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Quinones-Olvera N, Owen SV, McCully LM, Marin MG, Rand EA, Fan AC, Martins Dosumu OJ, Paul K, Sanchez Castaño CE, Petherbridge R, Paull JS, Baym M. Diverse and abundant phages exploit conjugative plasmids. Nat Commun 2024; 15:3197. [PMID: 38609370 PMCID: PMC11015023 DOI: 10.1038/s41467-024-47416-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Phages exert profound evolutionary pressure on bacteria by interacting with receptors on the cell surface to initiate infection. While the majority of phages use chromosomally encoded cell surface structures as receptors, plasmid-dependent phages exploit plasmid-encoded conjugation proteins, making their host range dependent on horizontal transfer of the plasmid. Despite their unique biology and biotechnological significance, only a small number of plasmid-dependent phages have been characterized. Here we systematically search for new plasmid-dependent phages targeting IncP and IncF plasmids using a targeted discovery platform, and find that they are common and abundant in wastewater, and largely unexplored in terms of their genetic diversity. Plasmid-dependent phages are enriched in non-canonical types of phages, and all but one of the 65 phages we isolated were non-tailed, and members of the lipid-containing tectiviruses, ssDNA filamentous phages or ssRNA phages. We show that plasmid-dependent tectiviruses exhibit profound differences in their host range which is associated with variation in the phage holin protein. Despite their relatively high abundance in wastewater, plasmid-dependent tectiviruses are missed by metaviromic analyses, underscoring the continued importance of culture-based phage discovery. Finally, we identify a tailed phage dependent on the IncF plasmid, and find related structural genes in phages that use the orthogonal type 4 pilus as a receptor, highlighting the evolutionarily promiscuous use of these distinct contractile structures by multiple groups of phages. Taken together, these results indicate plasmid-dependent phages play an under-appreciated evolutionary role in constraining horizontal gene transfer via conjugative plasmids.
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Affiliation(s)
- Natalia Quinones-Olvera
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Siân V Owen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Lucy M McCully
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Maximillian G Marin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Eleanor A Rand
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Alice C Fan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Boston University, Boston, MA, 02215, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Oluremi J Martins Dosumu
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Kay Paul
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Cleotilde E Sanchez Castaño
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Roxbury Community College, Boston, MA, 02120, USA
| | - Rachel Petherbridge
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jillian S Paull
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Michael Baym
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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Ramírez-Castillo FY, Guerrero-Barrera AL, Avelar-González FJ. An overview of carbapenem-resistant organisms from food-producing animals, seafood, aquaculture, companion animals, and wildlife. Front Vet Sci 2023; 10:1158588. [PMID: 37397005 PMCID: PMC10311504 DOI: 10.3389/fvets.2023.1158588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 05/23/2023] [Indexed: 07/04/2023] Open
Abstract
Carbapenem resistance (CR) is a major global health concern. CR is a growing challenge in clinical settings due to its rapid dissemination and low treatment options. The characterization of its molecular mechanisms and epidemiology are highly studied. Nevertheless, little is known about the spread of CR in food-producing animals, seafood, aquaculture, wildlife, their environment, or the health risks associated with CR in humans. In this review, we discuss the detection of carbapenem-resistant organisms and their mechanisms of action in pigs, cattle, poultry, seafood products, companion animals, and wildlife. We also pointed out the One Health approach as a strategy to attempt the emergency and dispersion of carbapenem-resistance in this sector and to determine the role of carbapenem-producing bacteria in animals among human public health risk. A higher occurrence of carbapenem enzymes in poultry and swine has been previously reported. Studies related to poultry have highlighted P. mirabilis, E. coli, and K. pneumoniae as NDM-5- and NDM-1-producing bacteria, which lead to carbapenem resistance. OXA-181, IMP-27, and VIM-1 have also been detected in pigs. Carbapenem resistance is rare in cattle. However, OXA- and NDM-producing bacteria, mainly E. coli and A. baumannii, are cattle's leading causes of carbapenem resistance. A high prevalence of carbapenem enzymes has been reported in wildlife and companion animals, suggesting their role in the cross-species transmission of carbapenem-resistant genes. Antibiotic-resistant organisms in aquatic environments should be considered because they may act as reservoirs for carbapenem-resistant genes. It is urgent to implement the One Health approach worldwide to make an effort to contain the dissemination of carbapenem resistance.
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Affiliation(s)
- Flor Y. Ramírez-Castillo
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Ags, Mexico
| | - Alma L. Guerrero-Barrera
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Ags, Mexico
| | - Francisco J. Avelar-González
- Laboratorio de Estudios Ambientales, Departamento de Fisiología y Farmacología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Ags, Mexico
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Mahazu S, Prah I, Ota Y, Hayashi T, Nukui Y, Suzuki M, Hoshino Y, Akeda Y, Suzuki T, Ishino T, Ablordey A, Saito R. Klebsiella Species and Enterobacter cloacae Isolates Harboring blaOXA-181 and blaOXA-48: Resistome, Fitness Cost, and Plasmid Stability. Microbiol Spectr 2022; 10:e0332022. [PMID: 36453894 PMCID: PMC9769605 DOI: 10.1128/spectrum.03320-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Abstract
IncX3 and IncL plasmids have been named as catalysts advancing dissemination of blaOXA-181 and blaOXA-48 genes. However, their impact on the performance of host cells is vastly understudied. Genetic characteristics of blaOXA-48- and blaOXA-181-containing Klebsiella pneumoniae (EFN299), Klebsiella quasipneumoniae (EFN262), and Enterobacter cloacae (EFN743) isolated from clinical samples in a Ghanaian hospital were investigated by whole-genome sequencing. Transfer of plasmids by conjugation and electroporation, plasmid stability, fitness cost, and genetic context of blaOXA-48, blaOXA-181, and blaDHA-1 were assessed. blaOXA-181 was carried on two IncX3 plasmids, an intact 51.5-kb IncX3 plasmid (p262-OXA-181) and a 45.3-kb IncX3 plasmid (p743-OXA-181) without replication protein sequence. The fluoroquinolone-resistant gene qnrS1 region was also excised, and unlike in p262-OXA-181, the blaOXA-181 drug-resistant region was not found on a composite transposon. blaOXA-48 was carried on a 74.6-kb conjugative IncL plasmid with unknown ~10.9-kb sequence insertion. This IncL plasmid proved to be highly transferable, with a conjugation efficiency of 1.8 × 10-2. blaDHA-1 was present on an untypeable 22.2 kb genetic structure. Plasmid stability test revealed plasmid loss rate between 4.3% and 12.4%. The results also demonstrated that carriage of IncX3-blaOXA-181 or IncL-blaOXA-48 plasmids was not associated with any fitness defect, but rather an enhanced competitive ability of host cells. This study underscores the significant contribution of IncX3 and IncL plasmids in the dissemination of resistance genes and their efficient transfer calls for regular monitoring to control the expansion of resistant strains. IMPORTANCE The growing rate of antibiotic resistance is an important global health threat. This threat is exacerbated by the lack of safe and potent alternatives to carbapenems in addition to the slow developmental process of newer and effective antibiotics. Infections by carbapenem-resistant Gram-negative bacteria are becoming almost untreatable, leading to poor clinical outcomes and high mortality rates. OXA-48-like carbapenemases are one of the most widespread carbapenemases accounting for resistance among Enterobacteriaecae. We characterized OXA-48- and OXA-181-producing Enterobacteriaecae to gain insights into the genetic basis and mechanism of resistance to carbapenems. Findings from the study showed that the genes encoding these enzymes were carried on highly transmissible plasmids, one of which had sequences absent in other similar plasmids. This implies that mobile genetic elements are important players in the dissemination of resistance genes. Further characterization of this plasmid is warranted to determine the role of this sequence in the spread of resistance genes.
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Affiliation(s)
- Samiratu Mahazu
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Parasitology and Tropical Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Isaac Prah
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yusuke Ota
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takaya Hayashi
- Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoko Nukui
- Department of Infection Control and Prevention, Tokyo Medical and Dental University Hospital, Tokyo, Japan
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshihiko Hoshino
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Toshihiko Suzuki
- Department of Bacterial Pathogenesis, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomoko Ishino
- Department of Parasitology and Tropical Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Anthony Ablordey
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Ryoichi Saito
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Infection Control and Prevention, Tokyo Medical and Dental University Hospital, Tokyo, Japan
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Genomic Analysis of Klebsiella pneumoniae ST258 Strain Coproducing KPC-2 and CTX-M-14 Isolated from Poultry in the Brazilian Amazon Region. Antibiotics (Basel) 2022; 11:antibiotics11121835. [PMID: 36551493 PMCID: PMC9774611 DOI: 10.3390/antibiotics11121835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
This study aimed to characterize a Klebsiella pneumoniae strain (KP411) recovered from the stool samples of poultry (Gallus gallus) in the Brazilian Amazon Region. The whole-genome sequencing of KP411 revealed the presence of an important arsenal of antimicrobial resistance genes to β-lactams (blaCTX-M-14, blaTEM-1B, blaKPC-2, blaSVH-11), aminoglycosides [aph(3″)- Ib, aph(6)-Id, aph(3')-Ia], sulfonamides (sul1, sul2), quinolones (oqxAB), fosfomycin (fosAKP), and macrolides [mph(A)]. Furthermore, our analyses revealed that the KP411 strain belongs to the ST258 clonal lineage, which is one of the main epidemic clones responsible for the dissemination of KPC-2 worldwide. Our data suggest that food-producing animals may act as reservoirs of multidrug-resistant K. pneumoniae belonging to the ST258 clone, and, consequently, contribute to their dissemination to humans and the environment.
