains isolated from pediatric patients between January and March 2017, indicating that the blaNDM-5 gene has spread to children. All 22 isolates, including 16 Klebsiella pneumoniae strains, four Klebsiella aerogenes strains, and two Escherichia coli strains, showed significantly high resistance to β-lactam antibiotics (except aztreonam) but remained susceptible to tigecycline and colistin. K. pneumoniae and K. aerogenes strains were respectively defined as homologous clonal isolates by pulsed-field gel electrophoresis (PFGE). Multilocus sequence typing (MLST) results confirmed the genetic relatedness with all K. pneumoniae strains belonging to sequence type (ST) 48. Two E. coli isolates (ST617 and ST1236) were considered genetically unrelated. Twenty-two blaNDM-5 plasmids were positive for the IncX3 amplicon and showed almost identical profiles after digestion with HindIII and EcoRI. Four representative strains (K. pneumoniae K725, K. aerogenes CR33, E. coli Z214, and E. coli Z244) were selected for further study. Plasmids harboring blaNDM-5 showed strong stability in both clinical isolates and transconjugants, without apparent plasmid loss after 100 serial generations. S1-PFGE followed by Southern blot analysis demonstrated that the blaNDM-5 gene was located on an ∼46-kb plasmid. Plasmid sequences of pNDM-K725, pNDM-CR33, and pNDM-Z214 were almost identical but were slightly different from that of pNDM-Z244. Compared with pNDM-Z244, ΔISAba125 and partial copies of IS3000 were missing. The genetic backgrounds of the blaNDM-5 gene in four strains were slightly different from that of the typical pNDM_MGR194. This study comprehensively characterized the horizontal gene transfer of the blaNDM-5 gene among different Enterobacteriaceae isolates in pediatric patients, and the IncX3-type plasmid was responsible for the spread. IMPORTANCE The emergence of CRE strains resistant to multiple antibiotics is considered a substantial threat to human health. Therefore, all the efforts to provide a detailed molecular transmission mechanism of specific drug resistance can contribute positively to prevent the further spread of multidrug-resistant bacteria. Although the new superbug harboring blaNDM-5 has been reported in many countries, it was mostly identified among E. coli strains, and the gene transfer mechanism has not been fully recognized and studied. In this work, we identified 22 blaNDM-5-positive strains in different species of Enterobacteriaceae, including 16 Klebsiella pneumoniae strains, four Klebsiella aerogenes strains, and two Escherichia coli strains, which indicated the horizontal gene transfer of blaNDM-5 among Enterobacteriaceae strains in pediatric patients. Moreover, blaNDM-5 was located on a 46-kb IncX3 plasmid, which is possibly responsible for this widespread horizontal gene transfer. The different genetic contexts of the blaNDM-5 gene indicated some minor evolutions of the plasmid, based on the complete sequences of the blaNDM-5 plasmids. These findings are of great significance to understand the transmission mechanism of drug resistance genes, develop anti-infection treatment, and take effective infection control measures.
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Ramadan H, Gupta SK, Sharma P, Ahmed M, Hiott LM, Barrett JB, Woodley TA, Frye JG, Jackson CR. Circulation of emerging NDM-5-producing Escherichia coli among humans and dogs in Egypt. Zoonoses Public Health 2019; 67:324-329. [PMID: 31867850 DOI: 10.1111/zph.12676] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 11/30/2022]
Abstract
The emergence of NDM-producing Escherichia coli has considerably threatened human and animal health worldwide. This study describes for the first time in Egypt, the draft genome sequences of emerging NDM-5-producing E. coli from humans and dogs, and investigates genetic relatedness between isolates from both sources. Two E. coli from human urine and seven from environmental clinical samples of dogs exhibited resistance to carbapenems and harbouring blaNDM were subjected to Illumina Miseq whole-genome sequencing (WGS). Assembly and analysis of the reads were performed to identify resistance genes, multilocus sequence types (MLST), plasmid replicon types (Inc) and insertion sequences (IS) of the blaNDM region; core genome MLST (cgMLST) analysis was also performed. Two different NDM alleles were identified; blaNDM-5 in E. coli HR119 from the urine of a healthy person and environmental samples of dogs, and blaNDM-1 in E. coli HR135 from a human patient's urine. Multiple mobilizable resistance genes to different antimicrobial classes were identified except the colistin resistance gene, mcr. E. coli isolates from humans and dogs were assigned to different sequence types (STs). Using cgMLST, dog isolates clustered together with only 1-2 allellic differences; however, human E. coli showed 1,978 different allelles compared with dog isolates. Plasmidfinder results indicated the presence of an IncX3 replicon in blaNDM-5 -producing E. coli; however, blaNDM-1 was linked to IncCoIKP3. Notably, the NDM region (3 Kb) in all isolates from humans and dogs was highly similar with variable flanking sequences that represented different IS elements. This study reports the first emergence of NDM-5-producing E. coli from dogs in Egypt that shared some genetic features with human isolates and could be considered potential public health threats.
