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El Zowalaty ME, Falgenhauer L, Ashour HM, Zishiri OT, Forsythe S, Helmy YA. Draft genome sequences of Bacillus licheniformis strains MEZBL63 and MEZBL64 harboring the lichenysin toxin operon isolated from livestock in South Africa. Microbiol Resour Announc 2024; 13:e0096723. [PMID: 38323846 DOI: 10.1128/mra.00967-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/05/2024] [Indexed: 02/08/2024] Open
Abstract
Here, we report the draft genome sequences of two Bacillus licheniformis strains harboring the lichenysin operon that were isolated from healthy goat and horse in South Africa. The genomes were sequenced using Illumina MiSeq and had a length of 4,152,826 and 4,110,075 bp, respectively, with a G + C content of 46%.
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Affiliation(s)
- Mohamed E El Zowalaty
- Veterinary Medicine and Food Security Research Group, Medical Laboratory Sciences Program, Faculty of Health Sciences, Abu Dhabi Women's Campus, Higher Colleges of Technology, Abu Dhabi, United Arab Emirates
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, German Center for Infection Research, Site Giessen-Marburg-Langen and Hessian University Competence Center for Hospital Hygiene (HuKKH), Justus Liebig University Giessen, Giessen, Germany
| | - Hossam M Ashour
- Department of Integrative Biology, College of Arts and Sciences, University of South Florida, St. Petersburg, Florida, USA
| | - Oliver T Zishiri
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Durban, South Africa
| | - Stephen Forsythe
- Foodmicrobe.com Ltd, Adams Hill, Keyworth, Nottingham, United Kingdom
| | - Yosra A Helmy
- Department of Veterinary Science, Martin-Gatton College of Agriculture, Food, and Environment, University of Kentucky, Lexington, Kentucky, USA
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Rahman MH, El Zowalaty ME, Falgenhauer L, Khan MFR, Alam J, Popy NN, Ashour HM, Rahman MB. Molecular identification and whole genome sequence analyses of methicillin-resistant and mastitis-associated Staphylococcus aureus sequence types 6 and 2454 isolated from dairy cows. J Genomics 2024; 12:19-25. [PMID: 38321997 PMCID: PMC10845239 DOI: 10.7150/jgen.90833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/19/2023] [Indexed: 02/08/2024] Open
Abstract
The emergence of antimicrobial-resistant and mastitis-associated Staphylococcus aureus is of great concern due to the huge economic losses worldwide. Here, we report draft genome sequences of two Staphylococcus aureus strains which were isolated from raw milk samples obtained from mastitis-infected cows in Bangladesh. The strains were isolated and identified using conventional microbiological and molecular polymerase chain reaction (PCR) methods. Antibiotic susceptibility testing was performed. Genomic DNA of the two strains was extracted and the strains were sequenced using the Illumina NextSeq 550 platform. The assembled contigs were analyzed for virulence determinants, antimicrobial resistance genes, extra-chromosomal plasmids, and multi-locus sequence type (MLST). The genomes of the two strains were compared with other publicly available genome sequences of Staphylococcus aureus strains. The raw read sequences were downloaded and all sequence files were analyzed identically to generate core genome phylogenetic trees. The genome of BR-MHR281strain did not harbour any antibiotic resistance determinants, however BR-MHR220 strain harbored mecA and blaZ genes. Analysis of BR-MHR220 strain revealed that it was assigned to sequence type (ST-6), clonal complex (CC) 5 and spa type t304, while BR-MHR281 strain belonged to ST-2454, CC8, and harbored the spa type t7867. The findings of the present study and the genome sequences of BR-MHR220 and BR-MHR281 strains will provide data on the detection and genomic analysis and characterization of mastitis-associated Staphylococcus aureus in Bangladesh. In addition, the findings of the present study will serve as reference genomes for future molecular epidemiological studies and will provide significant data which help understand the prevalence, pathogenesis and antimicrobial resistance of mastitis-associated Staphylococcus aureus.
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Affiliation(s)
- Mohammad H. Rahman
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Mohamed E. El Zowalaty
- Veterinary Medicine and Food Security Research Group, Medical Laboratory Sciences Program, Faculty of Health Sciences, Abu Dhabi Women's Campus, Higher Colleges of Technology, Abu Dhabi, UAE
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Biomedical research center Seltersberg, Schubertstrasse 81, 35392 Giessen, Germany
| | - Mohammad F. R. Khan
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Jahangir Alam
- National Institute of Biotechnology, Savar, Dhaka, Bangladesh
| | - Najmun N. Popy
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Hossam M. Ashour
- Department of Integrative Biology, College of Arts and Sciences, University of South Florida, St. Petersburg, Florida, USA
| | - Md. Bahanur Rahman
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
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Yao Y, Falgenhauer L, Rezazadeh Y, Falgenhauer J, Imirzalioglu C, Chakraborty T. Predominant transmission of KPC-2 carbapenemase in Germany by a unique IncN plasmid variant harboring a novel non-transposable element (NTE KPC -Y). Microbiol Spectr 2024; 12:e0256423. [PMID: 38084979 PMCID: PMC10790570 DOI: 10.1128/spectrum.02564-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/30/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Current infection control protocols assume that the spread of KPC-2 carbapenemase-producing Enterobacterales (KPC2-CPE) by detected carriers to other in-house patients is through clonal transmission and can be restricted by implementing containment measures. We examined the presence of the bla KPC-2 gene in different genera and species of Enterobacterales isolated from humans at different hospitals and surface waters between 2013 and 2019 in Germany. We found that a single IncN[pMLST15] plasmid carrying the bla KPC-2 gene on a novel non-Tn4401-element (NTEKPC-Y), flanked by an adjacent region encoding 12 other antibiotic resistance genes, was uniquely present in multiple species of KPC2-CPE isolates. These findings demonstrate the selective impact of specific IncN plasmids as major drivers of carbapenemase dissemination and suggest "plasmid-based endemicity" for KPC2-CPE. Studies on the dynamics of plasmid-based KPC2-CPE transmission and its presence in persistent reservoirs need to be urgently considered to implement effective surveillance and prevention measures in healthcare institutions.
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Affiliation(s)
- Yancheng Yao
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- Institute for Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Yalda Rezazadeh
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Jane Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - the IncN Study GroupHauriAnja M.1HeinmüllerPetra1DomannEugen2GhoshHiren2GoesmannAlexander2JanssenStefan2GatermannSören3KaaseMartin3PfennigwerthNiels3ExnerMartin4OvermannJörg5BunkBoyke5SpröerCathrin5Hessisches Landesprüfungs- und Untersuchungsamt im Gesundheitswesen - HLPUG, Dillenburg, GermanyJustus Liebig University Giessen, Giessen, GermanyGerman National Reference Centre for Multidrug-Resistant Gram-negative Bacteria, Ruhr-University Bochum, Bochum, GermanyUniversity of Bonn, Bonn, GermanyLeibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
- Institute for Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
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El Zowalaty ME, Lamichhane B, Falgenhauer L, Mowlaboccus S, Zishiri OT, Forsythe S, Helmy YA. Author Correction: Antimicrobial resistance and whole genome sequencing of novel sequence types of Enterococcus faecalis, Enterococcus faecium, and Enterococcus durans isolated from livestock. Sci Rep 2023; 13:19879. [PMID: 37963920 PMCID: PMC10645726 DOI: 10.1038/s41598-023-46976-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023] Open
Affiliation(s)
- Mohamed E El Zowalaty
- Veterinary Medicine and Food Security Research Group, Medical Laboratory Sciences Program, Faculty of Health Sciences, Abu Dhabi Women's Campus, Higher Colleges of Technology, Abu Dhabi, 41012, UAE.
| | - Bibek Lamichhane
- Department of Veterinary Science, Martin-Gatton College of Agriculture, Food, and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Biomedical Research Center Seltersberg, Schubertstrasse 81, 35392, Giessen, Germany
| | - Shakeel Mowlaboccus
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
- Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Oliver T Zishiri
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Private Bag X54001, Westville, Durban, 4000, South Africa
| | - Stephen Forsythe
- Foodmicrobe.com Ltd., Adams Hill, Keyworth, Nottingham, NG12 5GY, UK
| | - Yosra A Helmy
- Department of Veterinary Science, Martin-Gatton College of Agriculture, Food, and Environment, University of Kentucky, Lexington, KY, 40546, USA.
- Department of Zoonoses, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41522, Egypt.
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El Zowalaty ME, Lamichhane B, Falgenhauer L, Mowlaboccus S, Zishiri OT, Forsythe S, Helmy YA. Antimicrobial resistance and whole genome sequencing of novel sequence types of Enterococcus faecalis, Enterococcus faecium, and Enterococcus durans isolated from livestock. Sci Rep 2023; 13:18609. [PMID: 37903806 PMCID: PMC10616195 DOI: 10.1038/s41598-023-42838-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/15/2023] [Indexed: 11/01/2023] Open
Abstract
The emergence of antimicrobial-resistant, livestock-associated Enterococcus faecalis represents a public health concern. Here, we report the isolation, molecular detection of virulence and antimicrobial resistance determinants, in addition to the phylogenetic analyses of 20 Enterococcus species using whole genome sequencing analysis of 15 Enterococcus faecalis strains including six strains of three novel sequence types, three Enterococcus faecium and two Enterococcus durans. All strains were isolated from food chain animals in South Africa. Enterococcus strains were isolated on bile aesculin azide agar, followed by identification using MALDI-TOF MS analysis. Antibiotic susceptibility testing was performed using the Kirby-Bauer disk diffusion method. The genomic DNA of the isolates was extracted and sequencing was performed using the Illumina MiSeq platform. Sequence reads were trimmed and de novo assembled. The assembled contigs were analyzed for antimicrobial resistance genes and chromosomal mutations, extra-chromosomal plasmids, and multi-locus sequence type (MLST). Multidrug antimicrobial resistance genes conferring resistance to aminoglycosides (ant(6)-Ia, aph(3')-IIIa, sat4, and spw), lincosamides (lnu(B), lsa(A), and lsa(E)), macrolides (erm(B)), trimethoprim (dfrG) and tetracyclines (tet(L) and tet(M)) were identified. Plasmid replicons were detected in seven E. faecalis and three E. faecium isolates. The sequence type (ST) of each isolate was determined using the Enterococcus PubMLST database. Ten STs were identified in the collection, three of which (ST1240, ST1241, and ST1242) have not been previously reported and are described in the present study for the first time. To compare the sequenced strains to other previously sequenced E. faecalis strains, assembled sequences of E. faecalis from livestock were downloaded from the PubMLST database. Core genome-based phylogenetic analysis was performed using ParSNP. The detection of multiple drug-resistance in Enterococcus including E. faecalis and E. faecium highlights the significance of genomic surveillance to monitor the spread of antimicrobial resistance in food chain animals. In addition, the genome sequences of Enterococcus strains reported in the present study will serve as a reference point for future molecular epidemiological studies of livestock-associated and antibiotic-resistant E. faecalis in Africa. In addition, this study enables the in-depth analysis of E. faecalis genomic structure, as well as provides valuable information on the phenotypic and genotypic antimicrobial resistance, and the pathogenesis of livestock-associated E. faecalis and E. faecium.
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Affiliation(s)
- Mohamed E El Zowalaty
- Veterinary Medicine and Food Security Research Group, Medical Laboratory Sciences Program, Faculty of Health Sciences, Abu Dhabi Women's Campus, Higher Colleges of Technology, Abu Dhabi, 41012, UAE.
| | - Bibek Lamichhane
- Department of Veterinary Science, Martin-Gatton College of Agriculture, Food, and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Biomedical Research Center Seltersberg, Schubertstrasse 81, 35392, Giessen, Germany
| | - Shakeel Mowlaboccus
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
- Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Oliver T Zishiri
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Private Bag X54001, Westville, Durban, 4000, South Africa
| | - Stephen Forsythe
- Foodmicrobe.com Ltd., Adams Hill, Keyworth, Nottingham, NG12 5GY, UK
| | - Yosra A Helmy
- Department of Veterinary Science, Martin-Gatton College of Agriculture, Food, and Environment, University of Kentucky, Lexington, KY, 40546, USA.
- Department of Zoonoses, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41522, Egypt.
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Rahman MH, El Zowalaty ME, Falgenhauer L, Khan MFR, Alam J, Popy NN, Rahman MB. Draft Genome Sequences of Two Clinical Mastitis-Associated Escherichia coli Strains, of Sequence Type 101 and Novel Sequence Type 13054, Isolated from Dairy Cows in Bangladesh. Microbiol Resour Announc 2023; 12:e0016623. [PMID: 37428031 PMCID: PMC10443403 DOI: 10.1128/mra.00166-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/13/2023] [Indexed: 07/11/2023] Open
Abstract
Here, we report the draft genome sequences of two Escherichia coli strains that were isolated from raw milk samples obtained from lactating cows with mastitis in Bangladesh. One strain was assigned to a novel sequence type 13054, and the other strain belonged to sequence type 101.