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Srednik ME, Morningstar-Shaw BR, Hicks JA, Mackie TA, Schlater LK. Antimicrobial resistance and genomic characterization of Salmonella enterica serovar Senftenberg isolates in production animals from the United States. Front Microbiol 2022; 13:979790. [PMID: 36406424 PMCID: PMC9668867 DOI: 10.3389/fmicb.2022.979790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/02/2022] [Indexed: 07/22/2023] Open
Abstract
In the USA, Salmonella enterica subspecies enterica serovar Senftenberg is among the top five serovars isolated from food and the top 11 serovars isolated from clinically ill animals. Human infections are associated with exposure to farm environments or contaminated food. The objective of this study was to characterize S. Senftenberg isolates from production animals by analyzing phenotypic antimicrobial resistance profiles, genomic features and phylogeny. Salmonella Senftenberg isolates (n = 94) from 20 US states were selected from NVSL submissions (2014-2017), tested against 14 antimicrobial drugs, and resistance phenotypes determined. Resistance genotypes were determined using whole genome sequencing analysis with AMRFinder and the NCBI and ResFinder databases with ABRicate. Plasmids were detected using PlasmidFinder. Integrons were detected using IntFinder and manual alignment with reference genes. Multilocus-sequence-typing (MLST) was determined using ABRicate with PubMLST database, and phylogeny was determined using vSNP. Among 94 isolates, 60.6% were resistant to at least one antimicrobial and 39.4% showed multidrug resistance. The most prevalent resistance findings were for streptomycin (44.7%), tetracycline (42.6%), ampicillin (36.2%) and sulfisoxazole (32.9%). The most commonly found antimicrobial resistance genes were aac(6')-Iaa (100%), aph(3″)-Ib and aph(6)-Id (29.8%) for aminoglycosides, followed by bla TEM-1 (26.6%) for penicillins, sul1 (25.5%) and sul2 (23.4%) for sulfonamides and tetA (23.4%) for tetracyclines. Quinolone-resistant isolates presented mutations in gyrA and/or parC genes. Class 1 integrons were found in 37 isolates. Thirty-six plasmid types were identified among 77.7% of the isolates. Phylogenetic analysis identified two distinct lineages of S. Senftenberg that correlated with the MLST results. Isolates were classified into two distinct sequence types (ST): ST14 (97.9%) and ST 185 (2.1%). The diversity of this serotype suggests multiple introductions into animal populations from outside sources. This study provided antimicrobial susceptibility and genomic characteristics of S. Senftenberg clinical isolates from production animals in the USA during 2014 to 2017. This study will serve as a base for future studies focused on the phenotypic and molecular antimicrobial characterization of S. Senftenberg isolates in animals. Monitoring of antimicrobial resistance to detect emergence of multidrug-resistant strains is critical.
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Guo X, Chen R, Wang Q, Li C, Ge H, Qiao J, Li Y. Global prevalence, characteristics, and future prospects of IncX3 plasmids: A review. Front Microbiol 2022; 13:979558. [PMID: 36147856 PMCID: PMC9485871 DOI: 10.3389/fmicb.2022.979558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
IncX3 plasmids are narrow host range plasmids mostly found in Enterobacteriaceae with great conjugation ability, high stability, no fitness cost, and the ability to improve biofilm formation in their bacterial hosts. IncX3 plasmids have spread swiftly, primarily in several nations and among different species over the last 10 years. blaNDM, blaKPC, and blaOXA-181 are the carbapenemase genes carried by IncX3 plasmids. Among them, blaNDM is often located on the IncX3 plasmid, which is deemed as the primary vehicle of blaNDM transmission. Isolates harboring IncX3 plasmids are found in nations all over the world from human, animal, and environmental sources. Cointegrate plasmids related to IncX3 have recently been discovered to increase the antibiotic resistance spectrum and potentially broaden the host range of plasmids, restricting the use of antibiotics in the clinic. There are, however, few reviews based on the physiological and epidemiological properties of IncX3 plasmid, as well as studies on the plasmid itself. Hence, we conducted a retrospective literature review to summarize the characteristics of IncX3 plasmids aiming to provide a theoretical basis for controlling the global prevalence of IncX3 plasmids and directions for further research on the functions of the related genes on the IncX3 plasmid.
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Affiliation(s)
- Xiaobing Guo
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Xiaobing Guo,
| | - Ruyan Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qian Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Chenyu Li
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haoyu Ge
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jie Qiao
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuan Li
- Department of Nuclear Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Nohejl T, Valcek A, Papousek I, Palkovicova J, Wailan AM, Pratova H, Minoia M, Dolejska M. Genomic analysis of qnr-harbouring IncX plasmids and their transferability within different hosts under induced stress. BMC Microbiol 2022; 22:136. [PMID: 35590235 PMCID: PMC9118779 DOI: 10.1186/s12866-022-02546-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 04/27/2022] [Indexed: 11/26/2022] Open
Abstract
Background Conjugative plasmids play a major role in the dissemination of antibiotic resistance genes. Knowledge of the plasmid characteristics and behaviour can allow development of control strategies. Here we focus on the IncX group of plasmids carrying genes conferring quinolone resistance (PMQR), reporting their transfer and persistence within host bacteria of various genotypes under distinct conditions and levels of induced stress in form of temperature change and various concentrations of ciprofloxacin supplementation. Methods Complete nucleotide sequences were determined for eight qnr-carrying IncX-type plasmids, of IncX1 (3), IncX2 (3) and a hybrid IncX1-2 (2) types, recovered from Escherichia coli of various origins. This data was compared with further complete sequences of IncX1 and IncX2 plasmids carrying qnr genes (n = 41) retrieved from GenBank and phylogenetic tree was constructed. Representatives of IncX1 (pHP2) and IncX2 (p194) and their qnrS knockout mutants, were studied for influence of induced stress and genetic background on conjugative transfer and maintenance. Results A high level of IncX core-genome similarity was found in plasmids of animal, environmental and clinical origin. Significant differences were found between the individual IncX plasmids, with IncX1 subgroup plasmids showing higher conjugative transfer rates than IncX2 plasmids. Knockout of qnr modified transfer frequency of both plasmids. Two stresses applied simultaneously were needed to affect transfer rate of wildtype plasmids, whereas a single stress was sufficient to affect the IncX ΔqnrS plasmids. The conjugative transfer was shown to be biased towards the host phylogenetic proximity. A long-term cultivation experiment pointed out the persistence of IncX plasmids in the antibiotic-free environment. Conclusions The study indicated the stimulating effect of ciprofloxacin supplementation on the plasmid transfer that can be nullified by the carriage of a single PMQR gene. The findings present the significant properties and behaviour of IncX plasmids carrying antibiotic resistance genes that are likely to play a role in their dissemination and stability in bacterial populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02546-6.
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Affiliation(s)
- Tomas Nohejl
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic.,CEITEC, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Adam Valcek
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic.,CEITEC, University of Veterinary Sciences Brno, Brno, Czech Republic.,Faculty of Medicine, Biomedical Center, Charles University, Pilsen, Czech Republic
| | - Ivo Papousek
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Jana Palkovicova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic.,CEITEC, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Alexander M Wailan
- Parasites and Microbes, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Hana Pratova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic.,CEITEC, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Marco Minoia
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic.,CEITEC, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Monika Dolejska
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic. .,CEITEC, University of Veterinary Sciences Brno, Brno, Czech Republic. .,Faculty of Medicine, Biomedical Center, Charles University, Pilsen, Czech Republic. .,Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno, Brno, Czech Republic.
