Genome Sequences of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Recovered from Mid-Stream Urine Samples in Accra, Ghana
Abstract
:1. Introduction
2. Materials and Methods
2.1. Phenotypic Investigations
2.2. Whole-Genome Sequence Analysis of the Isolates
3. Results
3.1. Antimicrobial Resistance and Serotypes of the Isolates
3.2. Overview of the Identified Genomes
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Larramendy, S.; Deglaire, V.; Dusollier, P.; Fournier, J.-P.; Caillon, J.; Beaudeau, F.; Moret, L. Risk Factors of Extended-Spectrum Beta-Lactamases-Producing Escherichia coli Community Acquired Urinary Tract Infections: A Systematic Review. Infect. Drug Resist. 2020, 13, 3945–3955. [Google Scholar] [CrossRef] [PubMed]
- Aminov, R.I. Horizontal Gene Exchange in Environmental Microbiota. Front. Microbiol. 2011, 2, 158. [Google Scholar] [CrossRef] [PubMed]
- Samaha-Kfoury, J.N.; Araj, G.F. Recent developments in beta lactamases and extended spectrum beta lactamases. BMJ 2003, 327, 1209–1213. [Google Scholar] [CrossRef] [PubMed]
- Jacoby, G.A.; Munoz-Price, L.S. The new beta-lactamases. N. Engl. J. Med. 2005, 352, 380–391. [Google Scholar] [CrossRef] [PubMed]
- Paterson, D.L.; Bonomo, R.A. Extended-spectrum beta-lactamases: A clinical update. Clin. Microbiol. Rev. 2005, 18, 657–686. [Google Scholar] [CrossRef] [PubMed]
- Pitout, J.D.; Laupland, K.B. Extended-spectrum beta-lactamase-producing Enterobacteriaceae: An emerging public-health concern. Lancet Infect. Dis. 2008, 8, 159–166. [Google Scholar] [CrossRef] [PubMed]
- Shaikh, S.; Fatima, J.; Shakil, S.; Rizvi, S.M.D.; Kamal, M.A. Antibiotic resistance and extended spectrum beta-lactamases: Types, epidemiology and treatment. Saudi J. Biol. Sci. 2014, 22, 90–101. [Google Scholar] [CrossRef]
- Tooke, C.L.; Hinchliffe, P.; Bragginton, E.C.; Colenso, C.K.; Hirvonen, V.H.; Takebayashi, Y.; Spencer, J. Beta-Lactamases and beta-Lactamase Inhibitors in the 21st Century. J. Mol. Biol. 2019, 431, 3472–3500. [Google Scholar] [CrossRef]
- Bajpai, T.; Pandey, M.; Varma, M.; Bhatambare, G.S. Prevalence of TEM, SHV, and CTX-M Beta-Lactamase genes in the urinary isolates of a tertiary care hospital. Avicenna J. Med. 2017, 7, 12–16. [Google Scholar] [CrossRef]
- Nordmann, P.; Dortet, L.; Poirel, L. Carbapenem resistance in Enterobacteriaceae: Here is the storm! Trends Mol. Med. 2012, 18, 263–272. [Google Scholar] [CrossRef]
- Poirel, L.; Potron, A.; Nordmann, P. OXA-48-like carbapenemases: The phantom menace. J. Antimicrob. Chemother. 2012, 67, 1597–1606. [Google Scholar] [CrossRef]
- Falgenhauer, L.; Imirzalioglu, C.; Oppong, K.; Akenten, C.W.; Hogan, B.; Krumkamp, R.; Poppert, S.; Levermann, V.; Schwengers, O.; Sarpong, N.; et al. Detection and Characterization of ESBL-Producing Escherichia coli From Humans and Poultry in Ghana. Front. Microbiol. 2019, 9, 3358. [Google Scholar] [CrossRef] [PubMed]