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Affiliation(s)
- Mohammad H. Rahman
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Mohamed E. El Zowalaty
- Veterinary Medicine and Food Security Research Group, Medical Laboratory Sciences Program, Faculty of Health Sciences, Abu Dhabi Women's Campus, Higher Colleges of Technology, Abu Dhabi, United Arab Emirates
| | - Linda Falgenhauer
- German Center for Infection Research, Site Giessen-Marburg-Langen, Giessen, Germany
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
- Hessian University Competence Center for Hospital Hygiene, Justus Liebig University Giessen, Giessen, Germany
| | | | - Jahangir Alam
- National Institute of Biotechnology, Savar, Dhaka, Bangladesh
| | - Najmun Nahar Popy
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - M. Bahanur Rahman
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
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Frantz R, Gwozdzinski K, Gisch N, Doijad SP, Hudel M, Wille M, Abu Mraheil M, Schwudke D, Imirzalioglu C, Falgenhauer L, Ehrmann M, Chakraborty T. A Single Residue within the MCR-1 Protein Confers Anticipatory Resilience. Microbiol Spectr 2023; 11:e0359222. [PMID: 37071007 PMCID: PMC10269488 DOI: 10.1128/spectrum.03592-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/21/2023] [Indexed: 04/19/2023] Open
Abstract
The envelope stress response (ESR) of Gram-negative enteric bacteria senses fluctuations in nutrient availability and environmental changes to avert damage and promote survival. It has a protective role toward antimicrobials, but direct interactions between ESR components and antibiotic resistance genes have not been demonstrated. Here, we report interactions between a central regulator of ESR viz., the two-component signal transduction system CpxRA (conjugative pilus expression), and the recently described mobile colistin resistance protein (MCR-1). Purified MCR-1 is specifically cleaved within its highly conserved periplasmic bridge element, which links its N-terminal transmembrane domain with the C-terminal active-site periplasmic domain, by the CpxRA-regulated serine endoprotease DegP. Recombinant strains harboring cleavage site mutations in MCR-1 are either protease resistant or degradation susceptible, with widely differing consequences for colistin resistance. Transfer of the gene encoding a degradation-susceptible mutant to strains that lack either DegP or its regulator CpxRA restores expression and colistin resistance. MCR-1 production in Escherichia coli imposes growth restriction in strains lacking either DegP or CpxRA, effects that are reversed by transactive expression of DegP. Excipient allosteric activation of the DegP protease specifically inhibits growth of isolates carrying mcr-1 plasmids. As CpxRA directly senses acidification, growth of strains at moderately low pH dramatically increases both MCR-1-dependent phosphoethanolamine (PEA) modification of lipid A and colistin resistance levels. Strains expressing MCR-1 are also more resistant to antimicrobial peptides and bile acids. Thus, a single residue external to its active site induces ESR activity to confer resilience in MCR-1-expressing strains to commonly encountered environmental stimuli, such as changes in acidity and antimicrobial peptides. Targeted activation of the nonessential protease DegP can lead to the elimination of transferable colistin resistance in Gram-negative bacteria. IMPORTANCE The global presence of transferable mcr genes in a wide range of Gram-negative bacteria from clinical, veterinary, food, and aquaculture environments is disconcerting. Its success as a transmissible resistance factor remains enigmatic, because its expression imposes fitness costs and imparts only moderate levels of colistin resistance. Here, we show that MCR-1 triggers regulatory components of the envelope stress response, a system that senses fluctuations in nutrient availability and environmental changes, to promote bacterial survival in low pH environments. We identify a single residue within a highly conserved structural element of mcr-1 distal to its catalytic site that modulates resistance activity and triggers the ESR. Using mutational analysis, quantitative lipid A profiling and biochemical assays, we determined that growth in low pH environments dramatically increases colistin resistance levels and promotes resistance to bile acids and antimicrobial peptides. We exploited these findings to develop a targeted approach that eliminates mcr-1 and its plasmid carriers.
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Affiliation(s)
- Renate Frantz
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Konrad Gwozdzinski
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Swapnil Prakash Doijad
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Martina Hudel
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Maria Wille
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Mobarak Abu Mraheil
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Dominik Schwudke
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site: Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Airway Research Center North, Partner Site: Research Center Borstel, Borstel, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- Hessian University Competence Center for Hospital Hygiene, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
- Hessian University Competence Center for Hospital Hygiene, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Michael Ehrmann
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- Hessian University Competence Center for Hospital Hygiene, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
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El Zowalaty ME, Falgenhauer L, Forsythe S, Helmy YA. Draft genome sequences of rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 carrying mobile colistin resistance gene mcr-9 isolated from wastewater in South Africa. J Glob Antimicrob Resist 2023; 33:231-237. [PMID: 36948496 DOI: 10.1016/j.jgar.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/23/2023] [Accepted: 03/07/2023] [Indexed: 03/24/2023] Open
Abstract
OBJECTIVES Antimicrobial-resistant bacteria of the order Enterobacterales are emerging threats to global public and animal health, leading to morbidity and mortality. The emergence of antimicrobial-resistant, livestock-associated pathogens is a great public health concern. The genera Enterobacter and Lelliottia are ubiquitous, facultatively anaerobic, motile, non-spore-forming, rod-shaped Gram-negative bacteria belonging to the Enterobacteriaceae family and include pathogens of public health importance. Here, we report the first draft genome sequences of a rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 in Africa. METHODS The bacteria were isolated from environmental wastewater samples. Bacteria were cultured on nutrient agar, and the pure cultures were subjected to whole-genome sequencing. Genomic DNA was sequenced using an Illumina MiSeq platform. Generated reads were trimmed and subjected to de novo assembly. The assembled contigs were analysed for virulence genes, antimicrobial resistance genes, and extra-chromosomal plasmids, and multilocus sequence typing was performed. To compare the sequenced strains with other, previously sequenced E. kobei and L. nimipressuralis strains, available raw read sequences were downloaded, and all sequence files were treated identically to generate core genome bootstrapped maximum likelihood phylogenetic trees. RESULTS Whole-genome sequencing analyses identified strain MEZLN61 as L. nimipressuralis and strains MEZEK193 and MEZEK194 as E. kobei. MEZEK193 and MEZEK194 carried genes encoding resistance to fosfomycin (fosA), beta-lactam antibiotics (blaACT-9), and colistin (mcr-9). Additionally, MEZEK193 harboured nine different virulence genes, while MEZEK194 harboured eleven different virulence genes. The phenotypic analysis showed that L. nimipressuralis strain MEZLN61 was susceptible to colistin (2 μg/mL), while E. kobei MEZEK193 (64 μg/mL) and MEZEK194 (32 μg/mL) were resistant to colistin. CONCLUSION The genome sequences of strains L. nimipressuralis MEZLN6, E. kobei MEZEK193, and E. kobei MEZEK194 will serve as a reference point for molecular epidemiological studies of L. nimipressuralis and E. kobei in Africa. In addition, this study provides an in-depth analysis of the genomic structure and offers important information that helps clarify the pathogenesis and antimicrobial resistance of L. nimipressuralis and E. kobei. The detection of mcr-9, which is associated with very low-level colistin resistance in Enterobacter species, is alarming and may indicate the undetected dissemination of mcr genes in bacteria of the order Enterobacterales. Continuous monitoring and surveillance of the prevalence of mcr genes and their associated phenotypic changes in clinically important pathogens and environmentally associated bacteria is necessary to control and prevent the spread of colistin resistance.
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Affiliation(s)
- Mohamed E El Zowalaty
- Veterinary Medicine and Food Security Research Group, Medical Laboratory Sciences Program, Faculty of Health Sciences, Abu Dhabi Women's Campus, Higher Colleges of Technology, Abu Dhabi 41012, UAE.
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany; German Center for Infection Research, Site Giessen-Marburg-Langen, Giessen, Germany; Hessian University Competence Center for Hospital Hygiene, Justus Liebig University Giessen, Giessen, Germany
| | | | - Yosra A Helmy
- Department of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky, Lexington, Kentucky, USA.
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9
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Doijad SP, Gisch N, Frantz R, Kumbhar BV, Falgenhauer J, Imirzalioglu C, Falgenhauer L, Mischnik A, Rupp J, Behnke M, Buhl M, Eisenbeis S, Gastmeier P, Gölz H, Häcker GA, Käding N, Kern WV, Kola A, Kramme E, Peter S, Rohde AM, Seifert H, Tacconelli E, Vehreschild MJGT, Walker SV, Zweigner J, Schwudke D, Chakraborty T, Thoma N, Weber A, Vavra M, Schuster S, Peyerl-Hoffmann G, Hamprecht A, Proske S, Stelzer Y, Wille J, Lenke D, Bader B, Dinkelacker A, Hölzl F, Kunstle L, Chakraborty T. Resolving colistin resistance and heteroresistance in Enterobacter species. Nat Commun 2023; 14:140. [PMID: 36627272 PMCID: PMC9832134 DOI: 10.1038/s41467-022-35717-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023] Open
Abstract
Species within the Enterobacter cloacae complex (ECC) include globally important nosocomial pathogens. A three-year study of ECC in Germany identified Enterobacter xiangfangensis as the most common species (65.5%) detected, a result replicated by examining a global pool of 3246 isolates. Antibiotic resistance profiling revealed widespread resistance and heteroresistance to the antibiotic colistin and detected the mobile colistin resistance (mcr)-9 gene in 19.2% of all isolates. We show that resistance and heteroresistance properties depend on the chromosomal arnBCADTEF gene cassette whose products catalyze transfer of L-Ara4N to lipid A. Using comparative genomics, mutational analysis, and quantitative lipid A profiling we demonstrate that intrinsic lipid A modification levels are genospecies-dependent and governed by allelic variations in phoPQ and mgrB, that encode a two-component sensor-activator system and specific inhibitor peptide. By generating phoPQ chimeras and combining them with mgrB alleles, we show that interactions at the pH-sensing interface of the sensory histidine kinase phoQ dictate arnBCADTEF expression levels. To minimize therapeutic failures, we developed an assay that accurately detects colistin resistance levels for any ECC isolate.
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Affiliation(s)
- Swapnil Prakash Doijad
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Justus Liebig University, Gießen, Germany
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Renate Frantz
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Justus Liebig University, Gießen, Germany
| | - Bajarang Vasant Kumbhar
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS (Deemed-to-be) University, Vile Parle, Mumbai, India
| | - Jane Falgenhauer
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Justus Liebig University, Gießen, Germany
| | - Can Imirzalioglu
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Justus Liebig University, Gießen, Germany
| | - Linda Falgenhauer
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Justus Liebig University, Gießen, Germany.,Institute of Hygiene and Environmental Medicine, Justus Liebig University, Gießen, Germany
| | - Alexander Mischnik
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Jan Rupp
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Michael Behnke
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität of Berlin and Berlin Institute of Health, Institute of Hygiene and Environmental Medicine, Berlin, Germany
| | - Michael Buhl
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology and Hygiene, Tübingen University, Tübingen, Germany.,Division of Infectious Diseases, Department of Internal Medicine I, Tübingen University, Tübingen, Germany.,Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Paracelsus Medical University, Klinikum Nürnberg, Nürnberg, Germany
| | - Simone Eisenbeis
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Division of Infectious Diseases, Department of Internal Medicine I, Tübingen University, Tübingen, Germany
| | - Petra Gastmeier
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität of Berlin and Berlin Institute of Health, Institute of Hygiene and Environmental Medicine, Berlin, Germany
| | - Hanna Gölz
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology and Hygiene, Albert-Ludwigs-University, Freiburg, Germany
| | - Georg Alexander Häcker
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology and Hygiene, Albert-Ludwigs-University, Freiburg, Germany
| | - Nadja Käding
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Winfried V Kern
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Division of Infectious Diseases, Department of Medicine II, Faculty of Medicine and University Hospital and Medical Center, Albert-Ludwigs-University, Freiburg, Germany
| | - Axel Kola
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität of Berlin and Berlin Institute of Health, Institute of Hygiene and Environmental Medicine, Berlin, Germany
| | - Evelyn Kramme
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität of Berlin and Berlin Institute of Health, Institute of Hygiene and Environmental Medicine, Berlin, Germany
| | - Silke Peter
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology and Hygiene, Tübingen University, Tübingen, Germany
| | - Anna M Rohde
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität of Berlin and Berlin Institute of Health, Institute of Hygiene and Environmental Medicine, Berlin, Germany
| | - Harald Seifert
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology, Immunology, and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Evelina Tacconelli
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Division of Infectious Diseases, Department of Internal Medicine I, Tübingen University, Tübingen, Germany
| | - Maria J G T Vehreschild
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - Sarah V Walker
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology, Immunology, and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Janine Zweigner
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology, Immunology, and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Dominik Schwudke
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany.,Airway Research Center North, Member of the German Center for Lung Research (DZL), Site: Research Center Borstel, Borstel, Germany
| | | | - Trinad Chakraborty
- German Center for Infection Research (DZIF), Braunschweig, Germany. .,Institute of Medical Microbiology, Justus Liebig University, Gießen, Germany.
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Rohde AM, Walker S, Behnke M, Eisenbeis S, Falgenhauer L, Falgenhauer JC, Häcker G, Hölzl F, Imirzalioglu C, Käding N, Kern WV, Kola A, Kramme E, Mischnik A, Peter S, Rieg S, Rupp J, Schneider C, Schwab F, Seifert H, Tacconelli E, Tobys D, Trauth J, Weber A, Xanthopoulou K, Zweigner J, Higgins PG, Gastmeier P. Vancomycin-resistant Enterococcus faecium: admission prevalence, sequence types and risk factors-a cross-sectional study in seven German university hospitals from 2014 to 2018. Clin Microbiol Infect 2022; 29:515-522. [PMID: 36481293 DOI: 10.1016/j.cmi.2022.11.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/11/2022] [Accepted: 11/27/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Assessment of vancomycin-resistant Enterococcus faecium (VREfm) prevalence upon hospital admission and analysis of risk factors for colonization. METHODS From 2014 to 2018, patients were recruited within 72 hours of admission to seven participating German university hospitals, screened for VREfm and questioned for potential risk factors (prior multidrug-resistant organism detection, current/prior antibiotic consumption, prior hospital, rehabilitation or long-term care facility stay, international travel, animal contact and proton pump inhibitor [PPI]/antacid therapy). Genotype analysis was done using cgMLST typing. Multivariable analysis was performed. RESULTS In 5 years, 265 of 17,349 included patients were colonized with VREfm (a prevalence of 1.5%). Risk factors for VREfm colonization were age (adjusted OR [aOR], 1.02; 95% CI, 1.01-1.03), previous (aOR, 2.71; 95% CI, 1.87-3.92) or current (aOR, 2.91; 95% CI, 2.60-3.24) antibiotic treatment, prior multidrug-resistant organism detection (aOR, 2.83; 95% CI, 2.21-3.63), prior stay in a long-term care facility (aOR, 2.19; 95% CI, 1.62-2.97), prior stay in a hospital (aOR, 2.91; 95% CI, 2.05-4.13) and prior consumption of PPI/antacids (aOR, 1.29; 95% CI, 1.18-1.41). Overall, the VREfm admission prevalence increased by 33% each year and 2% each year of life. 250 of 265 isolates were genotyped and 141 (53.2%) of the VREfm were the emerging ST117. Multivariable analysis showed that ST117 and non-ST117 VREfm colonized patients differed with respect to admission year and prior multidrug-resistant organism detection. DISCUSSION Age, healthcare contacts and antibiotic and PPI/antacid consumption increase the individual risk of VREfm colonization. The VREfm admission prevalence increase in Germany is mainly driven by the emergence of ST117.