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Wei H, Kong L, Wang Y, Huang Z, Yang X, Zhou C, Li C, Ma B, Li C, Lei C, Wang H. Characterization and Public Health Insights of the New Delhi Metallo-β-Lactamase-Producing Enterobacterales from Laying Hens in China. Microorganisms 2022; 10:microorganisms10040800. [PMID: 35456850 PMCID: PMC9029685 DOI: 10.3390/microorganisms10040800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/26/2022] [Accepted: 04/09/2022] [Indexed: 02/04/2023] Open
Abstract
The New Delhi metallo-β-lactamase (NDM) is a major element for the rapid expansion of the carbapenem-resistant Enterobacterales, which poses a great challenge to public health security. NDM-producing Enterobacterales strains (50 Escherichia coli, 40 Klebsiella pneumoniae, and 5 Enterobacter cloacae) were isolated from laying hens in China for the surveillance of antibiotic-resistant pathogens, and all were found to be multi-drug resistant bacteria. The genomic analysis of these NDM-positive bacteria revealed the ST167, ST617, and ST410 of the fifteen ST-type E. coli clones and ST37 of the four ST-type K. pneumoniae clones to be the same types as the human-derived strains. Among them, some new clone types were also found. Most of the blaNDM genes (blaNDM-1 or blaNDM-5) were on the IncX3 plasmids (n = 80) and were distributed in E. coli, K. pneumoniae, and E. cloacae, while the remaining blaNDM-5 genes were harbored in the E. coli ST167 with IncFII plasmids (n = 15). The typeⅠ1 of the eight IncX3 plasmid subtypes was consistent with the human-derived pNDM5_020001 plasmid (accession no. CP032424). In addition, these two plasmids did not affect the growth of the host bacteria and could be reproduced stably without antibiotics. Our study revealed the high genetic propensity of the NDM-positive Enterobacterales from the laying hens and human commensal Enterobacterales, suggesting the potentially enormous risk of its transmission to humans.
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Affiliation(s)
- Hongcheng Wei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Linghan Kong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Yulong Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Zheren Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Xue Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Changyu Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Chao Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Boheng Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Cui Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Changwei Lei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Hongning Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
- Correspondence: ; Tel.: +86-28-8547-1599
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9
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Hammer-Dedet F, Aujoulat F, Jumas-Bilak E, Licznar-Fajardo P. Persistence and Dissemination Capacities of a BlaNDM-5-Harboring IncX-3 Plasmid in Escherichia coli Isolated from an Urban River in Montpellier, France. Antibiotics (Basel) 2022; 11:antibiotics11020196. [PMID: 35203799 PMCID: PMC8868147 DOI: 10.3390/antibiotics11020196] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/24/2022] [Accepted: 01/28/2022] [Indexed: 02/01/2023] Open
Abstract
To investigate the capacities of persistence and dissemination of blaNDM-5 within Escherichia coli and in aquatic environment, we characterized E. coli (sequence type 636) strains B26 and B28 isolated one month apart from the same urban river in Montpellier, France. The two isolates carried a pTsB26 plasmid, which sized 45,495 Kb, harbored blaNDM-5 gene and belonged to IncX-3 incompatibility group. pTsB26 was conjugative in vitro at high frequency, it was highly stable after 400 generations and it exerted no fitness cost on its host. blaNDM-5harboring plasmids are widely dispersed in E. coli all around the world, with no lineage specialization. The genomic comparison between B26 and B28 stated that the two isolates probably originated from the same clone, suggesting the persistence of pTsB26 in an E. coli host in aquatic environment.
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Affiliation(s)
- Florence Hammer-Dedet
- HSM, University Montpellier, CNRS, IRD, 34090 Montpellier, France; (F.H.-D.); (F.A.)
| | - Fabien Aujoulat
- HSM, University Montpellier, CNRS, IRD, 34090 Montpellier, France; (F.H.-D.); (F.A.)
| | - Estelle Jumas-Bilak
- HSM, University of Montpellier, CNRS, IRD, CHU Montpellier, 34090 Montpellier, France;
| | - Patricia Licznar-Fajardo
- HSM, University of Montpellier, CNRS, IRD, CHU Montpellier, 34090 Montpellier, France;
- Correspondence:
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10
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Baomo L, Lili S, Moran RA, van Schaik W, Chao Z. Temperature-Regulated IncX3 Plasmid Characteristics and the Role of Plasmid-Encoded H-NS in Thermoregulation. Front Microbiol 2022; 12:765492. [PMID: 35069472 PMCID: PMC8770905 DOI: 10.3389/fmicb.2021.765492] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/17/2021] [Indexed: 12/03/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) are a critical public health problem worldwide. Globally, IncX3-type plasmids have emerged as the predominant vehicles carrying the metallo-β-lactamase gene bla NDM. Although bla NDM-bearing IncX3 plasmids have been found in various hosts from diverse environments, whether their transfer and persistence properties vary under different conditions and what factors influence any variation is unknown. By observing the effects of different temperatures on IncX3 plasmid conjugation rates, stability, and effects on host fitness in Escherichia coli, we demonstrate that temperature is an important determinant of plasmid phenotypes. The IncX3 plasmid pGZIncX3 transferred at highest frequencies, was most stable and imposed lower fitness costs at 37°C. Temperature-regulated variation in pGZIncX3 properties involved a thermoregulated plasmid-encoded H-NS-like protein, which was produced at higher levels at 30°C and 42°C and inhibited the expression of type IV secretion system genes involved in conjugation. These findings suggest that bla NDM-bearing IncX3 plasmids are adapted to carriage by enterobacteria that colonize mammalian hosts and could explain the rapid dissemination of these plasmids among human-associated species, particularly in hospital settings.
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Affiliation(s)
- Liu Baomo
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shui Lili
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Robert A. Moran
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Willem van Schaik
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Zhuo Chao
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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11
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Dissection of Highly Prevalent qnrS1-Carrying IncX Plasmid Types in Commensal Escherichia coli from German Food and Livestock. Antibiotics (Basel) 2021; 10:antibiotics10101236. [PMID: 34680816 PMCID: PMC8532951 DOI: 10.3390/antibiotics10101236] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 09/29/2021] [Accepted: 10/08/2021] [Indexed: 11/16/2022] Open
Abstract
Plasmids are mobile genetic elements, contributing to the spread of resistance determinants by horizontal gene transfer. Plasmid-mediated quinolone resistances (PMQRs) are important determinants able to decrease the antimicrobial susceptibility of bacteria against fluoroquinolones and quinolones. The PMQR gene qnrS1, especially, is broadly present in the livestock and food sector. Thus, it is of interest to understand the characteristics of plasmids able to carry and disseminate this determinant and therewith contribute to the resistance development against this class of high-priority, critically important antimicrobials. Therefore, we investigated all commensal Escherichia (E.) coli isolates, with reduced susceptibility to quinolones, recovered during the annual zoonosis monitoring 2017 in the pork and beef production chain in Germany (n = 2799). Through short-read whole-genome sequencing and bioinformatics analysis, the composition of the plasmids and factors involved in their occurrence were determined. We analysed the presence and structures of predominant plasmids carrying the PMQR qnrS1. This gene was most frequently located on IncX plasmids. Although the E. coli harbouring these IncX plasmids were highly diverse in their sequence types as well as their phenotypic resistance profiles, the IncX plasmids-carrying the qnrS1 gene were rather conserved. Thus, we only detected three distinct IncX plasmids carrying qnrS1 in the investigated isolates. The IncX plasmids were assigned either to IncX1 or to IncX3. All qnrS1-carrying IncX plasmids further harboured a β-lactamase gene (bla). In addition, all investigated IncX plasmids were transmissible. Overall, we found highly heterogenic E. coli harbouring conserved IncX plasmids as vehicles for the most prevalent qnr gene qnrS1. These IncX plasmids may play an important role in the dissemination of those two resistance determinants and their presence, transfer and co-selection properties require a deeper understanding for a thorough risk assessment.
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12
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Samajpati S, Pragasam AK, Mandal S, Balaji V, Dutta S. Emergence of ceftriaxone resistant Salmonella enterica serovar Typhi in Eastern India. INFECTION GENETICS AND EVOLUTION 2021; 96:105093. [PMID: 34592414 DOI: 10.1016/j.meegid.2021.105093] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 10/20/2022]
Abstract
In view of widespread isolation of fluoroquinolone (FQ) resistant Salmonella enterica serovar Typhi globally, third generation cephalosporins (ceftriaxone) are used as alternative drugs for treatment of typhoid fever in recent years. But reports on emergence of third generation cephalosporin resistant S. Typhi have been documented from various countries including India posing threat in future use of this drug for typhoid treatment. Here, we report on genomic analysis of a third generation cephalosporin resistant S. Typhi strain isolated for the first time from Eastern India, Kolkata during 2019. The study strain was phenotypically resistant to ceftriaxone, ampicillin. Whole genome sequencing revealed the presence of conjugative IncX3 plasmid carrying blaSHV-12 gene on it. The study strain belongs to H58 haplotype (4.3.1.2) and ST1 type. Comparison of phylogenetic analysis of the study strain with other cephalosporin resistant S. Typhi strains across the world revealed that three strains isolated from Western part of India during 2016 were its closest neighbours. Hence close monitoring of cephalosporin resistant S. Typhi strains are of great importance to control the furure use of this antibiotic for the treatment of typhoid fever.