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Affiliation(s)
- Hazem Ramadan
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA, USA.,Hygiene and Zoonoses Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Sushim K Gupta
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA, USA
| | - Poonam Sharma
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA, USA
| | - Marwa Ahmed
- Hygiene and Zoonoses Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Lari M Hiott
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA, USA
| | - John B Barrett
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA, USA
| | - Tiffanie A Woodley
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA, USA
| | - Jonathan G Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA, USA
| | - Charlene R Jackson
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA, USA
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Kong Z, Cai R, Cheng C, Zhang C, Kang H, Ma P, Gu B. First Reported Nosocomial Outbreak Of NDM-5-Producing Klebsiella pneumoniae In A Neonatal Unit In China. Infect Drug Resist 2019; 12:3557-3566. [PMID: 31814744 PMCID: PMC6863125 DOI: 10.2147/idr.s218945] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/20/2019] [Indexed: 12/20/2022] Open
Abstract
Purpose Carbapenem-resistant Klebsiella pneumoniae (CRKP) have emerged worldwide and also being a major threat to children and neonate. In this study, we describe a nosocomial outbreak of NDM-5-producing Klebsiella pneumoniae in neonatal unit of a teaching hospital in China from September 2015 to September 2016. Patients and methods We collected 12 carbapenem-resistant K. pneumoniae outbreak strains from 12 newborns and characterized these isolates for their antimicrobial susceptibility, clone relationships, and multi-locus sequence types using vitek-2 compact system, pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Resistant genes were detected by using PCR and sequencing. Plasmid conjugation experiment was carried out to determine the transferability of carbapenem resistance. PCR-based replicon typing (PBRT), S1 nuclease-PFGE, and southern blotting were conducted for plasmid profiling. Results All 12 K. pneumoniae isolates were resistant to carbapenems and carried blaNDM-5, blaTEM-1 and blaSHV-11. Furthermore, PFGE analysis showed that NDM-5-producing K. pneumoniae were clonally related and MLST assigned them to sequence type 337. Conjugative assays showed that plasmids harboring blaNDM-5 gene were self-transmissible. Plasmid analysis suggested that all blaNDM-5 gene located on a ~45 kb IncX3 type plasmid. Conclusion To the best of our knowledge, this is the first report of a clone outbreak of blaNDM-5-carrying K. pneumoniae isolates from neonates. There is an urgent need for effective infection control measures to prevent blaNDM-5 variants from becoming epidemic in the neonates in the future.
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Affiliation(s)
- Ziyan Kong
- Medical Technology School, Xuzhou Medical University, Xuzhou, Jiangsu Province, People's Republic of China
| | - Rui Cai
- Medical Technology School, Xuzhou Medical University, Xuzhou, Jiangsu Province, People's Republic of China
| | - Chen Cheng
- Medical Technology School, Xuzhou Medical University, Xuzhou, Jiangsu Province, People's Republic of China
| | - Chuanling Zhang
- Department of Laboratory Medicine, XuZhou Children's Hospital, Xuzhou, Jiangsu Province, People's Republic of China
| | - Haiquan Kang
- Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, People's Republic of China
| | - Ping Ma
- Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, People's Republic of China
| | - Bing Gu
- Medical Technology School, Xuzhou Medical University, Xuzhou, Jiangsu Province, People's Republic of China.,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, People's Republic of China
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Sun P, Xia W, Liu G, Huang X, Tang C, Liu C, Xu Y, Ni F, Mei Y, Pan S. Characterization Of bla NDM-5-Positive Escherichia coli Prevalent In A University Hospital In Eastern China. Infect Drug Resist 2019; 12:3029-3038. [PMID: 31576153 PMCID: PMC6767761 DOI: 10.2147/idr.s225546] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/13/2019] [Indexed: 11/24/2022] Open
Abstract
Purpose The emergence and spread of carbapenem-resistant Enterobacteriaceae deserves special concern worldwide. Unlike the epidemiological characteristics reported in other studies, we found that the production of New Delhi metallo-β-lactamase 5 was the main mechanism for the resistance of Escherichia coli to carbapenems. Methods All carbapenem-resistant strains were collected from July 2017 to July 2018 of the First Affiliated Hospital of Nanjing Medical University. The presence of carbapenemase-encoding genes was detected using PCR and gene sequencing. Genetic relatedness of the blaNDM-5-positive E. coli strains was determined with PFGE and MLST. Susceptibility profiles were measured with broth microdilution method and E-test strips. Transferability features of blaNDM-5 gene were assessed by conjugation experiments, S1-PFGE, southern blotting and PCR-based replicon typing methods. The genetic structures surrounding blaNDM-5 were acquired by whole genome sequencing and PCR mapping. Results Among the 28 carbapenem-resistant E. coli strains, 18 (64%) were verified as NDM-5 producers. The 18 blaNDM-5-positive E. coli strains showed high resistance to most antibiotics, but 100% were sensitive to colistin and tigecycline. In addition, the 18 blaNDM-5-positive E. coli strains belonged to eight STs, among which ST167, ST410 and ST101 were found to cause clonal spread in the hospital. Further studies found that the blaNDM-5 gene was located on an IncX3-type plasmid, and all plasmids harbored an IS3000-ΔISAba125-IS5-blaNDM-5-bleMBL-trpF-dsbC-IS26 structure. Conclusion The clonal spread of blaNDM-5-positive E. coli strains and horizontal dissemination via the pNDM-MGR 194-like plasmids should draw more attention. Appropriate infection control operations should be performed to prevent the further spread of blaNDM-5.