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Affiliation(s)
- Anna M Rohde
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Institute for Hygiene and Environmental Medicine, Charité-University Medicine Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
| | - Sarah Walker
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Michael Behnke
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Institute for Hygiene and Environmental Medicine, Charité-University Medicine Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Simone Eisenbeis
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Division of Infectious Diseases, Department of Internal Medicine 1, University Hospital Tübingen, Tübingen, Germany
| | - Linda Falgenhauer
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Institute of Hygiene and Environmental Medicine, Justus Liebig University, Giessen, Germany
| | - Jane C Falgenhauer
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany
| | - Georg Häcker
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Institute for Medical Microbiology and Hygiene, University Medical Centre Freiburg, University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Florian Hölzl
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Division of Infectious Diseases, Department of Internal Medicine 1, University Hospital Tübingen, Tübingen, Germany; Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Can Imirzalioglu
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany
| | - Nadja Käding
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein/Campus, Lübeck, Germany
| | - Winfried V Kern
- Division of Infectious Diseases, Department of Medicine II, University Medical Centre and Faculty of Medicine, Albert-Ludwigs-University, Freiburg, Freiburg, Germany
| | - Axel Kola
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Institute for Hygiene and Environmental Medicine, Charité-University Medicine Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Evelyn Kramme
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein/Campus, Lübeck, Germany
| | - Alexander Mischnik
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein/Campus, Lübeck, Germany
| | - Silke Peter
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Siegbert Rieg
- Division of Infectious Diseases, Department of Medicine II, University Medical Centre and Faculty of Medicine, Albert-Ludwigs-University, Freiburg, Freiburg, Germany
| | - Jan Rupp
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein/Campus, Lübeck, Germany
| | - Christian Schneider
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Institute for Medical Microbiology and Hygiene, University Medical Centre Freiburg, University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Frank Schwab
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Institute for Hygiene and Environmental Medicine, Charité-University Medicine Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Harald Seifert
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Evelina Tacconelli
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Division of Infectious Diseases, Department of Internal Medicine 1, University Hospital Tübingen, Tübingen, Germany
| | - David Tobys
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Janina Trauth
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Department of Internal Medicine (Infectiology), Uniklinikum, Giessen, Germany
| | - Anna Weber
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Institute for Hygiene and Environmental Medicine, Charité-University Medicine Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Kyriaki Xanthopoulou
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Janine Zweigner
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Department of Hospital Hygiene and Infection Control, University Hospital Cologne, Cologne, Germany
| | - Paul G Higgins
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Petra Gastmeier
- German Centre for Infection Research (DZIF), Braunschweig, Germany; Institute for Hygiene and Environmental Medicine, Charité-University Medicine Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
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Eze EC, Falgenhauer L, El Zowalaty ME. Draft genome sequences of extensively drug resistant and pandrug resistant Acinetobacter baumannii strains isolated from hospital wastewater in South Africa. J Glob Antimicrob Resist 2022; 31:286-291. [PMID: 36058511 DOI: 10.1016/j.jgar.2022.08.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/06/2022] [Accepted: 08/29/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES Acinetobacter baumannii is a significant opportunistic pathogen causing nosocomial infections. Infections caused by A. baumannii are often difficult to treat because this bacterium is often multidrug-resistant and shows high environmental adaptability. Here, we report on the analysis of three A. baumannii strains isolated from hospital effluents in South Africa. METHODS Strains were isolated on Leeds Acinetobacter agar and were identified using VITEK®2 platform. Antibiotic susceptibility testing was performed using the Kirby-Bauer Disk diffusion method. Whole-genome sequencing was performed. The assembled contigs were annotated. Multilocus sequence type, antimicrobial resistance, and virulence genes were identified. RESULTS The strains showed two multilocus sequence types, ST231 (FA34) and ST1552 (PL448, FG116). Based on their antibiotic susceptibility profiles, PL448 and FG116 were classified as extensively drug-resistant and FA34 as pandrug-resistant. FA34 harbored mutations in LpxA, LpxC, and PmrB, conferring resistance to colistin, but not mcr genes. All three strains encoded virulence genes for immune evasion (capsule, lipopolysaccharide [LPS]), iron uptake, and biofilm formation. FA34 was related to human strains from South Africa; PL448 and FG116 were related to a strain isolated in the United States from a human wound. CONCLUSIONS The detection of extensively drug- and pandrug-resistant A. baumannii strains in hospital effluents is of particular concern. It indicates that wastewater might play a role in the spread of these bacteria. Our data provide insight into the molecular epidemiology, resistance, pathogenicity, and distribution of A. baumannii in South Africa.
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Affiliation(s)
- Emmanuel C Eze
- Department of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, German Center for Infection Research, Site Giessen-Marburg-Langen and Hessian University Competence Center for Hospital Hygiene, Justus Liebig University Giessen, Germany
| | - Mohamed E El Zowalaty
- Veterinary Medicine and Food Security Research Group, Medical Laboratory Sciences Program, Division of Health Sciences, Abu Dhabi Women's Campus, Higher Colleges of Technology, Abu Dhabi, UAE; Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
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12
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Dahdouh E, Allander L, Falgenhauer L, Iorga BI, Lorenzetti S, Marcos-Alcalde Í, Martin NI, Martínez-Martínez L, Mingorance J, Naas T, Rubin JE, Spyrakis F, Tängdén T, Gómez-Puertas P. Computational Modeling and Design of New Inhibitors of Carbapenemases: A Discussion from the EPIC Alliance Network. Int J Mol Sci 2022; 23:ijms23179746. [PMID: 36077146 PMCID: PMC9456441 DOI: 10.3390/ijms23179746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/23/2022] Open
Abstract
The EPIC consortium brings together experts from a wide range of fields that include clinical, molecular and basic microbiology, infectious diseases, computational biology and chemistry, drug discovery and design, bioinformatics, biochemistry, biophysics, pharmacology, toxicology, veterinary sciences, environmental sciences, and epidemiology. The main question to be answered by the EPIC alliance is the following: “What is the best approach for data mining on carbapenemase inhibitors and how to translate this data into experiments?” From this forum, we propose that the scientific community think up new strategies to be followed for the discovery of new carbapenemase inhibitors, so that this process is efficient and capable of providing results in the shortest possible time and within acceptable time and economic costs.
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Affiliation(s)
- Elias Dahdouh
- Clinical Microbiology and Parasitology Department, Instituto de Investigación Sanitaria del Hospital, Universitario La Paz (IdiPAZ), 28046 Madrid, Spain
- Correspondence: (E.D.); (P.G.-P.)
| | - Lisa Allander
- Department of Medical Sciences, Uppsala University, 752 36 Uppsala, Sweden
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Bogdan I. Iorga
- Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Stefano Lorenzetti
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità (ISS), 00161 Rome, Italy
| | - Íñigo Marcos-Alcalde
- Molecular Modeling Group, Centro de Biología Molecular Severo Ochoa (CBMSO, CSIC-UAM), 28049 Madrid, Spain
| | - Nathaniel I. Martin
- Biological Chemistry Group, Institute of Biology Leiden (IBL), Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Luis Martínez-Martínez
- Unit of Microbiology, University Hospital Reina Sofía, 14004 Córdoba, Spain
- Department of Agricultural Chemistry, Edaphology and Microbiology, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Córdoba, Spain
| | - Jesús Mingorance
- Clinical Microbiology and Parasitology Department, Instituto de Investigación Sanitaria del Hospital, Universitario La Paz (IdiPAZ), 28046 Madrid, Spain
| | - Thierry Naas
- Department of Microbiology, Hôpital de Bicêtre, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Joseph E. Rubin
- Department of Veterinary Microbiology, University of Saskatchewan at Saskatoon, Saskatoon, SK S7N 5A2, Canada
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, 10125 Torino, Italy
| | - Thomas Tängdén
- Department of Medical Sciences, Uppsala University, 752 36 Uppsala, Sweden
| | - Paulino Gómez-Puertas
- Molecular Modeling Group, Centro de Biología Molecular Severo Ochoa (CBMSO, CSIC-UAM), 28049 Madrid, Spain
- Correspondence: (E.D.); (P.G.-P.)
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Perestrelo S, Correia Carreira G, Valentin L, Fischer J, Pfeifer Y, Werner G, Schmiedel J, Falgenhauer L, Imirzalioglu C, Chakraborty T, Käsbohrer A. Comparison of approaches for source attribution of ESBL-producing Escherichia coli in Germany. PLoS One 2022; 17:e0271317. [PMID: 35839265 PMCID: PMC9286285 DOI: 10.1371/journal.pone.0271317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 06/28/2022] [Indexed: 11/19/2022] Open
Abstract
Extended-spectrum beta-lactamase (ESBL)-producing Escherichia (E.) coli have been widely described as the cause of treatment failures in humans around the world. The origin of human infections with these microorganisms is discussed controversially and in most cases hard to identify. Since they pose a relevant risk to human health, it becomes crucial to understand their sources and the transmission pathways. In this study, we analyzed data from different studies in Germany and grouped ESBL-producing E. coli from different sources and human cases into subtypes based on their phenotypic and genotypic characteristics (ESBL-genotype, E. coli phylogenetic group and phenotypic antimicrobial resistance pattern). Then, a source attribution model was developed in order to attribute the human cases to the considered sources. The sources were from different animal species (cattle, pig, chicken, dog and horse) and also from patients with nosocomial infections. The human isolates were gathered from community cases which showed to be colonized with ESBL-producing E. coli. We used the attribution model first with only the animal sources (Approach A) and then additionally with the nosocomial infections (Approach B). We observed that all sources contributed to the human cases, nevertheless, isolates from nosocomial infections were more related to those from human cases than any of the other sources. We identified subtypes that were only detected in the considered animal species and others that were observed only in the human population. Some subtypes from the human cases could not be allocated to any of the sources from this study and were attributed to an unknown source. Our study emphasizes the importance of human-to-human transmission of ESBL-producing E. coli and the different role that pets, livestock and healthcare facilities may play in the transmission of these resistant bacteria. The developed source attribution model can be further used to monitor future trends. A One Health approach is necessary to develop source attribution models further to integrate also wildlife, environmental as well as food sources in addition to human and animal data.
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Affiliation(s)
- Sara Perestrelo
- Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
- * E-mail:
| | | | - Lars Valentin
- Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jennie Fischer
- Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Yvonne Pfeifer
- Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Guido Werner
- Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Judith Schmiedel
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Campus Giessen, Giessen, Germany
- Hessisches universitäres Kompetenzzentrum Krankenhaushygiene (HuKKH), Giessen, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Campus Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Campus Giessen, Giessen, Germany
| | - Annemarie Käsbohrer
- Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
- Veterinary Public Health and Epidemiology, University of Veterinary Medicine, Vienna, Austria
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Sváb D, Falgenhauer L, Mag T, Chakraborty T, Tóth I. Genomic Diversity, Virulence Gene, and Prophage Arrays of Bovine and Human Shiga Toxigenic and Enteropathogenic Escherichia coli Strains Isolated in Hungary. Front Microbiol 2022; 13:896296. [PMID: 35865933 PMCID: PMC9294531 DOI: 10.3389/fmicb.2022.896296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/13/2022] [Indexed: 11/23/2022] Open
Abstract
Escherichia coli belonging to the enterohemorrhagic (EHEC), Shiga toxin-producing (STEC) and atypical enteropathogenic (aEPEC) pathotypes are significant foodborne zoonotic pathogens posing serious health risks, with healthy cattle as their main reservoir. A representative sampling of Hungarian cattle farms during 2017–2018 yielded a prevalence of 6.5 and 5.8% for STEC and aEPEC out of 309 samples. The draft genomes of twelve STEC (of them 9 EHEC) and four aEPEC of bovine origin were determined. For comparative purposes, we also included 3 EHEC and 2 aEPEC strains of human origin, as well four commensal isolates and one extraintestinal pathogenic E. coli (ExPEC) obtained from animals in a final set of 26 strains for a WGS-based analysis. Apart from key virulence genes, these isolates harbored several additional virulence genes with arrays characteristic for the site of isolation. The most frequent insertion site of Shiga toxin (stx) encoding prophages was yehV for the Stx1 prophage and wrbA and sbcB for Stx2. For O157:H7 strains, the locus of enterocyte effacement pathogenicity island was present at the selC site, with integration at pheV for other serotypes, and pheU in the case of O26:H11 strains. Several LEE-negative STEC and aEPEC as well as commensal isolates carried additional prophages, with an average of ten prophage regions per isolate. Comparative phylogenomic analysis showed no clear separation between bovine and human lineages among the isolates characterized in the current study. Similarities in virulence gene arrays and close phylogenetic relations of bovine and human isolates underline the zoonotic potential of bovine aEPEC and STEC and emphasize the need for frequent monitoring of these pathogens in livestock.