- Hassuna, N.A.; Khairalla, A.S.; Farahat, E.M.; Hammad, A.M.; Abdel-Fattah, M. Molecular characterization of Extended-spectrum β lactamase-producing E. coli recovered from community-acquired urinary tract infections in Upper Egypt. Sci. Rep. 2020, 10, 2772. [Google Scholar] [CrossRef] [PubMed]
- Obeng-Nkrumah, N.; Twum-Danso, K.; Krogfelt, K.A.; Newman, M.J. High Levels of Extended-Spectrum Beta-Lactamases in a Major Teaching Hospital in Ghana: The Need for Regular Monitoring and Evaluation of Antibiotic Resistance. Am. J. Trop. Med. Hyg. 2013, 89, 960–964. [Google Scholar] [CrossRef] [PubMed]
- Toy, T.; Pak, G.D.; Duc, T.P.; Campbell, J.I.; El Tayeb, M.A.; Von Kalckreuth, V.; Im, J.; Panzner, U.; Cruz Espinoza, L.M.; Eibach, D.; et al. Multicountry Distribution and Characterization of Extended-spectrum β-Lactamase-associated Gram-negative Bacteria from Bloodstream Infections in Sub-Saharan Africa. Clin. Infect. Dis. 2019, 69, S449–S458. [Google Scholar] [CrossRef] [PubMed]
- CLSI. Performance Standards for Antimicrobial Susceptibility Testing, 33rd ed.; CLSI Supplement M100: Wayne PA, USA, 2023. [Google Scholar]
- Naseer, F. Phenotypic Cofirmatory Disc Diffusion Test (PCDDT), Double Disc Synergy Test (DDST), E-Test Os Diagnostic Tool for Detection of Extended Spectrum Beta Lactamase (ESΒL) Producing Uropathogens. J. Appl. Biotechnol. Bioeng. 2017, 3, 344–349. [Google Scholar] [CrossRef]
- Gurevich, A.; Saveliev, V.; Vyahhi, N.; Tesler, G. QUAST: Quality assessment tool for genome assemblies. Bioinformatics 2013, 29, 1072–1075. [Google Scholar] [CrossRef] [PubMed]
- Assefa, S.; Keane, T.M.; Otto, T.D.; Newbold, C.; Berriman, M. ABACAS: Algorithm-based automatic contiguation of assembled sequences. Bioinformatics 2009, 25, 1968–1969. [Google Scholar] [CrossRef]
- Walker, B.J.; Abeel, T.; Shea, T.; Priest, M.; Abouelliel, A.; Sakthikumar, S.; Cuomo, C.A.; Zeng, Q.; Wortman, J.; Young, S.K.; et al. Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS ONE 2014, 9, e112963. [Google Scholar] [CrossRef]
- Seemann, T. Prokka: Rapid Prokaryotic Genome Annotation. Bioinformatics 2014, 30, 2068–2069. [Google Scholar] [CrossRef]
- Joensen, K.G.; Tetzschner, A.M.; Iguchi, A.; Aarestrup, F.M.; Scheutz, F. Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data. J. Clin. Microbiol. 2015, 53, 2410–2426. [Google Scholar] [CrossRef] [PubMed]
- Opintan, J.A.; Newman, M.J. Prevalence of antimicrobial resistant pathogens from blood cultures: Results from a laboratory based nationwide surveillance in Ghana. Antimicrob. Resist. Infect. Control 2017, 6, 64. [Google Scholar] [CrossRef] [PubMed]
- Donkor, E.S.; Horlortu, P.Z.; Dayie, N.T.; Obeng-Nkrumah, N.; Labi, A.-K. Community acquired urinary tract infections among adults in Accra, Ghana. Infect. Drug Resist. 2019, 12, 2059–2067. [Google Scholar] [CrossRef] [PubMed]
- Deku, J.G.; Duedu, K.O.; Ativi, E.; Kpene, G.E.; Feglo, P.K. Occurrence and distribution of extended-spectrum β-lactamase in clinical Escherichia coli isolates at Ho Teaching Hospital in Ghana. Ghana Med. J. 2021, 55, 298–307. [Google Scholar] [CrossRef]