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Affiliation(s)
- Pengfei Sun
- Department of Laboratory Medicine, Jiangsu Province Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, People's Republic of China.,National Key Clinical Department of Laboratory Medicine, Nanjing, People's Republic of China
| | - Wenying Xia
- Department of Laboratory Medicine, Jiangsu Province Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, People's Republic of China.,National Key Clinical Department of Laboratory Medicine, Nanjing, People's Republic of China
| | - Genyan Liu
- Department of Laboratory Medicine, Jiangsu Province Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, People's Republic of China.,National Key Clinical Department of Laboratory Medicine, Nanjing, People's Republic of China
| | - Xu Huang
- Department of Laboratory Medicine, Jiangsu Province Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, People's Republic of China.,National Key Clinical Department of Laboratory Medicine, Nanjing, People's Republic of China
| | - Chenjie Tang
- Department of Laboratory Medicine, Jiangsu Province Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, People's Republic of China.,National Key Clinical Department of Laboratory Medicine, Nanjing, People's Republic of China
| | - Chengcheng Liu
- Department of Laboratory Medicine, Jiangsu Province Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, People's Republic of China.,National Key Clinical Department of Laboratory Medicine, Nanjing, People's Republic of China
| | - Yuqiao Xu
- Department of Laboratory Medicine, Jiangsu Province Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, People's Republic of China.,National Key Clinical Department of Laboratory Medicine, Nanjing, People's Republic of China
| | - Fang Ni
- Department of Laboratory Medicine, Jiangsu Province Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, People's Republic of China.,National Key Clinical Department of Laboratory Medicine, Nanjing, People's Republic of China
| | - Yaning Mei
- Department of Laboratory Medicine, Jiangsu Province Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, People's Republic of China.,National Key Clinical Department of Laboratory Medicine, Nanjing, People's Republic of China
| | - Shiyang Pan
- Department of Laboratory Medicine, Jiangsu Province Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, People's Republic of China.,National Key Clinical Department of Laboratory Medicine, Nanjing, People's Republic of China
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Kopotsa K, Osei Sekyere J, Mbelle NM. Plasmid evolution in carbapenemase-producing Enterobacteriaceae: a review. Ann N Y Acad Sci 2019; 1457:61-91. [PMID: 31469443 DOI: 10.1111/nyas.14223] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/22/2019] [Accepted: 07/26/2019] [Indexed: 12/17/2022]
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) have been listed by the WHO as high-priority pathogens owing to their high association with mortalities and morbidities. Resistance to multiple β-lactams complicates effective clinical management of CRE infections. Using plasmid typing methods, a wide distribution of plasmid replicon groups has been reported in CREs around the world, including IncF, N, X, A/C, L/M, R, P, H, I, and W. We performed a literature search for English research papers, published between 2013 and 2018, reporting on plasmid-mediated carbapenem resistance. A rise in both carbapenemase types and associated plasmid replicon groups was seen, with China, Canada, and the United States recording a higher increase than other countries. blaKPC was the most prevalent, except in Angola and the Czech Republic, where OXA-181 (n = 50, 88%) and OXA-48-like (n = 24, 44%) carbapenemases were most prevalent, respectively; blaKPC-2/3 accounted for 70% (n = 956) of all reported carbapenemases. IncF plasmids were found to be responsible for disseminating different antibiotic resistance genes worldwide, accounting for almost 40% (n = 254) of plasmid-borne carbapenemases. blaCTX-M , blaTEM , blaSHV , blaOXA-1/9 , qnr, and aac-(6')-lb were mostly detected concurrently with carbapenemases. Most reported plasmids were conjugative but not present in multiple countries or species, suggesting limited interspecies and interboundary transmission of a common plasmid. A major limitation to effective characterization of plasmid evolution was the use of PCR-based instead of whole-plasmid sequencing-based plasmid typing.
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Affiliation(s)
- Katlego Kopotsa
- Department of Medical Microbiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, Gauteng, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Nontombi Marylucy Mbelle
- Department of Medical Microbiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, Gauteng, South Africa.,National Health Laboratory Service, Tshwane Division, Department of Medical Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
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Rakhi NN, Alam ARU, Sultana M, Rahaman MM, Hossain MA. Diversity of carbapenemases in clinical isolates: The emergence of blaVIM-5 in Bangladesh. J Infect Chemother 2019; 25:444-451. [DOI: 10.1016/j.jiac.2019.01.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 10/27/2022]
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Plasmid analysis of Escherichia coli isolates from South Korea co-producing NDM-5 and OXA-181 carbapenemases. Plasmid 2019; 104:102417. [PMID: 31150689 DOI: 10.1016/j.plasmid.2019.102417] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/02/2019] [Accepted: 05/27/2019] [Indexed: 11/23/2022]
Abstract
Recently, Escherichia coli isolates co-producing New Delhi metallo-β-lactamase (NDM)-5 and oxacillinase (OXA)-181 were identified in a tertiary-care hospital of South Korea. Isolate CC1702-1 was collected from urine in January 2017 and isolate CC1706-1 was recovered from a transtracheal aspirate of a hospitalized patient in May 2017. Carbapenemase genes were identified by multiplex PCR and sequencing, and whole genome sequencing was performed subsequently using the PacBio RSII system. Both E. coli isolates belonged to the same clone (ST410) and were resistant to all β-lactams including carbapenems. We obtained whole plasmid sequences of the isolates: pCC1702-NDM-5 from CC1702-1 and pCC1706-NDM-5 and pCC1706-OXA-181 from CC1706-1. The two E. coli isolates belonged to the same clone (ST410) and they were completely resistant to all β-lactams, as well as carbapenems. Two blaNDM-5-harboring plasmids belonged to the same incompatibility group, IncFIA/B, and consisted of 79,613 bp and 111,890 bp with 87 and 130 coding sequences, respectively. The genetic structures of the two blaNDM-5-bearing plasmids, which were distinct from the blaNDM-5-bearing plasmids from the Klebsiella pneumoniae isolates previously transmitted from the United Arab Emirates (UAE) to South Korea, differed from each other. While pCC1702-NDM-5 showed high degree of identity with the plasmid from a multidrug-resistant isolate of Citrobacter fruendii P5571 found in China, pCC1706-NDM-5 was very similar to the plasmid from a multidrug-resistant isolate of E. coli AMA1176 found in Denmark. pCC1706-OXA-181, which was a 51 kb, self-transmissible IncX3 plasmid, was identical to the E. coli plasmids pAMA1167-OXA-181 from Denmark and pOXA-181-WCHEC14828 from China. Plasmids harboring blaNDM-5 in E. coli isolates might not be transferred from K. pneumoniae isolates co-producing NDM-5 and OXA-181. They probably originated from multiple sources.