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Affiliation(s)
- Domonkos Sváb
- Veterinary Medical Research Institute, Budapest, Hungary
- *Correspondence: Domonkos Sváb,
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine and German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany
| | - Tünde Mag
- National Public Health Center, Budapest, Hungary
| | - Trinad Chakraborty
- Institute of Medical Microbiology, German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany
| | - István Tóth
- Veterinary Medical Research Institute, Budapest, Hungary
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Eze EC, El Zowalaty ME, Falgenhauer L, Pillay M. Genome Sequence of a carbapenemase-encoding Acinetobacter baumannii isolate of the sequence type 231 isolated from hospital wastewater in South Africa. J Glob Antimicrob Resist 2022; 29:150-154. [DOI: 10.1016/j.jgar.2022.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/22/2022] [Accepted: 02/27/2022] [Indexed: 11/24/2022] Open
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Yao Y, Imirzalioglu C, Falgenhauer L, Chakraborty T. New Delhi Metallo-β-Lactamase-Producing Enterobacterales Bacteria. Emerg Infect Dis 2022; 28:265. [PMID: 34932454 PMCID: PMC8714229 DOI: 10.3201/eid2801.212106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Ren Y, Chakraborty T, Doijad S, Falgenhauer L, Falgenhauer J, Goesmann A, Schwengers O, Heider D. Multi-label classification for multi-drug resistance prediction of Escherichia coli. Comput Struct Biotechnol J 2022; 20:1264-1270. [PMID: 35317240 PMCID: PMC8918850 DOI: 10.1016/j.csbj.2022.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/08/2022] [Accepted: 03/08/2022] [Indexed: 11/03/2022] Open
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Yao Y, Falgenhauer L, Falgenhauer J, Hauri AM, Heinmüller P, Domann E, Chakraborty T, Imirzalioglu C. Carbapenem-Resistant Citrobacter spp. as an Emerging Concern in the Hospital-Setting: Results From a Genome-Based Regional Surveillance Study. Front Cell Infect Microbiol 2021; 11:744431. [PMID: 34858870 PMCID: PMC8632029 DOI: 10.3389/fcimb.2021.744431] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
The rise of Carbapenem-resistant Enterobacterales (CRE) represents an increasing threat to patient safety and healthcare systems worldwide. Citrobacter spp., long considered not to be a classical nosocomial pathogen, in contrast to Klebsiella pneumoniae and Escherichia coli, is fast gaining importance as a clinical multidrug-resistant pathogen. We analyzed the genomes of 512 isolates of 21 CRE species obtained from 61 hospitals within a three-year-period and found that Citrobacter spp. (C. freundii, C. portucalensis, C. europaeus, C. koseri and C. braakii) were increasingly detected (n=56) within the study period. The carbapenemase-groups detected in Citrobacter spp. were KPC, OXA-48/-like and MBL (VIM, NDM) accounting for 42%, 31% and 27% respectively, which is comparable to those of K. pneumoniae in the same study. They accounted for 10%, 17% and 14% of all carbapenemase-producing CRE detected in 2017, 2018 and 2019, respectively. The carbapenemase genes were almost exclusively located on plasmids. The high genomic diversity of C. freundii is represented by 22 ST-types. KPC-2 was the predominantly detected carbapenemase (n=19) and was located in 95% of cases on a highly-conserved multiple-drug-resistance-gene-carrying pMLST15 IncN plasmid. KPC-3 was rarely detected and was confined to a clonal outbreak of C. freundii ST18. OXA-48 carbapenemases were located on plasmids of the IncL/M (pOXA-48) type. About 50% of VIM-1 was located on different IncN plasmids (pMLST7, pMLST5). These results underline the increasing importance of the Citrobacter species as emerging carriers of carbapenemases and therefore as potential disseminators of Carbapenem- and multidrug-resistance in the hospital setting.
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Affiliation(s)
- Yancheng Yao
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Giessen, Germany
| | - Linda Falgenhauer
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Giessen, Germany.,Institute for Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Jane Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Giessen, Germany
| | - Anja M Hauri
- Department of Epimeiology, Hessisches Landesprüfungs- und Untersuchungsamt im Gesundheitswesen (HLPUG), Dillenburg, Germany.,Department of Epimeiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Petra Heinmüller
- Department of Epimeiology, Hessisches Landesprüfungs- und Untersuchungsamt im Gesundheitswesen (HLPUG), Dillenburg, Germany
| | - Eugen Domann
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Giessen, Germany.,Institute for Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Giessen, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus-Liebig University Giessen, Giessen, Germany
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Ren Y, Chakraborty T, Doijad S, Falgenhauer L, Falgenhauer J, Goesmann A, Hauschild AC, Schwengers O, Heider D. Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning. Bioinformatics 2021; 38:325-334. [PMID: 34613360 PMCID: PMC8722762 DOI: 10.1093/bioinformatics/btab681] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/27/2021] [Accepted: 09/24/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Antimicrobial resistance (AMR) is one of the biggest global problems threatening human and animal health. Rapid and accurate AMR diagnostic methods are thus very urgently needed. However, traditional antimicrobial susceptibility testing (AST) is time-consuming, low throughput and viable only for cultivable bacteria. Machine learning methods may pave the way for automated AMR prediction based on genomic data of the bacteria. However, comparing different machine learning methods for the prediction of AMR based on different encodings and whole-genome sequencing data without previously known knowledge remains to be done. RESULTS In this study, we evaluated logistic regression (LR), support vector machine (SVM), random forest (RF) and convolutional neural network (CNN) for the prediction of AMR for the antibiotics ciprofloxacin, cefotaxime, ceftazidime and gentamicin. We could demonstrate that these models can effectively predict AMR with label encoding, one-hot encoding and frequency matrix chaos game representation (FCGR encoding) on whole-genome sequencing data. We trained these models on a large AMR dataset and evaluated them on an independent public dataset. Generally, RFs and CNNs perform better than LR and SVM with AUCs up to 0.96. Furthermore, we were able to identify mutations that are associated with AMR for each antibiotic. AVAILABILITY AND IMPLEMENTATION Source code in data preparation and model training are provided at GitHub website (https://github.com/YunxiaoRen/ML-iAMR). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yunxiao Ren
- Department of Data Science in Biomedicine, Faculty of Mathematics and Computer Science, Philipps-University of Marburg, Marburg 35032, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen 35392, Germany,German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen 35392, Germany
| | - Swapnil Doijad
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen 35392, Germany,German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen 35392, Germany
| | - Linda Falgenhauer
- German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen 35392, Germany,Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen 35392, Germany,Hessisches universitäres Kompetenzzentrum Krankenhaushygiene, Giessen 35392, Germany
| | - Jane Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen 35392, Germany,German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen 35392, Germany
| | - Alexander Goesmann
- German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen 35392, Germany,Department of Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen 35392, Germany
| | - Anne-Christin Hauschild
- Department of Data Science in Biomedicine, Faculty of Mathematics and Computer Science, Philipps-University of Marburg, Marburg 35032, Germany
| | - Oliver Schwengers
- German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen 35392, Germany,Department of Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen 35392, Germany
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20
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Xanthopoulou K, Peter S, Tobys D, Behnke M, Dinkelacker AG, Eisenbeis S, Falgenhauer J, Falgenhauer L, Fritzenwanker M, Gölz H, Häcker G, Higgins PG, Imirzalioglu C, Käding N, Kern WV, Kramme E, Kola A, Mischnik A, Rieg S, Rohde AM, Rupp J, Tacconelli E, Vehreschild MJGT, Walker SV, Gastmeier P, Seifert H. Vancomycin-resistant Enterococcus faecium colonizing patients on hospital admission in Germany: prevalence and molecular epidemiology. J Antimicrob Chemother 2021; 75:2743-2751. [PMID: 32699884 DOI: 10.1093/jac/dkaa271] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/12/2020] [Accepted: 05/20/2020] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES To analyse the rectal carriage rate and the molecular epidemiology of vancomycin-resistant Enterococcus faecium (VREfm) recovered from patients upon hospital admission. METHODS Adult patients were screened at six German university hospitals from five different federal states upon hospital admission for rectal colonization with VREfm between 2014 and 2018. Molecular characterization of VREfm was performed by WGS followed by MLST and core-genome MLST analysis. RESULTS Of 16350 patients recruited, 263 were colonized with VREfm, with increasing prevalence rates during the 5 year study period (from 0.8% to 2.6%). In total, 78.5% of the VREfm were vanB positive and 20.2% vanA positive, while 1.2% harboured both vanA and vanB. The predominant ST was ST117 (56.7%) followed by ST80 (15%), ST203 (10.9%), ST78 (5.7%) and ST17 (3.2%). ST117/vanB VREfm isolates formed a large cluster of 96 closely related isolates extending across all six study centres and four smaller clusters comprising 13, 5, 4 and 3 isolates each. In contrast, among the other STs inter-regional clonal relatedness was rarely observed. CONCLUSIONS To our knowledge, this is the largest admission prevalence and molecular epidemiology study of VREfm. These data provide insight into the epidemiology of VREfm at six German university hospitals and demonstrate the remarkable inter-regional clonal expansion of the ST117/vanB VREfm clone.
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Affiliation(s)
- Kyriaki Xanthopoulou
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Silke Peter
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - David Tobys
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Michael Behnke
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Hygiene and Environmental Medicine, National Reference Centre for the Surveillance of Nosocomial Infections, Charité-University Hospital, Berlin, Germany
| | - Ariane G Dinkelacker
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Simone Eisenbeis
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Division of Infectious Disease, Department of Internal Medicine I, Tübingen University Hospital, Tübingen, Germany
| | - Jane Falgenhauer
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Linda Falgenhauer
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Moritz Fritzenwanker
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Hannah Gölz
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology and Hygiene, University Medical Centre Freiburg, Freiburg, Germany
| | - Georg Häcker
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology and Hygiene, University Medical Centre Freiburg, Freiburg, Germany
| | - Paul G Higgins
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Can Imirzalioglu
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Nadja Käding
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Winfried V Kern
- Division of Infectious Diseases, Department of Medicine II, University of Freiburg Medical Centre and Faculty of Medicine, Freiburg, Germany
| | - Evelyn Kramme
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Axel Kola
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Hygiene and Environmental Medicine, National Reference Centre for the Surveillance of Nosocomial Infections, Charité-University Hospital, Berlin, Germany
| | - Alexander Mischnik
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Siegbert Rieg
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Division of Infectious Diseases, Department of Medicine II, University of Freiburg Medical Centre and Faculty of Medicine, Freiburg, Germany
| | - Anna M Rohde
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Hygiene and Environmental Medicine, National Reference Centre for the Surveillance of Nosocomial Infections, Charité-University Hospital, Berlin, Germany
| | - Jan Rupp
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Evelina Tacconelli
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Division of Infectious Disease, Department of Internal Medicine I, Tübingen University Hospital, Tübingen, Germany
| | - Maria J G T Vehreschild
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,University of Cologne, Department I of Internal Medicine, Cologne, Germany.,Department of Internal Medicine, Infectious Diseases, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sarah V Walker
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Petra Gastmeier
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Hygiene and Environmental Medicine, National Reference Centre for the Surveillance of Nosocomial Infections, Charité-University Hospital, Berlin, Germany
| | - Harald Seifert
- German Centre for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
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Falgenhauer L, Zur Nieden A, Harpel S, Falgenhauer J, Domann E. Clonal CTX-M-15-Producing Escherichia coli ST-949 Are Present in German Surface Water. Front Microbiol 2021; 12:617349. [PMID: 33912141 PMCID: PMC8072356 DOI: 10.3389/fmicb.2021.617349] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/24/2021] [Indexed: 11/13/2022] Open
Abstract
Extended-spectrum beta-lactamase (ESBL)-producing bacterial isolates are emerging within the last years. To understand this emergence, a thorough genome-based analysis of ESBL isolates from different sources (One Health approach) is needed. Among these, analysis of surface water is underrepresented. Therefore, we performed a genome-based analysis of ESBL-producing Escherichia coli isolates from surface water samples. Water samples were collected from eleven different surface water sites (lakes, river). ESBL-producing E. coli were recovered from these samples using filters and chromogenic media. Whole-genome sequencing of ESBL-producing E. coli was performed followed by determination of the multilocus sequence type (ST), ESBL-type, and virulence genes. Phylogenetic analysis was done using single nucleotide analysis. From all water samples taken, nineteen ESBL-producing E. coli were recovered. All of them harbored an ESBL gene. Nine different multilocus STs were determined, among which ST-949 was the ST detected most frequently. Phylogenetic analysis of ST-949 isolates revealed that all those isolates were closely related. In addition, they harbored an identical chromosomal insertion of bla CTX-M-15 , indicating a clonal relationship among these isolates. Genetic comparison with isolates from all over the world revealed that these isolates were closely related to human clinical isolates derived from New Zealand and Sweden. An ESBL-producing E. coli ST-949 clone was detected in German surface waters. Its close relationship to human clinical isolates suggests its ability to colonize or even infect humans. Our findings reveal that water sources indeed may play a hitherto underreported role in spread of ESBL-producing isolates.
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Affiliation(s)
- Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany
| | - Anja Zur Nieden
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Susanne Harpel
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Jane Falgenhauer
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Eugen Domann
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany.,German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
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Falgenhauer L, Preuser I, Imirzalioglu C, Falgenhauer J, Fritzenwanker M, Mack D, Best C, Heudorf U, Chakraborty T. Changing epidemiology of vancomycin-resistant Enterococcus faecium: Results of a genome-based study at a regional neurological acute hospital with intensive care and early rehabilitation treatment. Infect Prev Pract 2021; 3:100138. [PMID: 34368749 PMCID: PMC8335922 DOI: 10.1016/j.infpip.2021.100138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/22/2021] [Indexed: 12/04/2022] Open
Abstract
Background Vancomycin-resistant Enterococcus faecium (VREfm) are an emerging threat worldwide. In Germany, a VRE-belt with higher VREfm prevalences transversing its central east-west axis and including the state of Hesse was previously described. Recently, we detected a predominant VREfm clone in hospitals throughout the Rhine-Main metropolitan area of Hesse. Aim Here we expanded our study on VREfm to a regional neurological acute hospital outside of the metropolitan area with patient referrals from throughout Hesse and the neighboring federal state of Rhineland-Palatinate. Material/Methods VREfm isolates obtained between 2016-2018 from a regional neurological acute hospital with intensive care and early rehabilitation units were investigated (n=55). Patient data was collected and analyzed together with whole-genome sequencing data to investigate antibiotic resistance and virulence determinants of the VREfm. The population structure of VREfm was investigated using the Core genome-based multilocus sequence typing (cgMLST). Findings The average age of the patients was 67.1 years. For 96% of the patients, a previous hospital stay was reported. 64% of the patients were treated with antibiotics. All VREfm harbored the vanB vancomycin resistance gene. The multilocus sequence types (STs) detected changed abruptly from four different STs in 2016 to a predominant ST in 2017 and 2018 (ST117). Most of the ST117 isolates were members of the cgMLST type CT71. Conclusion The results indicate a sudden shift of the VREfm population structure from a semi-heterogeneous population to a pre-dominant clone within an interval of two years. Further investigations are warranted to understand the epidemiology and emergence of this clone.