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Affiliation(s)
- Sriparna Samajpati
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, P-33 C.I.T Road, Kolkata, West Bengal 700010, India
| | | | - Subhranshu Mandal
- Microbiology Division, Calcutta Medical Research Institute, 7/2 Diamond Harbour Road, Kolkata, West Bengal 700027, India
| | | | - Shanta Dutta
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, P-33 C.I.T Road, Kolkata, West Bengal 700010, India.
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13
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Characterization of E. coli Isolates Producing Extended Spectrum Beta-Lactamase SHV-Variants from the Food Chain in Germany. Microorganisms 2021; 9:microorganisms9091926. [PMID: 34576822 PMCID: PMC8471341 DOI: 10.3390/microorganisms9091926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 11/25/2022] Open
Abstract
Resistance of bacteria to 3rd generation cephalosporins mediated by beta-lactamases (ESBL, pAmpC) is a public health concern. In this study, 1517 phenotypically cephalosporin-resistant E. coli were screened for the presence of blaSHV genes. Respective genes were detected in 161 isolates. Majority (91%) were obtained from poultry production and meat. The SHV-12 beta-lactamase was the predominant variant (n = 155), while the remaining isolates exhibited SHV-2 (n = 4) or SHV-2a (n = 2). A subset of the isolates (n = 51) was further characterized by PCR, PFGE, or whole-genome sequencing and bioinformatics analysis. The SHV-12-producing isolates showed low phylogenetic relationships, and dissemination of the blaSHV-12 genes seemed to be mainly driven by horizontal gene transfer. In most of the isolates, blaSHV-12 was located on transferable IncX3 (~43 kb) or IncI1 (~100 kb) plasmids. On IncX3, blaSHV-12 was part of a Tn6 composite transposon located next to a Tn3 transposon, which harbored the fluoroquinolone resistance gene qnrS1. On IncI1 plasmids, blaSHV-12 was located on an incomplete class 1 integron as part of a Tn21 transposon. In conclusion, SHV-12 is widely distributed in German poultry production and spreads via horizontal gene transfer. Consumers are at risk by handling raw poultry meat and should take care in appropriate kitchen hygiene.
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Lachowska M, Izdebski R, Urbanowicz P, Żabicka D, Królak-Olejnik B. Infection of Cronobacter sakazakii ST1 Producing SHV-12 in a Premature Infant Born from Triplet Pregnancy. Microorganisms 2021; 9:microorganisms9091878. [PMID: 34576773 PMCID: PMC8469300 DOI: 10.3390/microorganisms9091878] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023] Open
Abstract
Cronobacter sakazakii can cause severe life-threatening invasive infections in neonates, with a high mortality rate mostly associated with powdered infant formula consumption. The study describes a fatal C. sakazakii infection in premature infant fed only with expressed human milk. Despite the identification of etiological factor from patient's blood, the epidemiological investigation, including mother's skin, hospital surfaces, milk expressing devices, and milk samples, did not show bacterial contamination. The infection was caused by C. sakazakii ST1, being one of the leading genotypes reported in invasive infections. The phylogenetic analysis of the international collection of the ST1 organisms allowed us to identify the isolate as a member of the main cluster. The pathogenic potential of the isolate was augmented by the presence of IncFIB-like molecule representing virulence plasmids of pESA-3 family. Isolate presented ESBL phenotype associated with blaSHV-12 gene harboured by IncX3 plasmid. The described case gave valuable information to genetics of Cronobacter, and also urges the need of wider whole-genome sequencing implementation as a part of diagnostic procedure.
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Affiliation(s)
- Monika Lachowska
- Department of Neonatology, Wrocław Medical University, 50-556 Wrocław, Poland; (M.L.); (B.K.-O.)
| | - Radosław Izdebski
- Department of Molecular Microbiology, National Medicines Institute, 00-725 Warsaw, Poland;
- Correspondence:
| | - Paweł Urbanowicz
- Department of Molecular Microbiology, National Medicines Institute, 00-725 Warsaw, Poland;
| | - Dorota Żabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, 00-725 Warsaw, Poland;
| | - Barbara Królak-Olejnik
- Department of Neonatology, Wrocław Medical University, 50-556 Wrocław, Poland; (M.L.); (B.K.-O.)
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15
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Borelli TC, Lovate GL, Scaranello AFT, Ribeiro LF, Zaramela L, Pereira-dos-Santos FM, Silva-Rocha R, Guazzaroni ME. Combining Functional Genomics and Whole-Genome Sequencing to Detect Antibiotic Resistance Genes in Bacterial Strains Co-Occurring Simultaneously in a Brazilian Hospital. Antibiotics (Basel) 2021; 10:antibiotics10040419. [PMID: 33920372 PMCID: PMC8070361 DOI: 10.3390/antibiotics10040419] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 01/01/2023] Open
Abstract
(1) Background: The rise of multi-antibiotic resistant bacteria represents an emergent threat to human health. Here, we investigate antibiotic resistance mechanisms in bacteria of several species isolated from an intensive care unit in Brazil. (2) Methods: We used whole-genome analysis to identify antibiotic resistance genes (ARGs) and plasmids in 34 strains of Gram-negative and Gram-positive bacteria, providing the first genomic description of Morganella morganii and Ralstonia mannitolilytica clinical isolates from South America. (3) Results: We identified a high abundance of beta-lactamase genes in resistant organisms, including seven extended-spectrum beta-lactamases (OXA-1, OXA-10, CTX-M-1, KPC, TEM, HYDRO, BLP) shared between organisms from different species. Additionally, we identified several ARG-carrying plasmids indicating the potential for a fast transmission of resistance mechanism between bacterial strains. Furthermore, we uncovered two pairs of (near) identical plasmids exhibiting multi-drug resistance. Finally, since many highly resistant strains carry several different ARGs, we used functional genomics to investigate which of them were indeed functional. In this sense, for three bacterial strains (Escherichia coli, Klebsiella pneumoniae, and M. morganii), we identified six beta-lactamase genes out of 15 predicted in silico as those mainly responsible for the resistance mechanisms observed, corroborating the existence of redundant resistance mechanisms in these organisms. (4) Conclusions: Systematic studies similar to the one presented here should help to prevent outbreaks of novel multidrug-resistant bacteria in healthcare facilities.
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Affiliation(s)
- Tiago Cabral Borelli
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-901, Brazil; (T.C.B.); (G.L.L.); (A.F.T.S.); (L.F.R.)
| | - Gabriel Lencioni Lovate
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-901, Brazil; (T.C.B.); (G.L.L.); (A.F.T.S.); (L.F.R.)
| | - Ana Flavia Tonelli Scaranello
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-901, Brazil; (T.C.B.); (G.L.L.); (A.F.T.S.); (L.F.R.)
| | - Lucas Ferreira Ribeiro
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-901, Brazil; (T.C.B.); (G.L.L.); (A.F.T.S.); (L.F.R.)
| | - Livia Zaramela
- Department of Pediatrics, University of California San Diego, San Diego, CA 92161, USA;
| | - Felipe Marcelo Pereira-dos-Santos
- Department of Cell and Molecular Biology, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900, Brazil; (F.M.P.-d.-S.); (R.S.-R.)
| | - Rafael Silva-Rocha
- Department of Cell and Molecular Biology, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900, Brazil; (F.M.P.-d.-S.); (R.S.-R.)
| | - María-Eugenia Guazzaroni
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-901, Brazil; (T.C.B.); (G.L.L.); (A.F.T.S.); (L.F.R.)