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Bonardi S, Pitino R. Carbapenemase-producing bacteria in food-producing animals, wildlife and environment: A challenge for human health. Ital J Food Saf 2019; 8:7956. [PMID: 31316921 PMCID: PMC6603432 DOI: 10.4081/ijfs.2019.7956] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 05/09/2019] [Indexed: 01/11/2023] Open
Abstract
Antimicrobial resistance is an increasing global health problem and one of the major concerns for economic impacts worldwide. Recently, resistance against carbapenems (doripenem, ertapenem, imipenem, meropenem), which are critically important antimicrobials for human cares, poses a great risk all over the world. Carbapenemases are β-lactamases belonging to different Ambler classes (A, B, D) and encoded by both chromosomal and plasmidic genes. They hydrolyze a broad variety of β-lactams, including carbapenems, cephalosporins, penicillins and aztreonam. Despite several studies in human patients and hospital settings have been performed in European countries, the role of livestock animals, wild animals and the terrestrial and aquatic environment in the maintenance and transmission of carbapenemase- producing bacteria has been poorly investigated. The present review focuses on the carbapenemase-producing bacteria detected in pigs, cattle, poultry, fish, mollusks, wild birds and wild mammals in Europe as well as in non-European countries, investigating the genetic mechanisms for their transmission among food-producing animals and wildlife. To shed light on the important role of the environment in the maintenance and genetic exchange of resistance determinants between environmental and pathogenic bacteria, studies on aquatic sources (rivers, lakes, as well as wastewater treatment plants) are described.
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Affiliation(s)
- Silvia Bonardi
- Department of Veterinary Science, University of Parma, Italy
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Aghamohammad S, Badmasti F, Shirazi AS, Dabiri H, Solgi H, Sabeti S, Shahcheraghi F. Considerable rate of putative virulent phylo-groups in fecal carriage of extended-spectrum β-lactamase producing Escherichia coli. INFECTION GENETICS AND EVOLUTION 2019; 73:184-189. [PMID: 31054921 DOI: 10.1016/j.meegid.2019.04.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 04/22/2019] [Accepted: 04/30/2019] [Indexed: 12/22/2022]
Abstract
Extended-Spectrum Beta-lactamase producing Enterobacteriales (ESBL-PE) in fecal carriage have become a global health concern. Detection of putative virulent ESBL-producing E.coli (ESBL-EC) isolates among asymptomatic carriers is a threatening issue in public health. The aim of this study was to investigate the intestinal carriage of ESBL-EC, phylo-groups and clonal relatedness among putative virulent groups of ESBL-EC isolated from fecal carriages. A total of 120 rectal swabs; 50.8% (61/120) from inpatients of intensive care unit (ICU) and 49.2% (59/120) from outpatients were collected. The ESBL-EC screening was performed by using MacConkey agar supplemented with cefotaxime. PCR assays were applied for determination of phylo-groups, detection of ESBL and carbapenemase genes. Conjugation experiment, plasmid replicon typing and Multilocus Sequence Typing (MLST) were performed for putative virulent phylo-groups. Totally, of 120 studied individuals, 60.0% (72/120) were carrier for ESBL-EC. The rate of blaCTX-M-15, blaTEM, blaSHV was 90.2% (65/72), 50.0% (36/72) and 5.5% (4/72), respectively. The frequency of phylo-groups A, B1, B2, C, D, and F were 20.8% (15/72), 6.9% (5/72), 20.8% (15/72), 2.7% (2/72), 13.8 (10/72) and 12.5% (9/72), respectively. In conjugation experiments, of 6 tested isolates, 5 had conjugative plasmids. The most prevalent plasmid types belonged to IncF incompatibility groups. The MLST analysis showed that the main sequence types among ESBL-EC isolates were ST769 and ST472. The current study provides novel information about the presence of the ESBL-EC isolates, particularly putative virulent phylo-groups among fecal carriages in Iran. Our data revealed that there was almost high ST heterogeneity among putative ESBL-EC isolates. In order to implementation of effective infection control program, detection of fecal carriage in appropriate time typically at the beginning of admission to the hospital is recommended.