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Affiliation(s)
- Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany.,German Center for Infection Research (DZIF), Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany
| | - Ingeborg Preuser
- Department of Neurology, Vitos-Weil-Lahn, Weilstrasse 10, Weilmünster, 35789, Germany
| | - Can Imirzalioglu
- German Center for Infection Research (DZIF), Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany
| | - Jane Falgenhauer
- German Center for Infection Research (DZIF), Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany
| | - Moritz Fritzenwanker
- German Center for Infection Research (DZIF), Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany
| | - Dietrich Mack
- Institut für Medizinische Diagnostik GmbH, Bioscientia Labor Ingelheim, Konrad-Adenauer-Straße 17, Ingelheim am Rhein, 55218, Germany
| | - Christoph Best
- Department of Neurology, Vitos-Weil-Lahn, Weilstrasse 10, Weilmünster, 35789, Germany
| | - Ursel Heudorf
- Network on MDRO Rhine-Main, Breite Gasse 28, Frankfurt/Main, 60313, Germany
| | - Trinad Chakraborty
- German Center for Infection Research (DZIF), Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany.,Institute of Medical Microbiology, Justus Liebig University Giessen, Schubertstrasse 81, Giessen, 35392, Germany
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Sváb D, Falgenhauer L, Horváth B, Maróti G, Falgenhauer J, Chakraborty T, Tóth I. Genome Analysis of a Historical Shigella dysenteriae Serotype 1 Strain Carrying a Conserved Stx Prophage Region. Front Microbiol 2021; 11:614793. [PMID: 33488558 PMCID: PMC7819885 DOI: 10.3389/fmicb.2020.614793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/09/2020] [Indexed: 11/13/2022] Open
Abstract
Shigella dysenteriae are significant agents of bacillary dysentery, accounting for a considerable number of illnesses with high morbidity worldwide. The Shiga toxin (Stx) encoded by a defective prophage is the key virulence factor of S. dysenteriae type 1 (SD1) strains. Here we present the full genome sequence of an SD1 strain HNCMB 20080 isolated in 1954, compare it to other sequenced SD1 genomes, and assess the diversity of Stx-prophages harbored by previously sequenced SD1 strains. The genome of HNCMB 20080 consists of a chromosome sized 4,393,622 bp containing 5,183 CDSs, as well as two small plasmids. Comparative genomic analysis revealed a high degree of uniformity among SD1 genomes, including the structure of Stx prophage regions, which we found to form two subgroups termed PT-I and PT-II. All PT-I strains are members of the sequence type (ST) 146 or ST260, while the only PT-II harboring strain, Sd1617 proved to be ST untypeable. In accordance with data from previous reports, the Stx1 prophage could not be induced from HNCMB 20080. Our cumulative data do not support the notion that stx-harboring phages in STEC are derived from historical SD1 isolates.
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Affiliation(s)
- Domonkos Sváb
- Institue for Veterinary Medical Research, Centre for Agricultural Research, Martonvásár, Hungary
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany.,German Centre for Infection Research, Site Giessen-Marburg-Langen, Giessen, Germany
| | | | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary.,Faculty of Water Sciences, University of Public Service, Baja, Hungary
| | - Jane Falgenhauer
- German Centre for Infection Research, Site Giessen-Marburg-Langen, Giessen, Germany.,Institute for Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany.,Institute for Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - István Tóth
- Institue for Veterinary Medical Research, Centre for Agricultural Research, Martonvásár, Hungary
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Falgenhauer L, Nordmann P, Imirzalioglu C, Yao Y, Falgenhauer J, Hauri AM, Heinmüller P, Chakraborty T. Cross-border emergence of clonal lineages of ST38 Escherichia coli producing the OXA-48-like carbapenemase OXA-244 in Germany and Switzerland. Int J Antimicrob Agents 2020; 56:106157. [DOI: 10.1016/j.ijantimicag.2020.106157] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/31/2020] [Accepted: 09/06/2020] [Indexed: 10/23/2022]
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Prieto A, Bernabeu M, Falgenhauer L, Chakraborty T, Hüttener M, Juárez A. Overexpression of the third H-NS paralogue H-NS2 compensates fitness loss in hns mutants of the enteroaggregative Escherichia coli strain 042. Sci Rep 2020; 10:18131. [PMID: 33093592 PMCID: PMC7582179 DOI: 10.1038/s41598-020-75204-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/07/2020] [Indexed: 11/10/2022] Open
Abstract
Members of the H-NS protein family play a role both in the chromosome architecture and in the regulation of gene expression in bacteria. The genomes of the enterobacteria encode an H-NS paralogue, the StpA protein. StpA displays specific regulatory properties and provides a molecular backup for H-NS. Some enterobacteria also encode third H-NS paralogues. This is the case of the enteroaggregative E. coli (EAEC) strain 042, which encodes the hns, stpA and hns2 genes. We provide in this paper novel information about the role of the H-NS2 protein in strain 042. A C > T transition in the hns2 promoter leading to increased H-NS2 expression is readily selected in hns mutants. Increased H-NS2 expression partially compensates for H-NS loss. H-NS2 levels are critical for the strain 042 fitness. Under some circumstances, high H-NS2 expression levels dictated by the mutant hns2 promoter can be deleterious. The selection of T > C revertants or of clones harboring insertional inactivations of the hns2 gene can then occur. Temperature also plays a relevant role in the H-NS2 regulatory activity. At 37 °C, H-NS2 targets a subset of the H-NS repressed genes contributing to their silencing. When temperature drops to 25 °C, the repressory ability of H-NS2 is significantly reduced. At low temperature, H-NS plays the main repressory role.
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Affiliation(s)
- A Prieto
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - M Bernabeu
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - L Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Schubertstrasse 81, 35392, Giessen, Germany.,German Center for Infection Research DZIF, Partner Site Giessen-Marburg-Langen, Campus, Giessen, Germany
| | - T Chakraborty
- German Center for Infection Research DZIF, Partner Site Giessen-Marburg-Langen, Campus, Giessen, Germany.,Institute of Medical Microbiology, Justus-Liebig University, Schubertstrasse 81, 35392, Giessen, Germany
| | - M Hüttener
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - A Juárez
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain. .,Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain.
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Schwengers O, Barth P, Falgenhauer L, Hain T, Chakraborty T, Goesmann A. Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores. Microb Genom 2020; 6:mgen000398. [PMID: 32579097 PMCID: PMC7660248 DOI: 10.1099/mgen.0.000398] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 06/02/2020] [Indexed: 12/22/2022] Open
Abstract
Plasmids are extrachromosomal genetic elements that replicate independently of the chromosome and play a vital role in the environmental adaptation of bacteria. Due to potential mobilization or conjugation capabilities, plasmids are important genetic vehicles for antimicrobial resistance genes and virulence factors with huge and increasing clinical implications. They are therefore subject to large genomic studies within the scientific community worldwide. As a result of rapidly improving next-generation sequencing methods, the quantity of sequenced bacterial genomes is constantly increasing, in turn raising the need for specialized tools to (i) extract plasmid sequences from draft assemblies, (ii) derive their origin and distribution, and (iii) further investigate their genetic repertoire. Recently, several bioinformatic methods and tools have emerged to tackle this issue; however, a combination of high sensitivity and specificity in plasmid sequence identification is rarely achieved in a taxon-independent manner. In addition, many software tools are not appropriate for large high-throughput analyses or cannot be included in existing software pipelines due to their technical design or software implementation. In this study, we investigated differences in the replicon distributions of protein-coding genes on a large scale as a new approach to distinguish plasmid-borne from chromosome-borne contigs. We defined and computed statistical discrimination thresholds for a new metric: the replicon distribution score (RDS), which achieved an accuracy of 96.6 %. The final performance was further improved by the combination of the RDS metric with heuristics exploiting several plasmid-specific higher-level contig characterizations. We implemented this workflow in a new high-throughput taxon-independent bioinformatics software tool called Platon for the recruitment and characterization of plasmid-borne contigs from short-read draft assemblies. Compared to PlasFlow, Platon achieved a higher accuracy (97.5 %) and more balanced predictions (F1=82.6 %) tested on a broad range of bacterial taxa and better or equal performance against the targeted tools PlasmidFinder and PlaScope on sequenced Escherichia coli isolates. Platon is available at: http://platon.computational.bio/.
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Affiliation(s)
- Oliver Schwengers
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Patrick Barth
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Giessen, Germany
- Present address: Institute of Hygiene and Environmental Health, Justus Liebig University, Giessen, Germany
| | - Torsten Hain
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Giessen, Germany
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Ayeni FA, Falgenhauer J, Schmiedel J, Schwengers O, Chakraborty T, Falgenhauer L. Detection of blaCTX-M-27-encoding Escherichia coli ST206 in Nigerian poultry stocks. J Antimicrob Chemother 2020; 75:3070-3072. [PMID: 32688376 DOI: 10.1093/jac/dkaa293] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Funmilola A Ayeni
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Jane Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany.,German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Judith Schmiedel
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany.,German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Oliver Schwengers
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany.,German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen, Germany.,Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany.,German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany.,German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen, Germany
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28
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Masseron A, Poirel L, Falgenhauer L, Imirzalioglu C, Kessler J, Chakraborty T, Nordmann P. Ongoing dissemination of OXA-244 carbapenemase-producing Escherichia coli in Switzerland and their detection. Diagn Microbiol Infect Dis 2020; 97:115059. [PMID: 32387849 DOI: 10.1016/j.diagmicrobio.2020.115059] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/01/2020] [Accepted: 04/05/2020] [Indexed: 01/01/2023]
Abstract
OXA-244 is a derivative of OXA-48 showing weaker carbapenemase activity, compromising the detection of corresponding producers in clinical laboratories. Since 2017, the Swiss National Reference Center for Emerging Antibiotic Resistance noticed an increased identification of OXA-244-producing Escherichia coli (n=15) within the country. Different methods (biochemical and immunoassay tests, screening culture media) were tested for the detection of OXA-244 producers. Whole genome sequencing was used to investigate the genetic relatedness between the isolates and the genetic structures at the origin of the acquisition of the blaOXA-244 gene. The mSuperCARBA® medium and the NG-Test CARBA5 assay were found to be suitable tools for detecting all OXA-244-producing isolates. Other selective media did not perform optimally. Among the fifteen strains, five sequence types were identified, with ST38 being predominant. The blaOXA-244 gene was located on the chromosome for all isolates. Overall, detection of OXA-244 producers is challenging and specific guidelines must be followed.
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Affiliation(s)
- Amandine Masseron
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Switzerland
| | - Laurent Poirel
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Switzerland; INSERM European Unit (IAME, France), University of Fribourg, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Switzerland.
| | - Linda Falgenhauer
- Institute of Medical Microbiology, and German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany; Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, and German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany
| | - Julie Kessler
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Switzerland
| | - Trinad Chakraborty
- Institute of Medical Microbiology, and German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany
| | - Patrice Nordmann
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Switzerland; INSERM European Unit (IAME, France), University of Fribourg, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Switzerland; Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany; Institute for Microbiology, University of Lausanne and University Hospital Centre, Lausanne, Switzerland
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Schwengers O, Hoek A, Fritzenwanker M, Falgenhauer L, Hain T, Chakraborty T, Goesmann A. ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates. PLoS Comput Biol 2020; 16:e1007134. [PMID: 32134915 PMCID: PMC7077848 DOI: 10.1371/journal.pcbi.1007134] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 03/17/2020] [Accepted: 12/03/2019] [Indexed: 11/18/2022] Open
Abstract
Whole genome sequencing of bacteria has become daily routine in many fields. Advances in DNA sequencing technologies and continuously dropping costs have resulted in a tremendous increase in the amounts of available sequence data. However, comprehensive in-depth analysis of the resulting data remains an arduous and time-consuming task. In order to keep pace with these promising but challenging developments and to transform raw data into valuable information, standardized analyses and scalable software tools are needed. Here, we introduce ASA3P, a fully automatic, locally executable and scalable assembly, annotation and analysis pipeline for bacterial genomes. The pipeline automatically executes necessary data processing steps, i.e. quality clipping and assembly of raw sequencing reads, scaffolding of contigs and annotation of the resulting genome sequences. Furthermore, ASA3P conducts comprehensive genome characterizations and analyses, e.g. taxonomic classification, detection of antibiotic resistance genes and identification of virulence factors. All results are presented via an HTML5 user interface providing aggregated information, interactive visualizations and access to intermediate results in standard bioinformatics file formats. We distribute ASA3P in two versions: a locally executable Docker container for small-to-medium-scale projects and an OpenStack based cloud computing version able to automatically create and manage self-scaling compute clusters. Thus, automatic and standardized analysis of hundreds of bacterial genomes becomes feasible within hours. The software and further information is available at: asap.computational.bio.
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Affiliation(s)
- Oliver Schwengers
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Giessen, Germany
- * E-mail:
| | - Andreas Hoek
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Moritz Fritzenwanker
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Torsten Hain
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Giessen, Germany
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Falgenhauer L, Schwengers O, Schmiedel J, Baars C, Lambrecht O, Heß S, Berendonk TU, Falgenhauer J, Chakraborty T, Imirzalioglu C. Multidrug-Resistant and Clinically Relevant Gram-Negative Bacteria Are Present in German Surface Waters. Front Microbiol 2019; 10:2779. [PMID: 31849911 PMCID: PMC6896662 DOI: 10.3389/fmicb.2019.02779] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/14/2019] [Indexed: 11/13/2022] Open
Abstract
Water is considered to play a role in the dissemination of antibiotic-resistant Gram-negative bacteria including those encoding Extended-spectrum beta-lactamases (ESBL) and carbapenemases. To investigate the role of water for their spread in more detail, we characterized ESBL/Carbapenemase-producing bacteria from surface water and sediment samples using phenotypic and genotypic approaches. ESBL/Carbapenemase-producing isolates were obtained from water/sediment samples. Species and antibiotic resistance were determined. A subset of these isolates (n = 33) was whole-genome-sequenced and analyzed for the presence of antibiotic resistance genes and virulence determinants. Their relatedness to isolates associated with human infections was investigated using multilocus sequence type and cgMLST-based analysis. Eighty-nine percent of the isolates comprised of clinically relevant species. Fifty-eight percent exhibited a multidrug-resistance phenotype. Two isolates harbored the mobile colistin resistance gene mcr-1. One carbapenemase-producing isolate identified as Enterobacter kobei harbored bla VIM- 1. Two Escherichia coli isolates had sequence types (ST) associated with human infections (ST131 and ST1485) and a Klebsiella pneumoniae isolate was classified as hypervirulent. A multidrug-resistant (MDR) Pseudomonas aeruginosa isolate encoding known virulence genes associated with severe lung infections in cystic fibrosis patients was also detected. The presence of MDR and clinically relevant isolates in recreational and surface water underlines the role of aquatic environments as both reservoirs and hot spots for MDR bacteria. Future assessment of water quality should include the examination of the multidrug resistance of clinically relevant bacterial species and thus provide an important link regarding the spread of MDR bacteria in a One Health context.