- Correspondence:
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16
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Ewers C, de Jong A, Prenger-Berninghoff E, El Garch F, Leidner U, Tiwari SK, Semmler T. Genomic Diversity and Virulence Potential of ESBL- and AmpC-β-Lactamase-Producing Escherichia coli Strains From Healthy Food Animals Across Europe. Front Microbiol 2021; 12:626774. [PMID: 33868190 PMCID: PMC8047082 DOI: 10.3389/fmicb.2021.626774] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/02/2021] [Indexed: 01/07/2023] Open
Abstract
The role of livestock animals as a putative source of ESBL/pAmpC E. coli for humans is a central issue of research. In a large-scale pan-European surveillance, 2,993 commensal Escherichia spp. isolates were recovered from randomly collected fecal samples of healthy cattle, pigs and chickens in various abattoirs. One-hundred Escherichia spp. isolates (0.5% from cattle, 1.3% pigs, 8.0% chickens) fulfilled the criteria for cefotaxime and ceftazidime non-wildtype (EUCAST). In silico screening of WGS data of 99 isolates (98 E. coli and 1 E. fergusonii) revealed blaSHV–12 (32.3%), blaCTX–M–1 (24.2%), and blaCMY–2 (22.2%) as predominant ESBL/pAmpC types. Other types were blaSHV–2 (1.0%), blaCTX–M–2/–14/–15 (1.0/6.1/1.0%), and blaTEM–52 (5.1%). Six isolates revealed AmpC-promoter mutations (position −42 (C > T) and one carried mcr-1. The majority (91.3%) of ESBL/pAmpC genes were located on plasmids. SHV-12 was mainly (50%) encoded on IncI1α plasmids (pST-3/-26/-95), followed by IncX3 (12.5%) and IncK2 (3.1%). The blaTEM–52 genes were located on IncI1α-pST-36 (60%) and IncX1 plasmids (20%). The dominant plasmid lineage among CTX-M-1 isolates was IncI1α (pST-3/-295/-317) (87.5%), followed by IncN-pST-1 (8.3%). CMY-2 was mostly identified on IncI1α (pST-12/-2) (54.5%) and IncK2 (31.8%) plasmids. Several plasmids revealed high similarity to published plasmids from human and animal Enterobacteriaceae. The isolates were assigned to phylogroups A/C (34.7/7.1%), B1 (27.6%), B2 (3.1%), D/F (9.2/10.2%), E (5.1%), and to E. clades (3.0%). With 51 known and 2 novel MLST types, a wide variety of STs was found, including STs previously observed in human isolates (ST10/38/117/131/648). ESBL/AmpC types or STs were rarely correlated with the geographic origin of the isolates or animal species. Virulence gene typing identified extraintestinal pathogenic E. coli (ExPEC; 2.0%), avian pathogenic E. coli (APEC; 51.5%), and atypical enteropathogenic E. coli (EPEC; 6.1%). In conclusion, the high diversity of STs and phylogenetic groups provides hardly any hint for clonal spread of single lineages but hints toward the dissemination of cephalosporin resistance genes in livestock via distinct, globally successful plasmid lineages. Even though a number of isolates could not be assigned to a distinct pathotype, our finding of combined multidrug-resistance and virulence in this facultative pathogen should be considered an additional threat to public health.
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Affiliation(s)
- Christa Ewers
- Department of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Anno de Jong
- European Antimicrobial Susceptibility Surveillance in Animals (EASSA) Study Group, Executive Animal Health Study Center (CEESA), Brussels, Belgium
| | - Ellen Prenger-Berninghoff
- Department of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Farid El Garch
- European Antimicrobial Susceptibility Surveillance in Animals (EASSA) Study Group, Executive Animal Health Study Center (CEESA), Brussels, Belgium
| | - Ursula Leidner
- Department of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Sumeet K Tiwari
- NG1 Microbial Genomics, Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- NG1 Microbial Genomics, Robert Koch Institute, Berlin, Germany
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Shin H, Kim Y, Han D, Hur HG. Emergence of High Level Carbapenem and Extensively Drug Resistant Escherichia coli ST746 Producing NDM-5 in Influent of Wastewater Treatment Plant, Seoul, South Korea. Front Microbiol 2021; 12:645411. [PMID: 33833746 PMCID: PMC8021692 DOI: 10.3389/fmicb.2021.645411] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/04/2021] [Indexed: 12/26/2022] Open
Abstract
High level carbapenem and extensively drug resistant (XDR) Escherichia coli strain N7, which produces a variant of New Delhi metallo-β-lactamase (NDM-5), was isolated from the influent of the Jungnang wastewater treatment plant located on Han River, Seoul, South Korea. Phenotypic and genotypic resistances to carbapenem were tested using agar and broth dilution methods, and polymerase chain reaction. Whole-genome sequencing was performed to characterize the genetic structure of strain N7. E. coli strain N7, which harbors the bla NDM-5 gene, showed high level of carbapenem resistance at concentrations of doripenem (512 mg/L) and meropenem (256 mg/L), and XDR to 15 antibiotics. Based on the genomic sequence analysis, two plasmids, a hybrid IncHI2/N-type and an IncX3 type, were present. The former contains a cluster (bla NDM-5-ble MBL -trpF-dsbD) bracketed by multi-insertional sequences, IS3000, ISAba125, IS5, and IS26. The latter carries the following resistance genes: bla CTX-14, aac(3)-IV, aadA1, aadA2, aph(3')-Ia, aph(4)-Ia, sul1, sul2, sul3, dfrA12, fosA3, oqxA, oqxB, mph(A), and floR, and cmlA1. The chromosome, contig3, and contig5 also carry bla CTX-64 and mdf(A), tet(A), and erm(B), tet(M) and aadA22, respectively. Strain N7 also harbors virulence factors such as fimH, flu, ecpABCDE, sfmA, hlyE, and gadA. This study demonstrates the emergence of high level carbapenem resistant XDR E. coli strain N7 containing bla NDM-5 in aquatic environment, Seoul, South Korea. Due to the presence of mobile genetic elements, this strain could horizontally transfer resistance genes, including bla NDM-5 to environmental bacteria. Thus, it is necessary to conduct continuous surveillance for carbapenem resistance in various aquatic environments.
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Affiliation(s)
- Hanseob Shin
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Yeonghyeon Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Dukki Han
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, South Korea
- Department of Marine Molecular Bioscience, Gangneung-Wonju National University, Gangneung, South Korea
| | - Hor-Gil Hur
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, South Korea
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18
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Juraschek K, Borowiak M, Tausch SH, Malorny B, Käsbohrer A, Otani S, Schwarz S, Meemken D, Deneke C, Hammerl JA. Outcome of Different Sequencing and Assembly Approaches on the Detection of Plasmids and Localization of Antimicrobial Resistance Genes in Commensal Escherichia coli. Microorganisms 2021; 9:microorganisms9030598. [PMID: 33799479 PMCID: PMC8000739 DOI: 10.3390/microorganisms9030598] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 01/01/2023] Open
Abstract
Antimicrobial resistance (AMR) is a major threat to public health worldwide. Currently, AMR typing changes from phenotypic testing to whole-genome sequence (WGS)-based detection of resistance determinants for a better understanding of the isolate diversity and elements involved in gene transmission (e.g., plasmids, bacteriophages, transposons). However, the use of WGS data in monitoring purposes requires suitable techniques, standardized parameters and approved guidelines for reliable AMR gene detection and prediction of their association with mobile genetic elements (plasmids). In this study, different sequencing and assembly strategies were tested for their suitability in AMR monitoring in Escherichia coli in the routines of the German National Reference Laboratory for Antimicrobial Resistances. To assess the outcomes of the different approaches, results from in silico predictions were compared with conventional phenotypic- and genotypic-typing data. With the focus on (fluoro)quinolone-resistant E.coli, five qnrS-positive isolates with multiple extrachromosomal elements were subjected to WGS with NextSeq (Illumina), PacBio (Pacific BioSciences) and ONT (Oxford Nanopore) for in depth characterization of the qnrS1-carrying plasmids. Raw reads from short- and long-read sequencing were assembled individually by Unicycler or Flye or a combination of both (hybrid assembly). The generated contigs were subjected to bioinformatics analysis. Based on the generated data, assembly of long-read sequences are error prone and can yield in a loss of small plasmid genomes. In contrast, short-read sequencing was shown to be insufficient for the prediction of a linkage of AMR genes (e.g., qnrS1) to specific plasmid sequences. Furthermore, short-read sequencing failed to detect certain duplications and was unsuitable for genome finishing. Overall, the hybrid assembly led to the most comprehensive typing results, especially in predicting associations of AMR genes and mobile genetic elements. Thus, the use of different sequencing technologies and hybrid assemblies currently represents the best approach for reliable AMR typing and risk assessment.
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Affiliation(s)
- Katharina Juraschek
- Epidemiology, Zoonoses and Antimicrobial Resistance, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany;
- Correspondence: (K.J.); (J.A.H.)
| | - Maria Borowiak
- Study Centre for Genome Sequencing and Analysis, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany; (M.B.); (S.H.T.); (B.M.); (C.D.)
| | - Simon H. Tausch
- Study Centre for Genome Sequencing and Analysis, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany; (M.B.); (S.H.T.); (B.M.); (C.D.)
| | - Burkhard Malorny
- Study Centre for Genome Sequencing and Analysis, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany; (M.B.); (S.H.T.); (B.M.); (C.D.)
| | - Annemarie Käsbohrer
- Epidemiology, Zoonoses and Antimicrobial Resistance, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany;
- Unit for Veterinary Public Health and Epidemiology, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Saria Otani
- DTU Food, National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, 2800 Kgs Lyngby, Denmark;
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany;
| | - Diana Meemken
- Institute of Food Safety and Food Hygiene, Working Group Meat Hygiene, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany;
| | - Carlus Deneke
- Study Centre for Genome Sequencing and Analysis, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany; (M.B.); (S.H.T.); (B.M.); (C.D.)
| | - Jens Andre Hammerl
- Epidemiology, Zoonoses and Antimicrobial Resistance, German Federal Institute for Risk Assessment (BfR), Max-Dohrn Str. 8-10, 10589 Berlin, Germany;
- Correspondence: (K.J.); (J.A.H.)