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Affiliation(s)
| | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Hossein Dabiri
- Department of Medical Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Solgi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Amin Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shahram Sabeti
- Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Brinkac LM, White R, D'Souza R, Nguyen K, Obaro SK, Fouts DE. Emergence of New Delhi Metallo-β-Lactamase (NDM-5) in Klebsiella quasipneumoniae from Neonates in a Nigerian Hospital. mSphere 2019; 4:e00685-18. [PMID: 30867330 PMCID: PMC6416368 DOI: 10.1128/msphere.00685-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/25/2019] [Indexed: 01/08/2023] Open
Abstract
Outbreaks of infection occur more often than they are reported in most developing countries, largely due to poor diagnostic services. A Klebsiella species bacteremia outbreak in a newborn unit with high mortality was recently encountered at a location being surveilled for childhood bacteremia. These surveillance efforts offered the opportunity to determine the cause of this neonatal outbreak. In this report, we present the whole-genome sequences of New Delhi metallo-β-lactamase (NDM-5)-containing Klebsiella quasipneumoniae subsp. similipneumoniae bloodstream isolates from a neonatal bacteremia outbreak at a tertiary hospital in Nigeria and as part of the largest collection of K. pneumoniae bloodstream isolates from children in Africa. Comparative analysis of the genetic environment surrounding the NDM-5 genes revealed nearly perfect sequence identity to blaNDM-5-bearing IncX3-type plasmids from other members of the EnterobacteriaceaeIMPORTANCE Carbapenem-resistant Klebsiella pneumoniae is of global health importance, yet there is a paucity of genome-based studies in Africa. Here we report fatal blood-borne NDM-5-producing K. quasipneumoniae subsp. similipneumoniae infections from Nigeria, Africa. New Delhi metallo-β-lactamase (NDM)-producing Klebsiella spp. are responsible for high mortality and morbidity, with the NDM-5 variant showing elevated carbapenem resistance. The prevalence of NDM-5 in Klebsiella has been limited primarily to K. pneumoniae, with only one isolate being collected from Africa. During an outbreak of sepsis in a teaching hospital in Nigeria, five NDM-5-producing K. quasipneumoniae subsp. similipneumoniae sequence type 476 isolates were identified. Given the increased resistance profile of these strains, this study highlights the emerging threat of blaNDM-5 dissemination in hospital environments. The observation of these NDM-5-producing isolates in Africa stresses the urgency to improve monitoring and clinical practices to reduce or prevent the further spread of resistance.
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Affiliation(s)
| | | | | | - Kevin Nguyen
- J. Craig Venter Institute, Rockville, Maryland, USA
| | - Stephen K Obaro
- University of Nebraska Medical Center, Omaha, Nebraska, USA
- Department of Pediatrics, University of Abuja Teaching Hospital, Abuja, Nigeria
- International Foundation against Infectious Diseases in Nigeria (IFAIN), Abuja, Nigeria
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NDM Metallo-β-Lactamases and Their Bacterial Producers in Health Care Settings. Clin Microbiol Rev 2019; 32:32/2/e00115-18. [PMID: 30700432 DOI: 10.1128/cmr.00115-18] [Citation(s) in RCA: 371] [Impact Index Per Article: 74.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
New Delhi metallo-β-lactamase (NDM) is a metallo-β-lactamase able to hydrolyze almost all β-lactams. Twenty-four NDM variants have been identified in >60 species of 11 bacterial families, and several variants have enhanced carbapenemase activity. Klebsiella pneumoniae and Escherichia coli are the predominant carriers of bla NDM, with certain sequence types (STs) (for K. pneumoniae, ST11, ST14, ST15, or ST147; for E. coli, ST167, ST410, or ST617) being the most prevalent. NDM-positive strains have been identified worldwide, with the highest prevalence in the Indian subcontinent, the Middle East, and the Balkans. Most bla NDM-carrying plasmids belong to limited replicon types (IncX3, IncFII, or IncC). Commonly used phenotypic tests cannot specifically identify NDM. Lateral flow immunoassays specifically detect NDM, and molecular approaches remain the reference methods for detecting bla NDM Polymyxins combined with other agents remain the mainstream options of antimicrobial treatment. Compounds able to inhibit NDM have been found, but none have been approved for clinical use. Outbreaks caused by NDM-positive strains have been reported worldwide, attributable to sources such as contaminated devices. Evidence-based guidelines on prevention and control of carbapenem-resistant Gram-negative bacteria are available, although none are specific for NDM-positive strains. NDM will remain a severe challenge in health care settings, and more studies on appropriate countermeasures are required.
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Lorme F, Maataoui N, Rondinaud E, Esposito-Farèse M, Clermont O, Ruppe E, Arlet G, Genel N, Matheron S, Andremont A, Armand-Lefevre L. Acquisition of plasmid-mediated cephalosporinase producing Enterobacteriaceae after a travel to the tropics. PLoS One 2018; 13:e0206909. [PMID: 30562395 PMCID: PMC6298645 DOI: 10.1371/journal.pone.0206909] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/22/2018] [Indexed: 12/31/2022] Open
Abstract
Travelers are at high risk of acquiring multi-drug resistant Enterobacteriaceae (MRE) while traveling abroad. Acquisition of extended spectrum beta-lactamase producing Enterobacteriaceae (ESBL-E) while traveling has been extensively described, but not that of plasmid-mediated cephalosporinase producing Enterobacteriaceae (pAmpC-E). Here, we characterized the pAmpC-E acquired in 574 French travelers to tropical areas enrolled in the VOYAG-R study. Among the 526 MRE isolated at return, 57 (10.8%) from 49 travelers were pAmpC-E. The acquisition rate of pAmpC-E was 8.5% (49/574) ranging from 12.8% (25/195) in Asia, 7.6% (14/184) in Latin America to 5.1% (10/195) in Africa. The highest acquisition rates were observed in Peru (21.9%), India (21.4%) and Vietnam (20%). The carriage of pAmpC-E decreased quickly after return with 92.5% of colonized travelers being negative at one month. Most enzymes were CMY types (96.5%, n = 55, only met in Escherichia coli), including 40 CMY-2 (70.2%), 12 CMY-42 (21.1%), 1 CMY-6 and two new CMY-2 variants. The remaining were two DHA observed in Klebsiella pneumoniae. CMY-2 producing strains were acquired worldwide whereas CMY-42, except for one, were all acquired in Asia. BlaCMY-2 genes were associated with different plasmid types, including IncI1 (45. 2%), IncF (10%), IncF-IncI (7.5%), IncA/C (5%) and IncR (2.5%) whereas blaCMY-42 were all associated with IncI1 plasmids. Even though the pAmpC-E acquisition rate was much lower than that of ESBL-E, it was significant, especially in Asia, showing that pAmpC-E, especially CMY-type producing E. coli have spread in the community settings of tropical regions.