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Affiliation(s)
- Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany
| | - Oliver Schwengers
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany
- Bioinformatics & Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Judith Schmiedel
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany
| | | | | | - Stefanie Heß
- Institute of Hydrobiology, Technical University of Dresden, Dresden, Germany
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Thomas U. Berendonk
- Institute of Hydrobiology, Technical University of Dresden, Dresden, Germany
| | - Jane Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Justus Liebig University Giessen, Giessen, Germany
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31
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Falgenhauer L, Fritzenwanker M, Imirzalioglu C, Steul K, Scherer M, Heudorf U, Chakraborty T. Near-ubiquitous presence of a vancomycin-resistant Enterococcus faecium ST117/CT71/ vanB -clone in the Rhine-Main metropolitan area of Germany. Antimicrob Resist Infect Control 2019; 8:128. [PMID: 31384433 PMCID: PMC6664515 DOI: 10.1186/s13756-019-0573-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/09/2019] [Indexed: 02/02/2023] Open
Abstract
Whole-genome sequencing analysis of Vancomycin-resistant Enterococcus faecium isolates from the Frankfurt metropolitan region revealed that 78/94 isolates were MLST type ST117, cgMLST complex type CT71 with a common vanB chromosomal insertion site. This indicates circulation of a single VRE clone in a catchment area of 5,000-km2 with 3 million inhabitants.
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Affiliation(s)
- Linda Falgenhauer
- 1Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Schubertstrasse 81, 35392 Giessen, Germany
| | - Moritz Fritzenwanker
- 1Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Schubertstrasse 81, 35392 Giessen, Germany
| | - Can Imirzalioglu
- 1Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Schubertstrasse 81, 35392 Giessen, Germany
| | - Katrin Steul
- Rhine-Main- Network on MDRO (multidrug-resistant organisms), Breite Gasse 28, 60313 Frankfurt/Main, Germany
| | - Marlene Scherer
- Rhine-Main- Network on MDRO (multidrug-resistant organisms), Breite Gasse 28, 60313 Frankfurt/Main, Germany
| | | | - Ursel Heudorf
- Rhine-Main- Network on MDRO (multidrug-resistant organisms), Breite Gasse 28, 60313 Frankfurt/Main, Germany
| | - Trinad Chakraborty
- 1Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Schubertstrasse 81, 35392 Giessen, Germany
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32
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Falgenhauer L, Fritzenwanker M, Imirzalioglu C, Steul K, Scherer M, Heudorf U, Chakraborty T. Near-ubiquitous presence of a vancomycin-resistant Enterococcus faecium ST117/CT71/vanB –clone in the Rhine-Main metropolitan area of Germany. Antimicrob Resist Infect Control 2019. [DOI: 10.1186/s13756-019-0573-8 ecollection 2019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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33
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Fischer D, Schlößer RL, Kempf VAJ, Wichelhaus TA, Klingebiel T, Philippi S, Falgenhauer L, Imirzalioglu C, Dahl U, Brandt C, Reinheimer C. Overcrowding in a neonatal intermediate care unit: impact on the incidence of multidrug-resistant gram-negative organisms. BMC Infect Dis 2019; 19:357. [PMID: 31035966 PMCID: PMC6489334 DOI: 10.1186/s12879-019-3981-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 04/11/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Overcrowding, reduced nurse to patient ratio, limited distance between incubators and absence of microbiological surveillance have been shown to promote spread of multidrug-resistant gram-negative organisms (MDRGN) in patients with birthweight < 1500 g. Patients > 1500 g treated on an intermediate care unit are unrepresented in recent literature. We therefore intended to present data obtained from a short-term overcrowded neonatal intermediate care unit (NIMCU) at a level III (international categorization) perinatal center at University Hospital Frankfurt, Germany. METHODS During a 25 day overcrowding (OV) and 28 day post-overcrowding period (POST-OV) on NIMCU, epidemiological data obtained from continuously hold microbiological surveillance were investigated and compared to the last 12 months of ward-regular bed occupancy preceding OV (PRAE-OV). RESULTS During OV, the number of patients simultaneously treated at the NIMCU increased from 18 to 22, resulting in a reduced bed-to-bed space. Nurse: patient ratio was 4:22 during OV compared to 3:18 during PRAE-OV. Cumulative incidence of MDRGN was 4.7% in OV and 2.4% POST-OV compared to 4.8% to PRAE-OV, respectively, without any significant variations. During OV and POST-OV, septic episodes due to MDRGN were not observed. In one case, potential nosocomial transmission of Enterobacter cloacae resistant to Piperacillin and 3rd/4th generation cephalosporins was observed. CONCLUSIONS Prevention of nosocomial spread of MDRGN in an overcrowded NIMCU is based on staff's diligent training and adequate staffing. Concise microbiological surveillance should be guaranteed to escort through overcrowding periods. In our setting, impact of bed-to-bed distance on MDRGN transmission seemed to be less strong.
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Affiliation(s)
- Doris Fischer
- Department of Pediatrics, Division of Neonatology, University Hospital Frankfurt, St. Vincenz Hospital, Auf dem Schafsberg, 65549, Limburg, Germany.
| | - Rolf L Schlößer
- Department of Pediatrics, Division of Neonatology, University Hospital Frankfurt, St. Vincenz Hospital, Auf dem Schafsberg, 65549, Limburg, Germany
| | - Volkhard A J Kempf
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, 60590, Frankfurt at the Main, Germany
- University Center for Infectious Diseases (UCI), University Hospital Frankfurt, 60590, Frankfurt at the Main, Germany
| | - Thomas A Wichelhaus
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, 60590, Frankfurt at the Main, Germany
- University Center for Infectious Diseases (UCI), University Hospital Frankfurt, 60590, Frankfurt at the Main, Germany
| | - Thomas Klingebiel
- Department of Pediatrics, Division of Neonatology, University Hospital Frankfurt, St. Vincenz Hospital, Auf dem Schafsberg, 65549, Limburg, Germany
| | - Sabine Philippi
- Department of Pediatrics, Division of Neonatology, University Hospital Frankfurt, St. Vincenz Hospital, Auf dem Schafsberg, 65549, Limburg, Germany
| | - Linda Falgenhauer
- Justus Liebig University, Institute of Medical Microbiology, and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Can Imirzalioglu
- Justus Liebig University, Institute of Medical Microbiology, and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Udo Dahl
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, 60590, Frankfurt at the Main, Germany
- University Center for Infectious Diseases (UCI), University Hospital Frankfurt, 60590, Frankfurt at the Main, Germany
| | - Christian Brandt
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, 60590, Frankfurt at the Main, Germany
- University Center for Infectious Diseases (UCI), University Hospital Frankfurt, 60590, Frankfurt at the Main, Germany
| | - Claudia Reinheimer
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, 60590, Frankfurt at the Main, Germany
- University Center for Infectious Diseases (UCI), University Hospital Frankfurt, 60590, Frankfurt at the Main, Germany
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Falgenhauer L, Imirzalioglu C, Oppong K, Akenten CW, Hogan B, Krumkamp R, Poppert S, Levermann V, Schwengers O, Sarpong N, Owusu-Dabo E, May J, Eibach D. Detection and Characterization of ESBL-Producing Escherichia coli From Humans and Poultry in Ghana. Front Microbiol 2019; 9:3358. [PMID: 30697208 PMCID: PMC6340976 DOI: 10.3389/fmicb.2018.03358] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 12/31/2018] [Indexed: 11/13/2022] Open
Abstract
Introduction: The increasing incidence of infections caused by extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in sub-Saharan Africa is of serious concern. Studies from countries with a highly industrialized poultry industry suggest the poultry production-food-consumer chain as a potential transmission route. In Africa, integrated studies at this human-animal interface are still missing. Aim: To determine the molecular epidemiology of ESBL-producing E. coli from the intestinal tract of humans and poultry in rural Ghana. Methods: During a 6-month period, fecal samples from all children admitted to the Agogo Hospital (Ghana) and broilers at eight poultry farms located within the hospital catchment area were collected. After screening on selective ESBL agar, whole genome sequencing (WGS) was performed on all ESBL isolates. The genomes were analyzed using multilocus sequence typing (MLST), ESBL genotyping and genome-based phylogenetic analyses. Results: Of 140 broilers and 54 children, 41 (29%) and 33 (61%) harbored ESBL E. coli, respectively, with prevalences on farms ranging between 0 and 85%. No predominant sequence type (ST) was detected among humans. ST10 was most prevalent among broilers (n = 31, 69%). The ESBL gene bla CTX-M-15 was predominant among broilers (n = 43, 96%) and humans (n = 32, 97%). Whole-genome-based phylogenetic analysis revealed three very closely related broiler/human isolate clusters (10% of ESBL isolates) with chromosomal and plasmid-mediated ESBL genes. Conclusion: The findings demonstrate a high frequency of intestinal ESBL-producing E. coli in rural Ghana. Considering that animal and human samples are independent specimens from the same geographic location, the number of closely related ESBL isolates circulating across these two reservoirs is substantial. Hence, poultry farms or meat products might be an important source for ESBL-producing bacteria in rural Ghana leading to difficult-to-treat infections in humans.
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Affiliation(s)
- Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Kwabena Oppong
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | | | - Benedikt Hogan
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Ralf Krumkamp
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Sven Poppert
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Vinzent Levermann
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Oliver Schwengers
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Nimako Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Ellis Owusu-Dabo
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Jürgen May
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Daniel Eibach
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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Sváb D, Falgenhauer L, Rohde M, Chakraborty T, Tóth I. Complete genome sequence of C130_2, a novel myovirus infecting pathogenic Escherichia coli and Shigella strains. Arch Virol 2018; 164:321-324. [PMID: 30238162 DOI: 10.1007/s00705-018-4042-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 09/04/2018] [Indexed: 12/20/2022]
Abstract
The genome sequence of a novel virulent bacteriophage, named " C130_2", that is morphologically a member of the family Myoviridae is reported. The 41,775-base-pair double-stranded DNA genome of C130_2 contains 59 ORFs but exhibits overall low sequence similarity to bacteriophage genomes for which sequences are publicly available. Phylogenetic analysis indicated that C130_2 represents a new phage type. C130_2 could be propagated well on enterohemorrhagic Escherichia coli (EHEC) O157:H7 and other pathogenic E. coli strains, as well as on strains of various Shigella species.
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Affiliation(s)
- Domonkos Sváb
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, HZI, Braunschweig, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - István Tóth
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary.
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Sváb D, Falgenhauer L, Rohde M, Chakraborty T, Tóth I. Identification and characterization of new broad host-range rV5-like coliphages C203 and P206 directed against enterobacteria. Infect Genet Evol 2018; 64:254-261. [PMID: 30033383 DOI: 10.1016/j.meegid.2018.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/08/2018] [Accepted: 07/03/2018] [Indexed: 11/18/2022]
Abstract
We isolated and characterized two novel rV5-like lytic bacteriophages from independently collected food samples. Nucleotide sequence analysis revealed that these phages have linear double-stranded DNA genomes comprising 138,073 bp with 213 CDS and 5 tRNA genes. The two genomes contain completely identical nucleotide sequence, albeit there is a 10,718 bp-long shift in the sequence. The GC content of the phage genomes was 43.7% and they showed high general homology to rV5-like phages. The new phages were termed C203 and P206. The genome of both phages contains a unique ORF that encodes for a putative phage homing endonuclease. The phage produced clear plaques with a burst size of approx. 1000 viral particles and a latent period of 60 min. Morphological investigation indicated that the new phages are members of the family Myoviridae with an approximate head length of 85 nm, tail length of 75 nm, and a head width of 96 nm. C203 and P206 exhibit a broad and uniform host range, which included enterohemorrhagic Escherichia coli strains of serogroup O157, multi drug resistant (MDR) E. coli strains of various sero- and pathotypes, and both Shigella sonnei and S. dysenteriae strains. C203 and P206 both effectively reduced the number of living EHEC O157:H7 Sakai in experimentally inoculated minced meat. The same broad host range, the lack of any virulence related genes, the stability and its short latent period suggest that these newly found phages could be suitable candidates as a bio-control agents against food-borne pathogenic Enterobacteria.
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Affiliation(s)
- Domonkos Sváb
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary.
| | - Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen, German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, HZI, Braunschweig, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen, German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany
| | - István Tóth
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary.
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37
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Marando R, Seni J, Mirambo MM, Falgenhauer L, Moremi N, Mushi MF, Kayange N, Manyama F, Imirzalioglu C, Chakraborty T, Mshana SE. Predictors of the extended-spectrum-beta lactamases producing Enterobacteriaceae neonatal sepsis at a tertiary hospital, Tanzania. Int J Med Microbiol 2018; 308:803-811. [PMID: 29980372 PMCID: PMC6171784 DOI: 10.1016/j.ijmm.2018.06.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/25/2018] [Accepted: 06/28/2018] [Indexed: 11/27/2022] Open
Abstract
ESBL-PE sepsis was predicted by admission at ICU and ESBL-PE colonization. Neonates infected with ESBL-PE had significantly high mortality. ESBL-producing Klebsiella pneumoniae (ST45) carrying blaCTX-M-15 were predominant. Whole genome SNP analysis revealed clonal origin in 50% of ESBL-PE paired cases with similar sequence type.
The study was conducted to establish predictors of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) neonatal sepsis and mortality in a tertiary hospital, Tanzania. Between July and December 2016, blood culture was performed in neonates with clinical features of sepsis and neonates/mothers/guardians were screened for ESBL colonization. Selected isolates underwent whole genome sequencing to investigate relatedness. Logistic regression analysis was performed to determine predictors for ESBL-PE associated neonatal sepsis and mortality. Neonatal ESBL-PE sepsis was detected in 32(10.5%) of the 304 neonates investigated. Neonatal ESBL-PE sepsis was independently predicted by admission at the Intensive care Unit and positive mother and neonate ESBL-PE colonization. Deaths occurred in 55(18.1%) of neonates. Neonates infected with ESBL-PE, admitted at ICU, increased age and those transferred from other centres had significantly high mortality rates. Gram-negative bacteria formed the majority (76%) of the isolates, of which 77% were ESBL-PE. Virulent Klebsiella pneumoniae ST45 carrying blaCTX-M-15 were commonly isolated from neonates. Klebsiella pneumoniae (ST45) were the predominant cause of ESBL-PE neonatal sepsis and mortality. Improved infection control and antibiotic stewardship are crucial in controlling the spread of resistant strains. Rapid diagnostic tests to detect ESBL-PE in low-income countries are needed to guide treatment and reduce ESBL-PE-associated mortality.
