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Agustinho DP, Fu Y, Menon VK, Metcalf GA, Treangen TJ, Sedlazeck FJ. Unveiling microbial diversity: harnessing long-read sequencing technology. Nat Methods 2024; 21:954-966. [PMID: 38689099 DOI: 10.1038/s41592-024-02262-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 03/29/2024] [Indexed: 05/02/2024]
Abstract
Long-read sequencing has recently transformed metagenomics, enhancing strain-level pathogen characterization, enabling accurate and complete metagenome-assembled genomes, and improving microbiome taxonomic classification and profiling. These advancements are not only due to improvements in sequencing accuracy, but also happening across rapidly changing analysis methods. In this Review, we explore long-read sequencing's profound impact on metagenomics, focusing on computational pipelines for genome assembly, taxonomic characterization and variant detection, to summarize recent advancements in the field and provide an overview of available analytical methods to fully leverage long reads. We provide insights into the advantages and disadvantages of long reads over short reads and their evolution from the early days of long-read sequencing to their recent impact on metagenomics and clinical diagnostics. We further point out remaining challenges for the field such as the integration of methylation signals in sub-strain analysis and the lack of benchmarks.
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Affiliation(s)
- Daniel P Agustinho
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA
| | - Yilei Fu
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Vipin K Menon
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA
- Senior research project manager, Human Genetics, Genentech, South San Francisco, CA, USA
| | - Ginger A Metcalf
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA
| | - Todd J Treangen
- Department of Computer Science, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
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Sobkowiak A, Scherff N, Schuler F, Bletz S, Mellmann A, Schwierzeck V, van Almsick V. Plasmid-encoded gene duplications of extended-spectrum β-lactamases in clinical bacterial isolates. Front Cell Infect Microbiol 2024; 14:1343858. [PMID: 38469349 PMCID: PMC10925753 DOI: 10.3389/fcimb.2024.1343858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/02/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction The emergence of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is an urgent and alarming One Health problem. This study aimed to investigate duplications of plasmid-encoded ESBL genes and their impact on antimicrobial resistance (AMR) phenotypes in clinical and screening isolates. Methods Multi-drug-resistant bacteria from hospitalized patients were collected during routine clinical surveillance from January 2022 to June 2023, and their antimicrobial susceptibility patterns were determined. Genotypes were extracted from long-read whole-genome sequencing data. Furthermore, plasmids and other mobile genetic elements associated with ESBL genes were characterized, and the ESBL genes were correlated to ceftazidime minimal inhibitory concentration (MIC). Results In total, we identified four cases of plasmid-encoded ESBL gene duplications that match four genetically similar plasmids during the 18-month surveillance period: five Escherichia coli and three Klebsiella pneumoniae isolates. As the ESBL genes were part of transposable elements, the surrounding sequence regions were duplicated as well. In-depth analysis revealed insertion sequence (IS)-mediated transposition mechanisms. Isolates with duplicated ESBL genes exhibited a higher MIC for ceftazidime in comparison to isolates with a single gene copy (3-256 vs. 1.5-32 mg/L, respectively). Conclusion ESBL gene duplications led to an increased phenotypic resistance against ceftazidime. Our data suggest that ESBL gene duplications by an IS-mediated transposition are a relevant mechanism for how AMR develops in the clinical setting and is part of the microevolution of plasmids.
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Affiliation(s)
- Annika Sobkowiak
- Institute of Hygiene, University Hospital Münster, Münster, Germany
- Department of Cardiology I – Coronary and Peripheral Vascular Disease, Heart Failure, University Hospital Münster, Münster, Germany
| | - Natalie Scherff
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | - Franziska Schuler
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Stefan Bletz
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | | | - Vera Schwierzeck
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | - Vincent van Almsick
- Institute of Hygiene, University Hospital Münster, Münster, Germany
- Department of Cardiology I – Coronary and Peripheral Vascular Disease, Heart Failure, University Hospital Münster, Münster, Germany
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Blau K, Berger FK, Mellmann A, Gallert C. Clostridioides difficile from Fecally Contaminated Environmental Sources: Resistance and Genetic Relatedness from a Molecular Epidemiological Perspective. Microorganisms 2023; 11:2497. [PMID: 37894155 PMCID: PMC10608975 DOI: 10.3390/microorganisms11102497] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Clostridioides difficile is the most important pathogen causing antimicrobial-associated diarrhea and has recently been recognized as a cause of community-associated C. difficile infection (CA-CDI). This study aimed to characterize virulence factors, antimicrobial resistance (AMR), ribotype (RT) distribution and genetic relationship of C. difficile isolates from diverse fecally contaminated environmental sources. C. difficile isolates were recovered from different environmental samples in Northern Germany. Antimicrobial susceptibility testing was determined by E-test or disk diffusion method. Toxin genes (tcdA and tcdB), genes coding for binary toxins (cdtAB) and ribotyping were determined by PCR. Furthermore, 166 isolates were subjected to whole genome sequencing (WGS) for core genome multi-locus sequence typing (cgMLST) and extraction of AMR and virulence-encoding genes. Eighty-nine percent (148/166) of isolates were toxigenic, and 51% (76/148) were positive for cdtAB. Eighteen isolates (11%) were non-toxigenic. Thirty distinct RTs were identified. The most common RTs were RT127, RT126, RT001, RT078, and RT014. MLST identified 32 different sequence types (ST). The dominant STs were ST11, followed by ST2, ST3, and ST109. All isolates were susceptible to vancomycin and metronidazole and displayed a variable rate of resistance to moxifloxacin (14%), clarithromycin (26%) and rifampicin (2%). AMR genes, such as gyrA/B, blaCDD-1/2, aph(3')-llla-sat-4-ant(6)-la cassette, ermB, tet(M), tet(40), and tetA/B(P), conferring resistance toward fluoroquinolone, beta-lactam, aminoglycoside, macrolide and tetracycline antimicrobials, were found in 166, 137, 29, 32, 21, 72, 17, and 9 isolates, respectively. Eleven "hypervirulent" RT078 strains were detected, and several isolates belonged to RTs (i.e., RT127, RT126, RT023, RT017, RT001, RT014, RT020, and RT106) associated with CA-CDI, indicating possible transmission between humans and environmental sources pointing out to a zoonotic potential.