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Affiliation(s)
- Florian Lorme
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Paris, France
| | - Naouale Maataoui
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Paris, France
- INSERM, IAME, UMR 1137 France, Université Paris Diderot, Sorbonne Paris Cité, Paris, France, AP-HP, Hôpital Bichat, URC Paris-Nord, Paris, France
| | - Emilie Rondinaud
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Paris, France
- INSERM, IAME, UMR 1137 France, Université Paris Diderot, Sorbonne Paris Cité, Paris, France, AP-HP, Hôpital Bichat, URC Paris-Nord, Paris, France
| | - Marina Esposito-Farèse
- AP-HP, Hôpital Bichat, URC Paris-Nord, Paris, France
- INSERM, CIC 1425-EC, UMR1123, Paris, France
| | - Olivier Clermont
- INSERM, IAME, UMR 1137 France, Université Paris Diderot, Sorbonne Paris Cité, Paris, France, AP-HP, Hôpital Bichat, URC Paris-Nord, Paris, France
| | - Etienne Ruppe
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Paris, France
- INSERM, IAME, UMR 1137 France, Université Paris Diderot, Sorbonne Paris Cité, Paris, France, AP-HP, Hôpital Bichat, URC Paris-Nord, Paris, France
| | - Guillaume Arlet
- AP-HP, Groupe Hospitalier des Hôpitaux Universitaires de l'Est Parisien, Département de Bactériologie, Paris, France
- INSERM U1135, CIMI, Team E13, Paris, France, Sorbonne Université, UPMC Université Paris, Paris, France
| | - Nathalie Genel
- AP-HP, Groupe Hospitalier des Hôpitaux Universitaires de l'Est Parisien, Département de Bactériologie, Paris, France
- INSERM U1135, CIMI, Team E13, Paris, France, Sorbonne Université, UPMC Université Paris, Paris, France
| | | | - Sophie Matheron
- INSERM, IAME, UMR 1137 France, Université Paris Diderot, Sorbonne Paris Cité, Paris, France, AP-HP, Hôpital Bichat, URC Paris-Nord, Paris, France
- AP-HP, Hôpital Bichat, Maladies Infectieuses et Tropicales, Paris, France
| | - Antoine Andremont
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Paris, France
- INSERM, IAME, UMR 1137 France, Université Paris Diderot, Sorbonne Paris Cité, Paris, France, AP-HP, Hôpital Bichat, URC Paris-Nord, Paris, France
| | - Laurence Armand-Lefevre
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Paris, France
- INSERM, IAME, UMR 1137 France, Université Paris Diderot, Sorbonne Paris Cité, Paris, France, AP-HP, Hôpital Bichat, URC Paris-Nord, Paris, France
- * E-mail:
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Barrado L, Pérez-Vázquez M, del Pozo JL, Martín-Salas C, Leiva J, Mazón A, Ezpeleta C, Oteo J. Clonal transmission of NDM-5-producing Escherichia coli belonging to high-risk sequence type ST405. Int J Antimicrob Agents 2018; 52:123-124. [DOI: 10.1016/j.ijantimicag.2018.05.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/22/2018] [Accepted: 05/26/2018] [Indexed: 10/14/2022]
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Li X, Fu Y, Shen M, Huang D, Du X, Hu Q, Zhou Y, Wang D, Yu Y. Dissemination of blaNDM-5 gene via an IncX3-type plasmid among non-clonal Escherichia coli in China. Antimicrob Resist Infect Control 2018; 7:59. [PMID: 29713466 PMCID: PMC5918551 DOI: 10.1186/s13756-018-0349-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/16/2018] [Indexed: 12/02/2022] Open
Abstract
Background The emergence and spread of New Delhi metallo-β-lactamase-producing Enterobacteriaceae has been a serious challenge to manage in the clinic due to its rapid dissemination of multi-drug resistance worldwide. As one main type of carbapenemases, New Delhi metallo-β-lactamase (NDM)is able to confer resistance to almost all β-lactams, including carbapenems, in Enterobacteriaceae. Recently, New Delhi metallo-β-lactamase-5 attracted extensive attention because of increased resistance to carbapenems and widespread dissemination. However, the dissemination mechanism of blaNDM-5 gene remains unclear. Methods A total of 224 carbapenem-resistant Enterobacteriaceae isolates (CRE) were collected from different hospitals in Zhejiang province. NDM-5-positive isolates were identified and subjected to genotyping, susceptibility testing, and clinical data analysis. We established the genetic location of blaNDM-5 with southern blot hybridisation, and analysed plasmids containing blaNDM-5 with filter mating and DNA sequencing. Results Eleven New Delhi metallo-β-lactamase-5 (NDM-5)-producing strains were identified, including 9 Escherichia coli strains, 1 Klebsiella pneumoniae strain, and 1 Citrobacter freundii strain. No epidemiological links for E. coli isolates were identified by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). S1-PFGE and southern blot suggested that the blaNDM-5 gene was located on a 46-kb IncX3-type plasmid in all isolates. Nine of the 11 isolates (81.8%) tested could successfully transfer their carbapenem-resistant phenotype to E. coli strain C600. Moreover, sequence analysis further showed that this plasmid possessed high sequence similarity to most of previously reported blaNDM-5-habouring plasmids in China. Conclusion The present data in this study showed the IncX3 type plasmid played an important role in the dissemination of blaNDM-5 in Enterobacteriaceae. In addition, to the best of our knowledge, this report is the first to isolate both E. coli and C. freundii strains carrying blaNDM-5 from one single patient, which further indicated the possibility of blaNDM-5 transmission among diverse species. Close surveillance is urgently needed to monitor the further dissemination of NDM-5-producing isolates.