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Affiliation(s)
- Rehema Marando
- Department of Pediatrics and Child Health, Weill Bugando School of Medicine, P.O. Box 1464, Mwanza, Tanzania
| | - Jeremiah Seni
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, P.O. Box 1464, Mwanza, Tanzania
| | - Mariam M Mirambo
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, P.O. Box 1464, Mwanza, Tanzania
| | - Linda Falgenhauer
- Institute of Medical Microbiology, Justus-Liebig University, Schubertstrasse 81, 35392, Giessen, Germany; German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Campus Giessen, Schubertstrasse 81, 35392, Giessen, Germany
| | - Nyambura Moremi
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, P.O. Box 1464, Mwanza, Tanzania
| | - Martha F Mushi
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, P.O. Box 1464, Mwanza, Tanzania
| | - Neema Kayange
- Department of Pediatrics and Child Health, Weill Bugando School of Medicine, P.O. Box 1464, Mwanza, Tanzania
| | - Festo Manyama
- Department of Pediatrics and Child Health, Weill Bugando School of Medicine, P.O. Box 1464, Mwanza, Tanzania
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus-Liebig University, Schubertstrasse 81, 35392, Giessen, Germany; German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Campus Giessen, Schubertstrasse 81, 35392, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus-Liebig University, Schubertstrasse 81, 35392, Giessen, Germany; German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Campus Giessen, Schubertstrasse 81, 35392, Giessen, Germany
| | - Stephen E Mshana
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, P.O. Box 1464, Mwanza, Tanzania.
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Ayandiran TO, Falgenhauer L, Schmiedel J, Chakraborty T, Ayeni FA. High resistance to tetracycline and ciprofloxacin in bacteria isolated from poultry farms in Ibadan, Nigeria. J Infect Dev Ctries 2018; 12:462-470. [PMID: 31940298 DOI: 10.3855/jidc.9862] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/07/2018] [Indexed: 10/31/2022] Open
Abstract
INTRODUCTION Resistance to ciprofloxacin and tetracycline is increasing in the food chain especially in E. coli strains and more worrisome will be occurrence of extended-spectrum beta-lactamase (ESBL) producers among ciprofloxacin- and tetracycline-resistant isolates. This study was undertaken to investigate the occurrence and mechanism of ciprofloxacin-, tetracycline- and ESBL-resistant bacteria in poultry in Ibadan, Nigeria. METHODOLOGY Bacteria were isolated from poultry feces in two farms in Ibadan and identified by MALDI-TOF. Antibiotic susceptibility patterns of the isolates were determined by disc diffusion and Minimum Inhibitory Concentration (MIC) using Vitek-2 apparatus. Four tetracycline genes and six plasmids mediated quinolone resistance genes (PMQR) were investigated by PCR. Whole genome sequencing was done for strains that were ESBL producers. RESULTS Bacterial strains (≥ 105 cfu/mL) were counted on ciprofloxacin and tetracycline supplemented plates. 106 bacteria from 14 different species were identified with high resistance to quinolones, tetracycline and trimethoprim. 49% of the strains were E. coli with 90% resistance for nalidixic acid, moxifloxacin (94%), ciprofloxacin (88%) levofloxacin (78%) and tetracycline (77%). The genes tetA, tetB, qnrB, qnrS and qepA were detected with 37%, 4%, 35%, 4% and 2% prevalence in E. coli respectively. Three ESBL-producing E. coli of the sequence type ST-6359 were found and harboured blaCTX-M-15 located in the chromosome, at the same insertion site. All the ESBL producers harboured mutations in gyrA (S83L/D87N/D678E) and parC (S80I). CONCLUSION The observed high quinolones and tetracycline resistance with ESBL producers in this study calls for caution in the use of these antibiotics in poultry feeds.
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Affiliation(s)
| | - Linda Falgenhauer
- Justus Liebig University and German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen, Germany.
| | - Judith Schmiedel
- Justus Liebig University and German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen, Germany.
| | - Trinad Chakraborty
- Justus Liebig University and German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen, Germany.
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Ghosh H, Doijad S, Falgenhauer L, Fritzenwanker M, Imirzalioglu C, Chakraborty T. bla CTX-M-27-Encoding Escherichia coli Sequence Type 131 Lineage C1-M27 Clone in Clinical Isolates, Germany. Emerg Infect Dis 2018; 23:1754-1756. [PMID: 28930021 PMCID: PMC5621564 DOI: 10.3201/eid2310.170938] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We examined extended-spectrum β-lactamase-producing isolates from livestock, humans, companion animals, food, and the environment during 2009-2016 in Germany for the presence of CTX-M-27 allele within Escherichia coli sequence type (ST) 131. E. coli ST131 C1-M27 was exclusively present in humans; its incidence increased from 0% in 2009 to 45% in 2016.
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Roschanski N, Fischer J, Falgenhauer L, Pietsch M, Guenther S, Kreienbrock L, Chakraborty T, Pfeifer Y, Guerra B, Roesler UH. Retrospective Analysis of Bacterial Cultures Sampled in German Chicken-Fattening Farms During the Years 2011-2012 Revealed Additional VIM-1 Carbapenemase-Producing Escherichia coli and a Serologically Rough Salmonella enterica Serovar Infantis. Front Microbiol 2018; 9:538. [PMID: 29636734 PMCID: PMC5880886 DOI: 10.3389/fmicb.2018.00538] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/08/2018] [Indexed: 11/30/2022] Open
Abstract
Carbapenems are last-resort antibiotics used in human medicine. The increased detection of carbapenem-resistant Enterobacteriaceae (CRE) is therefore worrying. In 2011 we reported the first livestock-associated VIM-1-producing Salmonella (S.) enterica serovar Infantis (R3) isolate from dust, sampled in a German chicken fattening farm. Due to this observation we retrospectively investigated more than 536 stored bacterial cultures, isolated from 45 chicken fattening farms during the years 2011 and 2012. After a non-selective overnight incubation, the bacteria were transferred to selective media. Escherichia (E.) coli and Salmonella growing on these media were further investigated, including antibiotic susceptibility testing, carbapenemase gene screening and whole genome sequencing (WGS). In total, four CRE were found in three out of 45 investigated farms: Besides R3, one additional Salmonella (G-336-1a) as well as two E. coli isolates (G-336-2, G-268-2). All but G-268-2 harbored the blaVIM-1 gene. Salmonella isolates R3 and G-336-1 were closely related although derived from two different farms. All three blaVIM-1-encoding isolates possessed identical plasmids and the blaVIM-1- containing transposon showed mobility at least in vitro. In isolate G-268-2, the AmpC beta-lactamase gene blaCMY-2 but no known carbapenemase gene was identified. However, a transfer of the phenotypic resistance was possible. Furthermore, G-268-2 contained the mcr-1 gene, combining phenotypical carbapenem- as well as colistin resistance in one isolate. Carbapenem-resistant Enterobacteriaceae have been found in three out of 45 investigated chicken flocks. This finding is alarming and emphasizes the importance of intervention strategies to contain the environmental spread of resistant bacteria in animals and humans.
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Affiliation(s)
- Nicole Roschanski
- Institute for Animal Hygiene and Environmental Health, Freie Universitaet Berlin, Berlin, Germany
| | - Jennie Fischer
- Department for Biological Safety, Federal Institute for Risk Assessment, Berlin, Germany
| | - Linda Falgenhauer
- German Center for Infection Research, Institute of Medical Microbiology, Justus Liebig University Giessen, Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Michael Pietsch
- FG13 Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Sebastian Guenther
- Institute for Animal Hygiene and Environmental Health, Freie Universitaet Berlin, Berlin, Germany
| | - Lothar Kreienbrock
- Epidemiology and Information Processing and WHO Collaborating Center for Research and Training for Health at the Human-Animal-Environment Interface, Institute for Biometry, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Trinad Chakraborty
- German Center for Infection Research, Institute of Medical Microbiology, Justus Liebig University Giessen, Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Yvonne Pfeifer
- FG13 Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Beatriz Guerra
- Department for Biological Safety, Federal Institute for Risk Assessment, Berlin, Germany
| | - Uwe H Roesler
- Institute for Animal Hygiene and Environmental Health, Freie Universitaet Berlin, Berlin, Germany
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Sváb D, Falgenhauer L, Rohde M, Szabó J, Chakraborty T, Tóth I. Identification and Characterization of T5-Like Bacteriophages Representing Two Novel Subgroups from Food Products. Front Microbiol 2018; 9:202. [PMID: 29487585 PMCID: PMC5816814 DOI: 10.3389/fmicb.2018.00202] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/29/2018] [Indexed: 12/11/2022] Open
Abstract
During recent years, interest in the use of bacteriophages as biocontrol agents against foodborne pathogens has increased, particularly for members of the family Enterobacteriaceae, with pathogenic Escherichia coli, Shigella, and Salmonella strains among them. Here, we report the isolation and characterisation of 12 novel T5-like bacteriophages from confiscated food samples. All bacterophages effectively lysed E. coli K-12 strains and were able to infect pathogenic E. coli strains representing enterohaemorrhagic (EHEC), enteropathogenic (EPEC), enterotoxigenic (ETEC), and enteroinvasive (EIEC) pathotypes, Shigella dysenteriae, S. sonnei strains, as well as multidrug-resistant (MDR) E. coli and multiple strains representing different Salmonella enterica serovars. All the bacteriophages exhibited Siphoviridae morphology. Whole genome sequencing of the novel T5-like bacteriophages showed that they represent two distinct groups, with the genome-based grouping correlating to the different host spectra. As these bacteriophages are of food origin, their stability and lack of any virulence genes, as well as their broad and mutually complementary host spectrum makes these new T5-like bacteriophages valuable candidates for use as biocontrol agents against foodborne pathogenic enterobacteria.
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Affiliation(s)
- Domonkos Sváb
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, HZI, Braunschweig, Germany
| | - Judit Szabó
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - István Tóth
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
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Irrgang A, Falgenhauer L, Fischer J, Ghosh H, Guiral E, Guerra B, Schmoger S, Imirzalioglu C, Chakraborty T, Hammerl JA, Käsbohrer A. CTX-M-15-Producing E. coli Isolates from Food Products in Germany Are Mainly Associated with an IncF-Type Plasmid and Belong to Two Predominant Clonal E. coli Lineages. Front Microbiol 2017; 8:2318. [PMID: 29209306 PMCID: PMC5702323 DOI: 10.3389/fmicb.2017.02318] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 11/09/2017] [Indexed: 01/06/2023] Open
Abstract
Extended-spectrum beta-lactamases (ESBL) mediating resistance to 3rd generation cephalosporins are a major public health issue. As food may be a vehicle in the spread of ESLB-producing bacteria, a study on the occurrence of cephalosporin-resistantu Escherichia coli in food was initiated. A total of 404 ESBL-producing isolates were obtained from animal-derived food samples (e.g., poultry products, pork, beef and raw milk) between 2011 and 2013. As CTX-M-15 is the most abundant enzyme in ESBL-producing E. coli causing human infections, this study focusses on E. coli isolates from food samples harboring the blaCTX-M-15 gene. The blaCTX-M-15 gene was detected in 5.2% (n = 21) of all isolates. Molecular analyses revealed a phylogenetic group A ST167 clone that was repeatedly isolated from raw milk and beef samples over a period of 6 months. The analyses indicate that spread of CTX-M-15-producing E. coli in German food samples were associated with a multireplicon IncF (FIA FIB FII) plasmid and additional antimicrobial resistance genes such as aac(6)-Ib-cr, blaOXA-1, catB3, different tet-variants as well as a class 1 integron with an aadA5/dfrA17 gene cassette. In addition, four phylogenetic group A ST410 isolates were detected. Three of them carried a chromosomal copy of the blaCTX-M-15 gene and a single isolate with the gene on a 90 kb IncF plasmid. The blaCTX-M-15 gene was always associated with the ISEcp1 element. In conclusion, CTX-M-15-producing E. coli were detected in German food samples. Among isolates of different matrices, two prominent clonal lineages, namely A-ST167 and A-ST410, were identified. These lineages may be important for the foodborne dissemination of CTX-M-15-producing E. coli in Germany. Interestingly, these clonal lineages were reported to be widely distributed and especially prevalent in isolates from humans and livestock. Transmission of CTX-M-15-harboring isolates from food-producing animals to food appears probable, as isolates obtained from livestock and food samples within the same time period exhibit comparable characteristics as compared to isolates detected from human. However, the routes and direction of transmission need further investigation.