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Trotta A, Cirilli M, Marinaro M, Bosak S, Diakoudi G, Ciccarelli S, Paci S, Buonavoglia D, Corrente M. Detection of multi-drug resistance and AmpC β-lactamase/extended-spectrum β-lactamase genes in bacterial isolates of loggerhead sea turtles (Caretta caretta) from the Mediterranean Sea. MARINE POLLUTION BULLETIN 2021; 164:112015. [PMID: 33513540 DOI: 10.1016/j.marpolbul.2021.112015] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/11/2021] [Accepted: 01/14/2021] [Indexed: 06/12/2023]
Abstract
Sea turtles are useful sentinels to monitor the dissemination of antimicrobial resistance (AMR) in the marine coastal ecosystems. Forty Gram negative bacteria were isolated from wounds of 52 injured Caretta caretta, living in the Mediterranean Sea. Bacteria were identified using 16S rRNA gene sequencing and tested for susceptibility to 15 antibiotics. In addition, NGS amplicon sequencing was performed to detect the presence of AmpC β-lactamase genes (blaAmpC) and extended-spectrum β-lactamase (ESBL) genes (blaCTX-M,blaSHV,blaTEM). Seventy-five percent of the isolates (30/40 isolates) exhibited multidrug resistance (MDR) phenotypes and 32.5% (13/40 isolates) were confirmed to be positive for at least one gene. The variants of ESBLs genes were blaCTX-M-3,blaTEM-236 and blaSHV-12. Variants of the blaAmpCβ-lactamase gene i.e., blaACT-24, blaACT-2, blaACT-17, blaDHA-4 and blaCMY-37, were also detected. In addition, 4 isolates were found simultaneously harboring CTX and AmpC genes while 2 strains harbored 3 genes (blaACT-2+TEM-236+SHV-12, and blaCTX-M-3+ACT-24+TEM-236).
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Affiliation(s)
- Adriana Trotta
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. per Casamassima Km 3, 70010 Valenzano, BA, Italy.
| | - Margie Cirilli
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. per Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Mariarosaria Marinaro
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Sunčica Bosak
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia
| | - Georgia Diakoudi
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. per Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Stefano Ciccarelli
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. per Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Serena Paci
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. per Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Domenico Buonavoglia
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. per Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Marialaura Corrente
- Department of Veterinary Medicine, University of Bari "Aldo Moro", Str. Prov. per Casamassima Km 3, 70010 Valenzano, BA, Italy
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20
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Rochegüe T, Haenni M, Cazeau G, Metayer V, Madec JY, Ferry T, Lupo A. An inventory of 44 qPCR assays using hydrolysis probes operating with a unique amplification condition for the detection and quantification of antibiotic resistance genes. Diagn Microbiol Infect Dis 2021; 100:115328. [PMID: 33819858 DOI: 10.1016/j.diagmicrobio.2021.115328] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/22/2021] [Accepted: 01/24/2021] [Indexed: 01/28/2023]
Abstract
Early antibiotic resistance determinants (ARDs) detection in humans or animals is crucial to counteract their propagation. The ARDs quantification is fundamental to understand the perturbation caused by disruptors, such as antibiotics, during therapies. Forty-three qPCRs on the most diffused ARDs and integrons among human and animal Enterobacterales, and one on the 16S rDNA for bacteria quantification, were developed. The qPCRs, using hydrolysis probes, operated with a unique amplification condition and were tested analytically and diagnostically performing 435 reactions on five positive and negative controls for each qPCR. Diagnostic sensitivity and specificity were confirmed by PCR and genome sequencing of control isolates, demonstrating 100% performance for all qPCRs. An easy and rapid discrimination method for the epidemiologically relevant blaCTX-Ms is provided. This large, noncommercial qPCRs inventory could serve for precise quantification of ARDs, but also as a rapid screening tool for surveillance purposes, providing the basis for further high-throughput developments.
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Affiliation(s)
- Tony Rochegüe
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Lyon, France
| | - Marisa Haenni
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Lyon, France
| | - Géraldine Cazeau
- ANSES - Université de Lyon, Unité Epidémiologie et Appui à la Surveillance (EAS), Lyon, France
| | - Véronique Metayer
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Lyon, France
| | - Jean-Yves Madec
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Lyon, France
| | - Tristan Ferry
- Service des maladies infectieuses et tropicales, CHU de Lyon, Hôpital de la Croix-Rousse, Lyon, France; Centre International de Recherche en Infectiologie, CIRI, Inserm U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Lyon, France
| | - Agnese Lupo
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Lyon, France.
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21
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Liu B, Shui L, Zhou K, Jiang Y, Li X, Guan J, Li Q, Zhuo C. Impact of Plasmid-Encoded H-NS-like Protein on blaNDM-1-Bearing IncX3 Plasmid in Escherichia coli. J Infect Dis 2021; 221:S229-S236. [PMID: 32176784 DOI: 10.1093/infdis/jiz567] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND This study was performed to assess the role of the histone-like nucleoid-structuring (H-NS)-like protein, carried by blaNDM-1-encoding IncX3-type plasmids, in the dissemination of IncX3 plasmids. METHODS The blaNDM-1-encoding IncX3 plasmids were analyzed using southern blot, conjugation, and competition assays. Virulence was evaluated with a Galleria mellonella infection model. An hns-knockout IncX3 plasmid was also constructed to identify the functions of plasmid-borne H-NS-like protein in Escherichia coli. RESULTS The assasys detected blaNDM-1-encoding IncX3-type plasmids with similar fingerprint patterns in all New Delhi metallo-β-lactamase (NDM) 1-producing carbapenem-resistant Enterobacteriaceae. The IncX3 plasmid conferred a fitness advantage to E. coli J53 but had no effect on host virulence. Moreover, the transconjugation frequency of the hns-null IncX3 plasmid pHN330-△hns was increased by 2.5-fold compared with the wild type. This was caused by up-regulation of conjugation-related plasmid-borne genes and the partition-related gene, in the J330-pHN330-△hns strain. In addition, decreased virulence was detected with this variant. CONCLUSIONS Our results highlight the important role of IncX3 plasmids in the dissemination of blaNDM-1 in south China. Plasmid-encoded H-NS-like protein can inhibit plasmid conjugation, partition, and the expression of related genes, in addition to promoting virulence in the host.
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Affiliation(s)
- Baomo Liu
- State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lili Shui
- State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Kai Zhou
- Shenzhen Institute of Respiratory Diseases, the First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen, China
| | - Ying Jiang
- State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaoyu Li
- State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jing Guan
- State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qi Li
- Pulmonary and Critical Care Medicine Center, Chinese PLA Respiratory Disease Institute, Xinqiao hospital, Army Medical University, Shapingba District, Chongqing, China
| | - Chao Zhuo
- State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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22
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The importance of using whole genome sequencing and extended spectrum beta-lactamase selective media when monitoring antimicrobial resistance. Sci Rep 2020; 10:19880. [PMID: 33199763 PMCID: PMC7670430 DOI: 10.1038/s41598-020-76877-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
To tackle the problem of antimicrobial resistance (AMR) surveillance programmes are in place within Europe applying phenotypic methods, but there are plans for implementing whole genome sequencing (WGS). We tested the benefits of WGS using Escherichia coli collected from pig surveillance performed between 2013 to 2017. WGS was performed on 498 E. coli producing ESBL and AmpC enzymes, recovered from pig caeca on MacConkey + cefotaxime (McC + CTX) agar, as recommended by the European Commission, or ESBL agar, used additionally by United Kingdom. Our results indicated WGS was extremely useful for monitoring trends for specific ESBL genes, as well as a plethora of AMR genotypes, helping to establish their prevalence and co-linkage to certain plasmids. Recovery of isolates with multi-drug resistance (MDR) genotypes was lower from McC + CTX than ESBL agar. The most widespread ESBL genes belonged to the blaCTX-M family. blaCTX-M-1 dominated all years, and was common in two highly stable IncI1 MDR plasmids harbouring (blaCTX-M-1,sul2, tetA) or (blaCTX-M-1, aadA5, sul2, dfrA17), in isolates which were phylogenetically dissimilar, suggesting plasmid transmission. Therefore, WGS provided a wealth of data on prevalence of AMR genotypes and plasmid persistence absent from phenotypic data and, also, demonstrated the importance of culture media for detecting ESBL E. coli.