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Affiliation(s)
- Khald Blau
- Department of Microbiology–Biotechnology, Faculty of Technology, University of Applied Sciences Emden/Leer, 26723 Emden, Germany;
| | - Fabian K. Berger
- Institute of Medical Microbiology and Hygiene, Saarland University Medical Center, 66421 Homburg, Germany;
- German National Reference Center for Clostridioides Difficile, 66421 Homburg, Germany;
| | - Alexander Mellmann
- German National Reference Center for Clostridioides Difficile, 66421 Homburg, Germany;
- Institute of Hygiene, University of Münster, 48149 Münster, Germany
| | - Claudia Gallert
- Department of Microbiology–Biotechnology, Faculty of Technology, University of Applied Sciences Emden/Leer, 26723 Emden, Germany;
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Wiethoff JP, Sandmann S, Theiler T, Nze Nkogue C, Akomo-Okoue EF, Varghese J, Kreidenweiss A, Mellmann A, Lell B, Adegnika AA, Held J, Schaumburg F. Pharyngeal Communities and Antimicrobial Resistance in Pangolins in Gabon. Microbiol Spectr 2023; 11:e0066423. [PMID: 37338382 PMCID: PMC10434165 DOI: 10.1128/spectrum.00664-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023] Open
Abstract
Wildlife can be a reservoir and source of zoonotic pathogens for humans. For instance, pangolins were considered one of the potential animal reservoirs of SARS-CoV-2. The aim of this study was to assess the prevalence of antimicrobial-resistant species (e.g., extended-spectrum β-lactamase [ESBL]-producing Enterobacterales) and Staphylococcus aureus-related complex and to describe the bacterial community in wild Gabonese pangolins. The pharyngeal colonization of pangolins sold in Gabon (n = 89, 2021 to 2022) was analyzed using culture media selective for ESBL-producing Enterobacterales, S. aureus-related complex, Gram-positive bacteria and nonfermenters. Phylogenetic analyses of ESBL-producing Enterobacterales was done using core-genome multilocus sequence typing (cgMLST) and compared with publicly available genomes. Patterns of cooccurring species were detected by network analysis. Of the 439 bacterial isolates, the majority of species belonged to the genus Pseudomonas (n = 170), followed by Stenotrophomonas (n = 113) and Achromobacter (n = 37). Three Klebsiella pneumoniae isolates and one Escherichia coli isolate were ESBL-producers, which clustered with human isolates from Nigeria (MLST sequence type 1788 [ST1788]) and Gabon (ST38), respectively. Network analysis revealed a frequent cooccurrence of Stenotrophomonas maltophilia with Pseudomonas putida and Pseudomonas aeruginosa. In conclusion, pangolins can be colonized with human-related ESBL-producing K. pneumoniae and E. coli. Unlike in other African wildlife, S. aureus-related complex was not detected in pangolins. IMPORTANCE There is an ongoing debate if pangolins are a relevant reservoir for viruses such as SARS-CoV-2. Here, we wanted to know if African pangolins are colonized with bacteria that are relevant for human health. A wildlife reservoir of antimicrobial resistance would be of medical relevance in regions were consumption of so-called bushmeat is common. In 89 pangolins, we found three ESBL-producing Klebsiella pneumoniae strains and one ESBL-producing Escherichia coli strains, which were closely related to isolates from humans in Africa. This points toward either a transmission between pangolins and humans or a common source from which both humans and pangolins became colonized.