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Affiliation(s)
- Xi Li
- Centre of Laboratory Medicine, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, 158 Shangtang Road, Zhejiang, 310014 Hangzhou China
| | - Ying Fu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Zhejiang, 310016 Hangzhou China
| | - Mengyuan Shen
- Centre of Laboratory Medicine, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, 158 Shangtang Road, Zhejiang, 310014 Hangzhou China
| | - Danyan Huang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Zhejiang, 310016 Hangzhou China
| | - Xiaoxing Du
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Zhejiang, 310016 Hangzhou China
| | - Qingfeng Hu
- Centre of Laboratory Medicine, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, 158 Shangtang Road, Zhejiang, 310014 Hangzhou China
| | - Yonglie Zhou
- Centre of Laboratory Medicine, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, 158 Shangtang Road, Zhejiang, 310014 Hangzhou China
| | - Dairong Wang
- Blood Center of Zhejiang Province, 789 Jianye Road, Zhejiang, 310052 Hangzhou China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Zhejiang, 310016 Hangzhou China
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45
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Taylor E, Sriskandan S, Woodford N, Hopkins KL. High prevalence of 16S rRNA methyltransferases among carbapenemase-producing Enterobacteriaceae in the UK and Ireland. Int J Antimicrob Agents 2018; 52:278-282. [PMID: 29596903 DOI: 10.1016/j.ijantimicag.2018.03.016] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 03/12/2018] [Accepted: 03/21/2018] [Indexed: 11/18/2022]
Abstract
The emergence of 16S rRNA methyltransferases (16S RMTases) worldwide is a growing concern due to their ability to confer high-level resistance (minimum inhibitory concentrations (MICs) >256 mg/L) to all clinically relevant aminoglycosides. As the occurrence of 16S RMTases in the United Kingdom has not been investigated to date, we screened 806 Enterobacteriaceae isolates displaying high-level aminoglycoside resistance (amikacin, gentamicin and tobramycin MICs ≥64, ≥32 and ≥32 mg/L, respectively) for 16S RMTases either by analysing whole-genome sequence (WGS) data (which were available for 449 isolates) or by polymerase chain reaction. A total of 94.5% (762/806) pan-aminoglycoside-resistant Enterobacteriaceae were positive for one or more 16S RMTase genes; armA was the most common (340, 44.6%) followed by rmtC (146, 19.2%), rmtF (137, 18.0%), rmtB (87, 11.4%) and various two-gene combinations (52, 6.8%). Most (93.4%; 712/762) 16S RMTase producers also carried acquired carbapenemase genes, with blaNDM the most common (592/712; 83.1%). Additionally, high-risk bacterial clones associated with blaNDM were identified in the subset of isolates with WGS data. These included Escherichia coli sequence types (STs) 405 (21.8%, 19/87), 167 (20.7%, 18/87) 410 (12.6%, 11/87) and K. pneumoniae STs 14 (35.6%, 112/315), 231 (15.6%, 49/315) and 147 (10.5%, 33/315). These accounted for 4.2% (15/358), 5.0% (18/358), 3.1% (11/358), 28.2% (101/358), 3.1% (11/358) and 7.0% (25/358) blaNDM-producing isolates, respectively. This study shows that 16S RMTases occur in the UK and Ireland and carbapenemases are particularly prevalent in 16S RMTase-producing Enterobacteriaceae. This association poses a risk to the treatment of multidrug-resistant Gram-negative infections in the clinical setting.