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23
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Apostolakos I, Feudi C, Eichhorn I, Palmieri N, Fasolato L, Schwarz S, Piccirillo A. High-resolution characterisation of ESBL/pAmpC-producing Escherichia coli isolated from the broiler production pyramid. Sci Rep 2020; 10:11123. [PMID: 32636426 PMCID: PMC7341882 DOI: 10.1038/s41598-020-68036-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 05/29/2020] [Indexed: 12/16/2022] Open
Abstract
The presence of extended-spectrum β-lactamase (ESBL) or plasmid-mediated AmpC β-lactamase (pAmpC)-producing Escherichia coli (ESBL/pAmpC-EC) in livestock is a public health risk given the likelihood of their transmission to humans via the food chain. We conducted whole genome sequencing on 100 ESBL/pAmpC-EC isolated from the broiler production to explore their resistance and virulence gene repertoire, characterise their plasmids and identify transmission events derived from their phylogeny. Sequenced isolates carried resistance genes to four antimicrobial classes in addition to cephalosporins. Virulence gene analysis assigned the majority of ESBL/pAmpC-EC to defined pathotypes. In the complex genetic background of ESBL/pAmpC-EC, clusters of closely related isolates from various production stages were identified and indicated clonal transmission. Phylogenetic comparison with publicly available genomes suggested that previously uncommon ESBL/pAmpC-EC lineages could emerge in poultry, while others might contribute to the maintenance and dissemination of ESBL/pAmpC genes in broilers. The majority of isolates from diverse E. coli lineages shared four dominant plasmids (IncK2, IncI1, IncX3 and IncFIB/FII) with identical ESBL/pAmpC gene insertion sites. These plasmids have been previously reported in diverse hosts, including humans. Our findings underline the importance of specific plasmid groups in the dissemination of cephalosporin resistance genes within the broiler industry and across different reservoirs.
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Affiliation(s)
- Ilias Apostolakos
- Department of Comparative Biomedicine and Food Science, University of Padua, 35020, Padua, Italy
| | - Claudia Feudi
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
| | - Inga Eichhorn
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
| | - Nicola Palmieri
- Department for Farm Animals and Veterinary Public Health, University Clinic for Poultry and Fish Medicine, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Luca Fasolato
- Department of Comparative Biomedicine and Food Science, University of Padua, 35020, Padua, Italy
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
| | - Alessandra Piccirillo
- Department of Comparative Biomedicine and Food Science, University of Padua, 35020, Padua, Italy.
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24
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Zhai R, Fu B, Shi X, Sun C, Liu Z, Wang S, Shen Z, Walsh TR, Cai C, Wang Y, Wu C. Contaminated in-house environment contributes to the persistence and transmission of NDM-producing bacteria in a Chinese poultry farm. ENVIRONMENT INTERNATIONAL 2020; 139:105715. [PMID: 32315891 DOI: 10.1016/j.envint.2020.105715] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/28/2020] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
While carbapenem use is prohibited in the poultry production chain and carbapenem-resistant Enterobacteriaceae (CRE) are absent from hatchery farms, New Delhi metallo-β-lactamase-producing CRE contamination of commercial broiler chicken farms (grow-out farms) can occur via living hosts such as flies. However, it is not known whether the inanimate factors from in-house environment play a role in the persistence of CRE on commercial farms. Herein, we monitored one typical broiler house in Hebei Province, China, from January 2017 to April 2018. We collected 350 cloacal samples from four broiler batches along with 582 environmental samples (194 in the raising period and 388 in the vacancy period) from sites including the surfaces of drooping boards, feeding troughs, nipple drinkers, corridor floors, sewage trenches, and air. All samples were screened for blaNDM and cultured for NDM-producing isolates. The resistance profiles, genotypes, and genetic context of blaNDM in CRE isolates were further characterized. Results showed that 1-day-old broilers, which were transferred from a hatchery farm and negative for CRE, acquired blaNDM within 24 h of transfer (2 days of age), with a detection rate of up to 18.6%. High blaNDM detection rates (26.8%-31.4%) were obtained among all environmental samples except air after standard cleaning and disinfection during the vacancy period. blaNDM carriage rates (52.9%-72.9%) within the flocks remain stable and high across the next three broiler batches. Overall, 279 NDM-producing bacteria, including 259 Enterobacteriaceae (8 species), 14 Morganellaceae (3 species), three Alcaligenes faecalis and three Pseudomonas putida isolates, were recovered from 85 (24.3%) cloacal and 101 (17.4%) environmental samples. Three NDM variants, including NDM-5 (n = 181), NDM-1 (n = 92), and NDM-9 (n = 3), and a novel NDM-like-metallo-β-lactamase (NLM, n = 3) were identified among the samples. The predominant NDM-producing CRE species among the samples were Klebsiella pneumoniae (CRKP; 32.6%, n = 91) and Escherichia coli (CREC; 27.2%, n = 76). Both clonal and horizontal transmission of blaNDM and an overlap of sequence types (STs) were observed in both CREC and CRKP from chicken and environmental samples. Notably, ST6751 CREC and ST37 CRKP persisted throughout the 16-month surveillance period. IncX3 (n = 197, 7 species), IncA/C2 (n = 41, 5 species), and IncFII (n = 8, E. coli) were the three major blaNDM-carrying plasmid types among the isolates. Although routine cleaning and disinfection procedures and "all-in/all-out" management were performed, once introduced to the farm environment, a diverse range of NDM-positive isolates may survive and persist, becoming an important reservoir of NDM-positive CRE for broiler chickens. Therefore, cleaning and disinfection procedures should be improved on poultry farms to avoid cross-contamination of NDM-producing bacteria between different batches of chickens, as well as further downstream in the poultry production chain.
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Affiliation(s)
- Ruidong Zhai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Bo Fu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiaomin Shi
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chengtao Sun
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhihai Liu
- Agricultural Bio-pharmaceutical Laboratory, College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, China
| | - Shaolin Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhangqi Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Timothy R Walsh
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China; Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Heath Park Hospital, Cardiff, United Kingdom
| | - Chang Cai
- China Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology, Zhejiang Agricultural and Forestry University, Hangzhou, China; Research and Innovation Office, Murdoch University, Murdoch, Australia
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.
| | - Congming Wu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.
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25
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Flerlage T, Brazelton de Cardenas JN, Garner CD, Hasan NA, Karathia H, Qudeimat A, Maron G, Hayden R. Multiple NDM-5-Expressing Escherichia Coli Isolates From an Immunocompromised Pediatric Host. Open Forum Infect Dis 2020; 7:ofaa018. [PMID: 32047833 PMCID: PMC7003983 DOI: 10.1093/ofid/ofaa018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 01/09/2020] [Indexed: 11/17/2022] Open
Abstract
Background Genes conferring carbapenem resistance have disseminated worldwide among Gram-negative bacteria. Here we present longitudinal changes in clinically obtained Escherichia coli isolates from 1 immunocompromised pediatric patient. This report demonstrates potential for antibiotic resistance genes and plasmids to emerge over time in clinical isolates from patients receiving intensive anticancer chemotherapy and broad-spectrum antibiotics. Methods Thirty-three isolates obtained over 7 months from 1 patient were included. Clinical data were abstracted from the medical record. For each isolate, studies included phenotypic antibacterial resistance patterns, sequence typing, bacterial isolate sequencing, plasmid identification, and antibiotic resistance gene identification. Results Sites of isolation included blood, wound culture, and culture for surveillance purposes from the perianal area. Isolates were of 5 sequence types (STs). All were resistant to multiple classes of antibiotics; 23 (69.6%) were phenotypically resistant to all carbapenems. The blaNDM-5 gene was identified in 22 (67%) isolates, all of ST-167 and ST-940, and appeared to coincide with the presence of the IncFII and IncX3 plasmid. Conclusions We present unique microbiologic data from 33 multidrug-resistant E. coli isolates obtained over the course of 7 months from an individual patient in the United States. Two E. coli sequence types causing invasive infection in the same patient and harboring the blaNDM-5 gene, encoded on the IncX3 plasmid and the IncFII plasmid, were identified. This study highlights the emergence of multidrug-resistant bacteria on antibiotic therapy and the necessity of adequate neutrophil number and function in the clearance of bacteremia.