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Affiliation(s)
- Johanna P. Wiethoff
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Tübingen, Germany
| | - Sarah Sandmann
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Tom Theiler
- Institute of Medical Microbiology, University of Münster, Münster, Germany
| | | | | | - Julian Varghese
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Andrea Kreidenweiss
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Tübingen, Germany
| | | | - Bertrand Lell
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Tübingen, Germany
| | - Ayôla A. Adegnika
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Tübingen, Germany
| | - Jana Held
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Tübingen, Germany
| | - Frieder Schaumburg
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- Institute of Medical Microbiology, University of Münster, Münster, Germany
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Editorial for the Special Issue “Antimicrobial Resistance and Genetic Elements in Bacteria”. Microorganisms 2023; 11:microorganisms11030670. [PMID: 36985240 PMCID: PMC10058548 DOI: 10.3390/microorganisms11030670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Throughout human history, bacterial infections have been an omnipresent threat, which have, on occasion, resulted in devastating pandemics affecting humanity [...]
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Ghenea AE, Zlatian OM, Cristea OM, Ungureanu A, Mititelu RR, Balasoiu AT, Vasile CM, Salan AI, Iliuta D, Popescu M, Udriștoiu AL, Balasoiu M. TEM,CTX-M,SHV Genes in ESBL-Producing Escherichia coli and Klebsiella pneumoniae Isolated from Clinical Samples in a County Clinical Emergency Hospital Romania-Predominance of CTX-M-15. Antibiotics (Basel) 2022; 11:antibiotics11040503. [PMID: 35453254 PMCID: PMC9028254 DOI: 10.3390/antibiotics11040503] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 02/01/2023] Open
Abstract
Background: CTX-M betalactamases have shown a rapid spread in the recent years among Enterobacteriaceae and have become the most prevalent Extended Spectrum Beta-Lactamases (ESBLs) in many parts of the world. The introduction and dissemination of antibiotic-resistant genes limits options for treatment, increases mortality and morbidity in patients, and leads to longer hospitalization and expensive costs. We aimed to identify the beta-lactamases circulating encoded by the genes blaCTX-M-15, blaSHV-1 and blaTEM-1 in Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) strains. Furthermore, we established the associated resistance phenotypes among patients hospitalized in the Intensive Care Unit (ICU) from County Clinical Emergency Hospital of Craiova, Romania. Methods: A total of 46 non-duplicated bacterial strains (14 strains of E. coli and 32 strains of K. pneumoniae), which were resistant to ceftazidime (CAZ) and cefotaxime (CTX) by Kirby–Bauer disk diffusion method, were identified using the automated VITEK2 system. Detection of ESBL-encoding genes and other resistance genes was carried out by PCR. Results. E. coli strains were resistant to 3rd generation cephalosporins and moderately resistant to quinolones, whereas K. pneumoniae strains were resistant to penicillins, cephalosporins, and sulfamides, and moderately resistant to quinolones and carbapenems. Most E. coli strains harbored blaCTX-M-15 gene (13/14 strains), a single strain had the blaSHV-1 gene, but 11 strains harbored blaTEM-1 gene. The mcr-1 gene was not detected. We detected tet(A) gene in six strains and tet(B) in one strain. In K. pneumoniae strains we detected blaCTX-M-15 in 23 strains, blaSHV-1 in all strains and blaTEM-1 in 14 strains. The colistin resistance gene mcr-1 was not detected. The tetracycline gene tet(A) was detected in 11 strains, but the gene tet(B) was not detected in any strains. Conclusions. The development in antibiotic resistance highlights the importance of establishing policies to reduce antibiotic use and improving the national resistance surveillance system in order to create local antibiotic therapy guidelines.
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Affiliation(s)
- Alice Elena Ghenea
- Department of Bacteriology-Virology-Parasitology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania; (A.E.G.); (O.M.Z.); (A.U.); (R.R.M.); (M.B.)
| | - Ovidiu Mircea Zlatian
- Department of Bacteriology-Virology-Parasitology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania; (A.E.G.); (O.M.Z.); (A.U.); (R.R.M.); (M.B.)
| | - Oana Mariana Cristea
- Department of Bacteriology-Virology-Parasitology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania; (A.E.G.); (O.M.Z.); (A.U.); (R.R.M.); (M.B.)
- Correspondence: (O.M.C.); (C.M.V.)
| | - Anca Ungureanu
- Department of Bacteriology-Virology-Parasitology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania; (A.E.G.); (O.M.Z.); (A.U.); (R.R.M.); (M.B.)
| | - Radu Razvan Mititelu
- Department of Bacteriology-Virology-Parasitology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania; (A.E.G.); (O.M.Z.); (A.U.); (R.R.M.); (M.B.)
| | - Andrei Theodor Balasoiu
- Department of Ophthalmology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania;
| | - Corina Maria Vasile
- Department of Paediatrics, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
- Correspondence: (O.M.C.); (C.M.V.)
| | - Alex-Ioan Salan
- Department of Oral and Maxillofacial Surgery, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania;
| | - Daniel Iliuta
- Department of Psychiatry, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania;
| | - Mihaela Popescu
- Department of Endocrinology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania;
| | - Anca-Loredana Udriștoiu
- Faculty of Automation, Computers and Electronics, University of Craiova, 200776 Craiova, Romania;
| | - Maria Balasoiu
- Department of Bacteriology-Virology-Parasitology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania; (A.E.G.); (O.M.Z.); (A.U.); (R.R.M.); (M.B.)
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