- Mahazu, S.; Sato, W.; Ayibieke, A.; Prah, I.; Hayashi, T.; Suzuki, T.; Iwanaga, S.; Ablordey, A.; Saito, R. Insights and genetic features of extended-spectrum beta-lactamase producing Escherichia coli isolates from two hospitals in Ghana. Sci. Rep. 2022, 12, 1843. [Google Scholar] [CrossRef]
- Eibach, D.; Dekker, D.; Boahen, K.G.; Akenten, C.W.; Sarpong, N.; Campos, C.B.; Berneking, L.; Aepfelbacher, M.; Krumkamp, R.; Owusu-Dabo, E.; et al. Extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae in local and imported poultry meat in Ghana. Vet. Microbiol. 2018, 217, 7–12. [Google Scholar] [CrossRef] [PubMed]
- Rasmussen, M.M.; Opintan, J.A.; Frimodt-Møller, N.; Styrishave, B. Beta-Lactamase Producing Escherichia coli Isolates in Imported and Locally Produced Chicken Meat from Ghana. PLoS ONE 2015, 10, e0139706. [Google Scholar] [CrossRef] [PubMed]
- Agyekum, A.; Fajardo-Lubián, A.; Ansong, D.; Partridge, S.R.; Agbenyega, T.; Iredell, J.R. blaCTX-M-15 carried by IncF-type plasmids is the dominant ESBL gene in Escherichia coli and Klebsiella pneumoniae at a hospital in Ghana. Diagn. Microbiol. Infect. Dis. 2016, 84, 328–333. [Google Scholar] [CrossRef]
- Hackman, H.K.; Brown, C.A.; Twum-Danso, K. Antibiotic Resistance Profile of CTX-M-type Extended-Spectrum Be-ta-Lactamases in Escherichia coli and Klebsiella pneumoniae in Accra. Ghana. J. Nat. Sci. Res. 2014, 4, 24–29. [Google Scholar]
- Seni, J.; Sweya, E.; Mabewa, A.; Mshana, S.E.; Gilyoma, J.M. Comparison of antimicrobial resistance patterns of ESBL and non ESBL bacterial isolates among patients with secondary peritonitis at Bugando Medical Centre, Mwanza—Tanzania. BMC Emerg. Med. 2016, 16, 41. [Google Scholar] [CrossRef]
- Ojo, O.E.; Schwarz, S.; Michael, G.B. Detection and characterization of extended-spectrum beta-lactamase-producing Esche-richia coli from chicken production chains in Nigeria. Vet. Microbiol. 2016, 194, 62–68. [Google Scholar] [CrossRef] [PubMed]
- van Hoek, A.H.A.M.; Veenman, C.; Florijn, A.; Huijbers, P.M.C.; Graat, E.A.M.; de Greeff, S.; Dierikx, C.M.; van Duijkeren, E. Longitudinal study of ESBL Escherichia coli carriage on an organic broiler farm. J. Antimicrob. Chemother. 2018, 73, 3298–3304. [Google Scholar] [CrossRef] [PubMed]
- Ueda, S.; Ngan, B.T.K.; Huong, B.T.M.; Hirai, I.; Tuyen, L.D.; Yamamoto, Y. Limited Transmission of bla CTX-M-9-Type-Positive Escherichia coli between Humans and Poultry in Vietnam. Antimicrob. Agents Chemother. 2015, 59, 3574–3577. [Google Scholar] [CrossRef] [PubMed]
- Blaak, H.; Van Hoek, A.H.A.M.; Hamidjaja, R.A.; van der Plaats, R.Q.; Kerkhof-de Heer, L.; de Roda Husman, A.M.; Schets, F.M. Distribution, Numbers, and Diversity of ESBL-Producing E. coli in the Poultry Farm Environment. PLoS ONE 2015, 10, e0135402. [Google Scholar] [CrossRef]
- Peirano, G.; Pitout, J.D. Molecular epidemiology of Escherichia coli producing CTX-M beta-lactamases: The worldwide emergence of clone ST131 O25:H4. Int. J. Antimicrob. Agents 2010, 35, 316–321. [Google Scholar] [CrossRef]