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Affiliation(s)
- Tim Flerlage
- Division of Pediatric Critical Care Medicine, Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA.,Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Cherilyn D Garner
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Nur A Hasan
- CosmosID Incorporated, Rockville, Maryland, USA
| | | | - Amr Qudeimat
- Department of Bone Marrow Transplant and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Gabriela Maron
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Randall Hayden
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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26
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Mouftah SF, Pál T, Darwish D, Ghazawi A, Villa L, Carattoli A, Sonnevend Á. Epidemic IncX3 plasmids spreading carbapenemase genes in the United Arab Emirates and worldwide. Infect Drug Resist 2019; 12:1729-1742. [PMID: 31417290 PMCID: PMC6593741 DOI: 10.2147/idr.s210554] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/27/2019] [Indexed: 12/31/2022] Open
Abstract
Purpose Plasmids of the incompatibility group X type 3 (IncX3) were described carrying various carbapenemase genes in carbapenemase-producing Enterobacteriaceae (CPE) worldwide and in the United Arab Emirates (UAE), as well. To understand the driving force behind the emergence of such plasmids in the UAE, the relationship between IncX3 plasmids encountered locally and globally was investigated. Methods CPE strains isolated in the UAE during 2009-2014 were screened by X3 PCR-based replicon typing. The clonal relationship of CPE carrying IncX3 plasmids was determined by multi-locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Complete sequence of selected IncX3 plasmids was determined. Phylogenetic relationship between the carbapenemase carrying IncX3 plasmids from the UAE and of those reported worldwide was established by comparing the plasmid backbones. Results 10.2% of the 295 CPE tested were identified to carry IncX3 plasmids: 13 Escherichia coli, 13 Klebsiella pneumoniae, two Enterobacter cloacae, one Citrobacter freundii and one Morganella morganii isolate, respectively. Most of them were non-clonal; with small clusters of triplets and pairs of E. coli and K. pneumoniae, and a cluster of five K. pneumoniae ST11 exhibiting >90% similar PFGE patterns, respectively. The 30 isolates harbored either bla NDM-1, bla NDM-4, bla NDM-5, bla NDM-7, bla OXA-181 or bla KPC-2 carbapenemase genes on IncX3 plasmids. Phylogenetic analysis of the backbone region of IncX3 plasmids carrying various beta-lactamase genes from the UAE (n=23) and that of North-America, Europe, Asia and Australia (n=35) revealed three clusters based on the carbapenemase genes carried: plasmids harboring bla OXA-181 and bla NDM-5 formed two distinct groups, whereas backbones of plasmids with bla NDM-1, bla NDM-4 and bla NDM-7 clustered together. Each cluster contained plasmids of diverse geographical origin. Conclusion The findings suggest that different carbapenemase gene carrying IncX3 plasmids encountered in the UAE do not evolve locally, rather are subtypes of this epidemic plasmid emerging in this country due to international transfer.
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Affiliation(s)
- Shaimaa F Mouftah
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Tibor Pál
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Dania Darwish
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Akela Ghazawi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Laura Villa
- Department of Infectious Diseases, Istituto Superiore di Sanitá, Rome, Italy
| | - Alessandra Carattoli
- Department of Molecular Microbiology, University of Rome La Sapienza, Rome, Italy
| | - Ágnes Sonnevend
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates.,Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
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27
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Brinkac LM, White R, D'Souza R, Nguyen K, Obaro SK, Fouts DE. Emergence of New Delhi Metallo-β-Lactamase (NDM-5) in Klebsiella quasipneumoniae from Neonates in a Nigerian Hospital. mSphere 2019; 4:e00685-18. [PMID: 30867330 PMCID: PMC6416368 DOI: 10.1128/msphere.00685-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/25/2019] [Indexed: 01/08/2023] Open
Abstract
Outbreaks of infection occur more often than they are reported in most developing countries, largely due to poor diagnostic services. A Klebsiella species bacteremia outbreak in a newborn unit with high mortality was recently encountered at a location being surveilled for childhood bacteremia. These surveillance efforts offered the opportunity to determine the cause of this neonatal outbreak. In this report, we present the whole-genome sequences of New Delhi metallo-β-lactamase (NDM-5)-containing Klebsiella quasipneumoniae subsp. similipneumoniae bloodstream isolates from a neonatal bacteremia outbreak at a tertiary hospital in Nigeria and as part of the largest collection of K. pneumoniae bloodstream isolates from children in Africa. Comparative analysis of the genetic environment surrounding the NDM-5 genes revealed nearly perfect sequence identity to blaNDM-5-bearing IncX3-type plasmids from other members of the EnterobacteriaceaeIMPORTANCE Carbapenem-resistant Klebsiella pneumoniae is of global health importance, yet there is a paucity of genome-based studies in Africa. Here we report fatal blood-borne NDM-5-producing K. quasipneumoniae subsp. similipneumoniae infections from Nigeria, Africa. New Delhi metallo-β-lactamase (NDM)-producing Klebsiella spp. are responsible for high mortality and morbidity, with the NDM-5 variant showing elevated carbapenem resistance. The prevalence of NDM-5 in Klebsiella has been limited primarily to K. pneumoniae, with only one isolate being collected from Africa. During an outbreak of sepsis in a teaching hospital in Nigeria, five NDM-5-producing K. quasipneumoniae subsp. similipneumoniae sequence type 476 isolates were identified. Given the increased resistance profile of these strains, this study highlights the emerging threat of blaNDM-5 dissemination in hospital environments. The observation of these NDM-5-producing isolates in Africa stresses the urgency to improve monitoring and clinical practices to reduce or prevent the further spread of resistance.
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Affiliation(s)
| | | | | | - Kevin Nguyen
- J. Craig Venter Institute, Rockville, Maryland, USA
| | - Stephen K Obaro
- University of Nebraska Medical Center, Omaha, Nebraska, USA
- Department of Pediatrics, University of Abuja Teaching Hospital, Abuja, Nigeria
- International Foundation against Infectious Diseases in Nigeria (IFAIN), Abuja, Nigeria
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28
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Ceccarelli D, Kant A, van Essen-Zandbergen A, Dierikx C, Hordijk J, Wit B, Mevius DJ, Veldman KT. Diversity of Plasmids and Genes Encoding Resistance to Extended Spectrum Cephalosporins in Commensal Escherichia coli From Dutch Livestock in 2007-2017. Front Microbiol 2019; 10:76. [PMID: 30778339 PMCID: PMC6369715 DOI: 10.3389/fmicb.2019.00076] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/15/2019] [Indexed: 11/13/2022] Open
Abstract
Extended-spectrum β-lactamase (ESBL) and plasmid-mediated AmpC β-lactamase (pAmpC) genes confer resistance to extended spectrum cephalosporin’s. The spread of these genes is mostly facilitated by plasmid-mediated horizontal transfer. National surveillance activities to detect ESBL/pAmpC-producers in commensal bacteria from livestock are in place in the Netherlands since several years. This study aimed at reporting gene and plasmid diversity of commensal ESBL/pAmpC-producing Escherichia coli isolated from healthy animals during surveillance activities between 2007 and 2017. A collection of 2304 extended-spectrum cephalosporin-resistant (ESC-R) E. coli isolated from feces of broilers, dairy cattle, slaughter pigs, turkeys, ducks, and veal calves was investigated and ESBL/pAmpC genes were determined. Gene location of a selection of 473 E. coli isolates was determined and typing of plasmids linked to the ESBL/pAmpC genes was performed. Twenty-two different ESBL/pAmpC genes were identified with blaCTX-M-1 being the most prevalent gene in livestock (43.7%), followed by blaCMY -2 and blaSHV -12, independent of the animal source. Prevalence of typically human associated blaCTX-M-15 was highest in cattle. Less than 10% E. coli isolates owed their ESC-R phenotype to promoter mutations of the chromosomal ampC gene. Majority (92%) of ESBL/pAmpC genes analyzed were plasmid located, with IncI1α being the most represented plasmid family in isolates from all animals, followed by IncF (veal calves, dairy cattle and slaughter pigs), IncK (broilers and laying hens), IncX1 in broilers, and emerging IncX3 in broilers and dairy cattle. Prevalence and molecular diversity of ESC-R E. coli isolated from livestock over an 11-year period revealed a composite scenario of gene-plasmid combinations.
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Affiliation(s)
- Daniela Ceccarelli
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Arie Kant
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | | | - Cindy Dierikx
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Joost Hordijk
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Ben Wit
- Netherlands Food and Consumer Product Safety Authority (NVWA), Utrecht, Netherlands
| | - Dik J Mevius
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands.,Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Kees T Veldman
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
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29
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Ball TA, Monte DF, Aidara-Kane A, Matheu-Alvarez J, Ru H, Thakur S, Horovitz J, Ejobi F, Lacher DW, Fedorka-Cray PJ. Phenotypic and Genotypic Characterization of Escherichia coli and Salmonella enterica from Dairy Cattle Farms in the Wakiso District, Uganda: A Cross-Sectional Study. Foodborne Pathog Dis 2019; 16:54-59. [DOI: 10.1089/fpd.2018.2528] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Takiyah A. Ball
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Daniel F. Monte
- Department of Food and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Awa Aidara-Kane
- Department of Food Safety and Zoonoses, World Health Organization (WHO), Geneva, Switzerland
| | - Jorge Matheu-Alvarez
- Department of Food Safety and Zoonoses, World Health Organization (WHO), Geneva, Switzerland
| | - Hongyu Ru
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Joy Horovitz
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
| | - Francis Ejobi
- Department of Bio Security, Ecosystems, and Veterinary Public Health, College of Veterinary Medicine, Animal Resources & Biosecurity, Makerere University, Kampala, Uganda
| | - David W. Lacher
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland
| | - Paula J. Fedorka-Cray
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina
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