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Affiliation(s)
- Alexandra Irrgang
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Linda Falgenhauer
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus Liebig University, Giessen, Germany
| | - Jennie Fischer
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Hiren Ghosh
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus Liebig University, Giessen, Germany
| | - Elisabet Guiral
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Beatriz Guerra
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,European Food Safety Authority, Parma, Italy
| | - Silvia Schmoger
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus Liebig University, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, German Center for Infection Research, Partner Site Giessen-Marburg-Langen, Justus Liebig University, Giessen, Germany
| | - Jens A Hammerl
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Annemarie Käsbohrer
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,Institute of Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
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43
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Yao Y, Lazaro-Perona F, Falgenhauer L, Valverde A, Imirzalioglu C, Dominguez L, Cantón R, Mingorance J, Chakraborty T. Insights into a Novel blaKPC-2-Encoding IncP-6 Plasmid Reveal Carbapenem-Resistance Circulation in Several Enterobacteriaceae Species from Wastewater and a Hospital Source in Spain. Front Microbiol 2017; 8:1143. [PMID: 28702005 PMCID: PMC5487458 DOI: 10.3389/fmicb.2017.01143] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/06/2017] [Indexed: 02/06/2023] Open
Abstract
Untreated wastewater, particularly from hospitals and other healthcare facilities, is considered to be a reservoir for multidrug-resistant bacteria. However, its role in the spread of antibiotic resistances in the human population remains poorly investigated. We used whole genome sequencing to analyze 25 KPC-2-producing Enterobacteriaceae isolates from sewage water collected during a 3-year period and three clinical Citrobacter freundii isolates from a tertiary hospital in the same collection area in Spain. We detected a common, recently described, IncP-6 plasmid carrying the gene blaKPC-2 in 21 isolates from both sources. The plasmid was present in diverse environmental bacterial species of opportunistic pathogens such as C. freundii, Enterobacter cloacae, Klebsiella oxytoca, and Raoultella ornithinolytica. The 40,186 bp IncP-6 plasmid encoded 52 coding sequences and was composed of three uniquely combined regions that were derived from other plasmids recently reported in different countries of South America. The region harboring the carbapenem resistance gene (14 kb) contained a Tn3 transposon disrupted by an ISApu-flanked element and the core sequence composed by ISKpn6/blaKPC-2/ΔblaTEM-1/ISKpn27. We document here the presence of a novel promiscuous blaKPC-2 plasmid circulating in environmental bacteria in wastewater and human populations.
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Affiliation(s)
- Yancheng Yao
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research, Partner Site Giessen-Marburg-LangenGiessen, Germany
| | - Fernando Lazaro-Perona
- Servicio de Microbiología, Hospital Universitario La Paz and Instituto de Investigación Sanitaria Hospital La PazMadrid, Spain
| | - Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research, Partner Site Giessen-Marburg-LangenGiessen, Germany
| | - Aránzazu Valverde
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de MadridMadrid, Spain.,Red Española de Investigación en Patología Infecciosa SpainMadrid, Spain
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research, Partner Site Giessen-Marburg-LangenGiessen, Germany
| | - Lucas Dominguez
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de MadridMadrid, Spain
| | - Rafael Cantón
- Red Española de Investigación en Patología Infecciosa SpainMadrid, Spain.,Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain
| | - Jesús Mingorance
- Servicio de Microbiología, Hospital Universitario La Paz and Instituto de Investigación Sanitaria Hospital La PazMadrid, Spain.,Red Española de Investigación en Patología Infecciosa SpainMadrid, Spain
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research, Partner Site Giessen-Marburg-LangenGiessen, Germany
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44
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Roschanski N, Falgenhauer L, Grobbel M, Guenther S, Kreienbrock L, Imirzalioglu C, Roesler U. Retrospective survey of mcr-1 and mcr-2 in German pig-fattening farms, 2011-2012. Int J Antimicrob Agents 2017; 50:266-271. [PMID: 28545990 DOI: 10.1016/j.ijantimicag.2017.03.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 02/02/2017] [Accepted: 03/02/2017] [Indexed: 01/12/2023]
Abstract
In November 2015, the first plasmid-encoded colistin resistance gene, mcr-1, was described in animals and in humans in China. Subsequently, a multitude of further studies was performed and quite recently the global spread of mcr-1 as well as the occurrence of a new gene variant, mcr-2, was reported. To obtain an overview of the occurrence of the colistin resistance genes mcr-1 and mcr-2 in German pig farms, a retrospective study, including 436 boot swab and pooled faecal samples collected from 58 pig-fattening farms throughout Germany, was performed. Whilst mcr-2 was not detected, the presence of mcr-1 was confirmed in 43 Escherichia coli isolates from 15 farms, indicating that the mcr-1 gene was present in 9.9% of the analysed samples and 25.9% of the investigated pig farms. Subsequent characterisation of the isolates showed colistin minimum inhibitory concentrations (MICs) of 4-8 µg/mL, with most isolates being resistant to several antibiotics including cephalosporins and/or fluoroquinolones. Pulsed-field gel electrophoresis (PFGE) showed great heterogeneity among the tested mcr-1-positive isolates. However, further analyses of 15 selected E. coli isolates (one per mcr-1-positive farm) indicated that the colistin resistance genes were predominantly located on IncX4 plasmids, highly similar to a plasmid initially isolated from an E. coli derived from a human patient in Brazil. The results described herein support the already expressed concern for public health and further underline the need for monitoring programmes in veterinary practice as well as in human medicine.
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Affiliation(s)
- Nicole Roschanski
- Freie Universität Berlin, Institute for Animal Hygiene and Environmental Health, Robert-von-Ostertag-Strasse 7-13, 14163 Berlin, Germany.
| | - Linda Falgenhauer
- Justus Liebig University Giessen, Institute of Medical Microbiology and German Center for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Schubertstrasse 81, 35392 Giessen, Germany
| | - Mirjam Grobbel
- Federal Institute for Risk Assessment, Department: Biological Safety, Diedersdorfer Weg 1, 12277 Berlin, Germany
| | - Sebastian Guenther
- Freie Universität Berlin, Institute for Animal Hygiene and Environmental Health, Robert-von-Ostertag-Strasse 7-13, 14163 Berlin, Germany
| | - Lothar Kreienbrock
- University of Veterinary Medicine Hannover, Institute for Biometry, Epidemiology and Information Processing, WHO Collaborating Center for Research and Training for Health at the Human-Animal-Environment Interface, Buenteweg 2, 30559 Hannover, Germany
| | - Can Imirzalioglu
- Justus Liebig University Giessen, Institute of Medical Microbiology and German Center for Infection Research (DZIF), partner site Giessen-Marburg-Langen, Schubertstrasse 81, 35392 Giessen, Germany
| | - Uwe Roesler
- Freie Universität Berlin, Institute for Animal Hygiene and Environmental Health, Robert-von-Ostertag-Strasse 7-13, 14163 Berlin, Germany
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45
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Pietsch M, Eller C, Wendt C, Holfelder M, Falgenhauer L, Fruth A, Grössl T, Leistner R, Valenza G, Werner G, Pfeifer Y. Molecular characterisation of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates from hospital and ambulatory patients in Germany. Vet Microbiol 2017; 200:130-137. [DOI: 10.1016/j.vetmic.2015.11.028] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 10/22/2022]
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46
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Guenther S, Falgenhauer L, Semmler T, Imirzalioglu C, Chakraborty T, Roesler U, Roschanski N. Environmental emission of multiresistantEscherichia colicarrying the colistin resistance genemcr-1from German swine farms. J Antimicrob Chemother 2017; 72:1289-1292. [DOI: 10.1093/jac/dkw585] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/21/2016] [Indexed: 12/17/2022] Open
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47
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Simon M, Melzl H, Hiergeist A, Richert K, Falgenhauer L, Pfeifer Y, Gerlach RG, Fuchs K, Reischl U, Gessner A, Jantsch J. Colistin- and carbapenem-resistant Klebsiella oxytoca harboring bla VIM-2 and an insertion in the mgrB gene isolated from blood culture. Int J Med Microbiol 2017; 307:113-115. [PMID: 28122677 DOI: 10.1016/j.ijmm.2017.01.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/24/2016] [Accepted: 01/13/2017] [Indexed: 12/11/2022] Open
Abstract
A carbapenemase-producing colistin-resistant Klebsiella oxytoca isolate was recovered from a blood culture of a female patient without previous report of risk factors to obtain multidrug-resistant Gram-negative bacilli. A combination of biochemical and molecular methods was used to identify the resistance mechanism of this isolate. Carbapenemase production was mediated by Verona integron-encoded metallo-β-lactamase (VIM)-2. Colistin resistance was not due to plasmid- borne mcr-1 gene, but we found an integration of IS5-like sequence in the mgrB gene of K. oxytoca. This gene is known to be an important regulator of the PhoPQ two-component system, and the disruption of this gene is most likely the cause of lipid A modification resulting in colistin resistance of our isolate. To the best of our knowledge this constitutes the first report of a carbapenemase-producing K. oxytoca with colistin resistance, a case that demonstrates the limited treatment options for infections with multidrug-resistant organisms.
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Affiliation(s)
- Michaela Simon
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Holger Melzl
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Andreas Hiergeist
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Katharina Richert
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Yvonne Pfeifer
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Roman G Gerlach
- Project Group 5, Robert KochInstitute, Wernigerode Branch, Wernigerode, Germany
| | - Kornelius Fuchs
- Department of Neurology, University Hospital Regensburg, Regensburg, Germany
| | - Udo Reischl
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - André Gessner
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Jonathan Jantsch
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany.
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48
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Moremi N, Manda EV, Falgenhauer L, Ghosh H, Imirzalioglu C, Matee M, Chakraborty T, Mshana SE. Predominance of CTX-M-15 among ESBL Producers from Environment and Fish Gut from the Shores of Lake Victoria in Mwanza, Tanzania. Front Microbiol 2016; 7:1862. [PMID: 27990135 PMCID: PMC5130978 DOI: 10.3389/fmicb.2016.01862] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/04/2016] [Indexed: 11/13/2022] Open
Abstract
Extended-Spectrum Beta-Lactamase (ESBL)-producing bacteria are a common cause of healthcare and community-associated infections worldwide. The distribution of such isolates in the environment and their presence in fish as a result of sewage contamination is not well-studied. Here we examined fish and environmental samples from Mwanza city for the presence of ESBL-producing bacteria. From 196 fish sampled from local markets, 26 (13.3%) contained lactose-fermenting ESBL-producing bacteria, while 39/73 (53.4%) environmental samples from the same area were ESBL producers. Antibiotic resistance genes, multi locus sequence types (MLST) and plasmid replicon types in 24 selected isolates from both populations were identified with whole genome sequencing using Illumina MiSeq. Nine of eleven sequenced fish isolates had the blaCTX-M-15 gene whereas 12/13 from environment carried blaCTX-M-15. Antibiotic resistance genes encoding resistance to sulfonamides (sul1/sul2), tetracyclines [tet(A)/tet(B)] fluoroquinolones [e.g., aac(6′)-Ib-cr, qnrS1], aminoglycosides [e.g., aac(3)-lld, strB, strA,] and trimethoprim (e.g., dfrA14) were detected. E. coli sequence type ST-38 (2) and ST-5173 (2) were detected in isolates both from the environment and fish. IncY plasmids carrying blaCTX-M-15, qnrS1, strA, and strB were detected in five environmental E. coli isolates and in one E. coli isolate from fish. Our data indicate spillage of resistant environmental isolates into Lake Victoria through the sewage system. Persistence of blaCTX-M-15 in the Mwanza city environment is complex, and involves both clonal spread of resistant strains as well as dissemination by commonly occurring IncY plasmids circulating in isolates present in humans, the environment as well as in the food chain.
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Affiliation(s)
- Nyambura Moremi
- Department of Microbiology and Immunology, Weill Bugando School of Medicine Mwanza, Tanzania
| | - Elizabeth V Manda
- Department of Microbiology and Immunology, Weill Bugando School of Medicine Mwanza, Tanzania
| | - Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig UniversityGiessen, Germany; German Center for Infection Research, Partner site Giessen-Marburg-Langen, Campus GiessenGiessen, Germany
| | - Hiren Ghosh
- Institute of Medical Microbiology, Justus Liebig UniversityGiessen, Germany; German Center for Infection Research, Partner site Giessen-Marburg-Langen, Campus GiessenGiessen, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig UniversityGiessen, Germany; German Center for Infection Research, Partner site Giessen-Marburg-Langen, Campus GiessenGiessen, Germany
| | - Mecky Matee
- Department of Microbiology/Immunology, Muhimbili University of Health and Allied Sciences Dar es Salaam, Tanzania
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig UniversityGiessen, Germany; German Center for Infection Research, Partner site Giessen-Marburg-Langen, Campus GiessenGiessen, Germany
| | - Stephen E Mshana
- Department of Microbiology and Immunology, Weill Bugando School of Medicine Mwanza, Tanzania
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49
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Falgenhauer L, Waezsada SE, Gwozdzinski K, Ghosh H, Doijad S, Bunk B, Spröer C, Imirzalioglu C, Seifert H, Irrgang A, Fischer J, Guerra B, Käsbohrer A, Overmann J, Goesmann A, Chakraborty T. Chromosomal Locations of mcr-1 and bla CTX-M-15 in Fluoroquinolone-Resistant Escherichia coli ST410. Emerg Infect Dis 2016; 22:1689-91. [PMID: 27322919 PMCID: PMC4994348 DOI: 10.3201/eid2209.160692] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
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50
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Fritzenwanker M, Imirzalioglu C, Gentil K, Falgenhauer L, Wagenlehner FM, Chakraborty T. Incidental detection of a urinary Escherichia coli isolate harbouring mcr-1 of a patient with no history of colistin treatment. Clin Microbiol Infect 2016; 22:954-955. [PMID: 27615721 DOI: 10.1016/j.cmi.2016.08.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 08/26/2016] [Accepted: 08/27/2016] [Indexed: 11/30/2022]
Affiliation(s)
- M Fritzenwanker
- Institut für Medizinische Mikrobiologie, Justus-Liebig Universität, Germany; German Center for Infection Research DZIF, Partner site Giessen-Marburg-Langen, Campus Giessen, Germany.
| | - C Imirzalioglu
- Institut für Medizinische Mikrobiologie, Justus-Liebig Universität, Germany; German Center for Infection Research DZIF, Partner site Giessen-Marburg-Langen, Campus Giessen, Germany
| | - K Gentil
- Institut für Medizinische Mikrobiologie, Justus-Liebig Universität, Germany; German Center for Infection Research DZIF, Partner site Giessen-Marburg-Langen, Campus Giessen, Germany
| | - L Falgenhauer
- Institut für Medizinische Mikrobiologie, Justus-Liebig Universität, Germany; German Center for Infection Research DZIF, Partner site Giessen-Marburg-Langen, Campus Giessen, Germany
| | - F M Wagenlehner
- German Center for Infection Research DZIF, Partner site Giessen-Marburg-Langen, Campus Giessen, Germany; Klinik und Poliklinik für Urologie, Kinderurologie und Andrologie, Universitätsklinikum Giessen und Marburg GmbH, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - T Chakraborty
- Institut für Medizinische Mikrobiologie, Justus-Liebig Universität, Germany; German Center for Infection Research DZIF, Partner site Giessen-Marburg-Langen, Campus Giessen, Germany
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