Isolate | AMP | CXM | CRO | CTX | CAZ | CFP | NOR | ETP | ST | CC | Predicted Serotype(s) |
---|---|---|---|---|---|---|---|---|---|---|---|
0190 | R | R | R | R | R | R | S | S | – * | – * | O96:H19 |
0198 | R | R | R | R | R | R | R | S | 617 | 10 | O101:H10 |
0232 | R | R | R | R | S | R | R | I | 205 | 205 | O100:H12 |
0320 | R | R | R | R | S | R | S | S | 34 | 10 | O62/O68:H30 [O62:H30] |
0456 | R | R | R | R | R | R | R | S | 2522 | – | H8 [O8:H8] |
0513 | R | R | R | R | R | R | S | S | 131 | 131 | O16:H5 |
0533 | R | R | R | R | R | R | S | S | 131 | 131 | O16:H5 |
0549 | R | R | R | R | R | R | S | S | 1722 | – | O1:H25 |
0492 | R | R | R | R | R | R | S | S | 12 | 12 | O4:H1 |
0135 | R | R | R | R | R | R | S | S | 44 | 10 | O101:H4 |
0350 | S | S | S | R | R | R | S | S | 69 | 69 | O45:H16 |
Assembly | Contig | Total Length (bp) | Largest Contig (bp) | N50 (bp) | GC (%) | CDS |
---|---|---|---|---|---|---|
0135 | 157 | 4,909,247 | 363,240 | 110,005 | 50.83 | 4567 |
0190 | 271 | 5,238,332 | 677,836 | 147,320 | 50.51 | 4960 |
0198 | 143 | 5,061,456 | 433,368 | 138,030 | 50.69 | 4710 |
0232 | 233 | 5,131,532 | 332,049 | 154,315 | 50.62 | 4877 |
0320 | 147 | 4,655,431 | 312,439 | 84,242 | 50.7 | 4380 |
0350 | 157 | 5,339,158 | 355,221 | 131,256 | 50.68 | 4957 |
0456 | 84 | 4,810,807 | 484,699 | 199,978 | 50.79 | 4465 |
0492 | 153 | 5,189,267 | 626,531 | 317,074 | 50.47 | 4808 |
0513 | 154 | 5,086,218 | 338,786 | 172,951 | 50.75 | 4727 |
0533 | 130 | 5,104,287 | 575,414 | 212,669 | 50.69 | 4747 |
0549 | 88 | 4,856,633 | 656,256 | 279,176 | 50.55 | 4461 |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Dayie, N.T.K.D.; Egyir, B.; Amoa-Owusu, F.; Owusu-Nyantakyi, C.; Adu, B.; Kotey, F.C.N.; Donkor, E.S.; Stabler, R.A. Genome Sequences of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Recovered from Mid-Stream Urine Samples in Accra, Ghana. Microorganisms 2024, 12, 1139. https://doi.org/10.3390/microorganisms12061139
Dayie NTKD, Egyir B, Amoa-Owusu F, Owusu-Nyantakyi C, Adu B, Kotey FCN, Donkor ES, Stabler RA. Genome Sequences of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Recovered from Mid-Stream Urine Samples in Accra, Ghana. Microorganisms. 2024; 12(6):1139. https://doi.org/10.3390/microorganisms12061139
Chicago/Turabian StyleDayie, Nicholas T. K. D., Beverly Egyir, Felicia Amoa-Owusu, Christian Owusu-Nyantakyi, Bright Adu, Fleischer C. N. Kotey, Eric S. Donkor, and Richard A. Stabler. 2024. "Genome Sequences of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Recovered from Mid-Stream Urine Samples in Accra, Ghana" Microorganisms 12, no. 6: 1139. https://doi.org/10.3390/microorganisms12061139
APA StyleDayie, N. T. K. D., Egyir, B., Amoa-Owusu, F., Owusu-Nyantakyi, C., Adu, B., Kotey, F. C. N., Donkor, E. S., & Stabler, R. A. (2024). Genome Sequences of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Recovered from Mid-Stream Urine Samples in Accra, Ghana. Microorganisms, 12(6), 1139. https://doi.org/10.3390/microorganisms12061139