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Affiliation(s)
- Emma Taylor
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance at Imperial College London, Hammersmith Hospital, Du Cane Road, London, UK; Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK.
| | - Shiranee Sriskandan
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance at Imperial College London, Hammersmith Hospital, Du Cane Road, London, UK
| | - Neil Woodford
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance at Imperial College London, Hammersmith Hospital, Du Cane Road, London, UK; Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - Katie L Hopkins
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance at Imperial College London, Hammersmith Hospital, Du Cane Road, London, UK; Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
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46
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Ahmad N, Ali SM, Khan AU. Detection of New Delhi Metallo-β-Lactamase Variants NDM-4, NDM-5, and NDM-7 in Enterobacter aerogenes Isolated from a Neonatal Intensive Care Unit of a North India Hospital: A First Report. Microb Drug Resist 2018; 24:161-165. [DOI: 10.1089/mdr.2017.0038] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Nayeem Ahmad
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh India
| | - Syed Manazir Ali
- Pediatrics Department, JN Medical College and Hospital, A.M.U, Aligarh India
| | - Asad U. Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh India
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47
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Luo Y, Luo R, Ding H, Ren X, Luo H, Zhang Y, Ye L, Cui S. Characterization of Carbapenem-Resistant Escherichia coli Isolates Through the Whole-Genome Sequencing Analysis. Microb Drug Resist 2018; 24:175-180. [PMID: 28686503 DOI: 10.1089/mdr.2017.0079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Yanping Luo
- Department of Microbiology, The General Hospital of PLA, Beijing, China
| | - Rong Luo
- Department of Microbiology, National Institutes for Food and Drug Control, The State Food and Drug Administration, Beijing, China
| | - Hong Ding
- Department of Microbiology, National Institutes for Food and Drug Control, The State Food and Drug Administration, Beijing, China
| | - Xiu Ren
- Department of Microbiology, National Institutes for Food and Drug Control, The State Food and Drug Administration, Beijing, China
| | - Haipeng Luo
- Department of Microbiology, National Institutes for Food and Drug Control, The State Food and Drug Administration, Beijing, China
| | - Ying Zhang
- Department of Microbiology, The General Hospital of PLA, Beijing, China
| | - Liyan Ye
- Department of Microbiology, The General Hospital of PLA, Beijing, China
| | - Shenghui Cui
- Department of Microbiology, National Institutes for Food and Drug Control, The State Food and Drug Administration, Beijing, China
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48
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Bitar I, Piazza A, Gaiarsa S, Villa L, Pedroni P, Oliva E, Nucleo E, Pagani L, Carattoli A, Migliavacca R. ST405 NDM-5 producing Escherichia coli in Northern Italy: the first two clinical cases. Clin Microbiol Infect 2017; 23:489-490. [DOI: 10.1016/j.cmi.2017.01.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/19/2017] [Accepted: 01/25/2017] [Indexed: 12/24/2022]
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49
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NDM-5 and OXA-181 Beta-Lactamases, a Significant Threat Continues To Spread in the Americas. Antimicrob Agents Chemother 2017; 61:AAC.00454-17. [PMID: 28461314 DOI: 10.1128/aac.00454-17] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 04/23/2017] [Indexed: 11/20/2022] Open
Abstract
Among Gram-negative bacteria, carbapenem-resistant infections pose a serious and life-threatening challenge. Here, the CRACKLE network reports a sentinel detection and characterization of a carbapenem-resistant Klebsiella pneumoniae ST147 isolate harboring blaNDM-5 and blaOXA-181 from a young man who underwent abdominal surgery in India. blaNDM-5 was located on an IncFII plasmid of ≈90 kb, whereas blaOXA-181 was chromosomally encoded. Resistome and genome analysis demonstrated multiple copies of the transposable element IS26 and a "hot-spot region" in the IncFII plasmid.
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50
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Espinal P, Miró E, Segura C, Gómez L, Plasencia V, Coll P, Navarro F. First Description of bla NDM-7 Carried on an IncX4 Plasmid in Escherichia coli ST679 Isolated in Spain. Microb Drug Resist 2017. [PMID: 28650275 DOI: 10.1089/mdr.2017.0039] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
This study describes the molecular characterization of an NDM-7 carbapenemase-producing Escherichia coli strain Ec188, recovered from a rectal swab of a male patient who had travelled to Pakistan before his hospitalization at the Hospital del Mar in Barcelona, Spain. The Ec188 isolate, assigned to a new multilocus sequence type ST679, was resistant to all beta-lactams, aminoglycosides (gentamicin, tobramycin, and with reduced susceptibility to amikacin), and ciprofloxacin. The blaNDM-7 gene was located on a 50 kb IncX4 plasmid (pEc188-NDM7), both in the original and transconjugant strains. In addition, blaCTX-M-15 was located on a 150 kb IncFIA plasmid and blaCMY-2 on a 95 kb undetermined plasmid type, only in the wild-type strain. The immediate genetic surroundings of blaNDM-7 included the bleo, trpf, and dsbC genes, and it was flanked by the insertion sequences IS26 and ISAba125, which appeared interrupted by IS5. The res and parA genes were found in the same orientation downstream of the IS26 element. To our knowledge, this is the first report of an NDM-7-carbapenemase carried on an IncX4 plasmid, as well as the first E. coli strain belonging to ST679 harboring an NDM β-lactamase, possibly associated with previous travel to Pakistan. In addition, this study highlights the dissemination of NDM variants accompanied by IncX-type plasmids.
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Affiliation(s)
- Paula Espinal
- 1 Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - Elisenda Miró
- 1 Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - Concepción Segura
- 2 Department of Microbiology, Reference Laboratory of Catalonia , Barcelona, Spain
| | - Laura Gómez
- 1 Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - Virginia Plasencia
- 2 Department of Microbiology, Reference Laboratory of Catalonia , Barcelona, Spain
| | - Pere Coll
- 1 Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain .,3 Department of Genètic and Microbiology, Universitat Autònoma de Barcelona , Barcelona, Spain
| | - Ferran Navarro
- 1 Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain .,3 Department of Genètic and Microbiology, Universitat Autònoma de Barcelona , Barcelona, Spain
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