Next Article in Journal
Occurrence, Impact, and Multilocus Sequence Analysis of Alder Yellows Phytoplasma Infecting Common Alder and Italian Alder in Southern Italy
Previous Article in Journal
Summatory Effects of Anaerobic Exercise and a ‘Westernized Athletic Diet’ on Gut Dysbiosis and Chronic Low-Grade Metabolic Acidosis
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Microorganisms
Volume 12
Issue 6
10.3390/microorganisms12061139
microorganisms-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles thumb_up
...
Endorse textsms
...
Comment
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Genome Sequences of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Recovered from Mid-Stream Urine Samples in Accra, Ghana

by
Nicholas T. K. D. Dayie
1,†,
Beverly Egyir
2,†,
Felicia Amoa-Owusu
2,
Christian Owusu-Nyantakyi
2,
Bright Adu
3,
Fleischer C. N. Kotey
1,
Eric S. Donkor
1 and
Richard A. Stabler
4,*
1
Department of Medical Microbiology, University of Ghana Medical School, Accra P.O. Box KB 4236, Ghana
2
Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
3
Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
4
Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Microorganisms 2024, 12(6), 1139; https://doi.org/10.3390/microorganisms12061139
Submission received: 8 May 2024 / Revised: 25 May 2024 / Accepted: 26 May 2024 / Published: 4 June 2024
(This article belongs to the Section Molecular Microbiology and Immunology)
Browse Figure
Versions Notes

Abstract

:
Escherichia coli, a member of the commensal intestinal microbiota, is a significant aetiology of urinary tract infections (UTIs) and has a propensity for acquiring multidrug resistance characteristics, such as extended-spectrum beta-lactamases (ESBLs). Despite the increase in the incidence of ESBL-producing E. coli infections in sub-Saharan Africa, routine ESBL detection in Ghana is often absent, and molecular data on ESBL genotypes is scarce. Eleven ESBL-producing E. coli recovered from mid-stream urine samples were subjected to antimicrobial susceptibility testing and whole-genome sequence analyses. All isolates exhibited multidrug resistance, demonstrating phenotypic resistance to third-generation cephalosporins, such as cefotaxime, ceftazidime, and cefpodoxime. Three isolates demonstrated resistance to norfloxacin (a fluoroquinolone), and one isolate demonstrated intermediate resistance to ertapenem (a carbapenem). Analysis of the draft genomes identified multiple antimicrobial resistance genes including ESBL genotypes blaTEM-1B/TEM-190 (6/11 and 1/11, respectively), blaCTX-M-15/CTX-M-3 (7/11 and 1/11) and blaOXA-1/OXA-181 (3/11 and 1/11). The strains belong to 10 different serotypes and 10 different multilocus sequence types. This study provides information on phenotypic resistance in 11 ESBL E. coli from Ghana and AMR genotypes within their genomes.

1. Introduction

Escherichia coli is a natural member of the human microbiota and is a significant aetiology of urinary tract infections (UTIs) [1]. E. coli is able to exchange genetic material, including antibiotic resistance determinants, which may be plasmids or other mobile genetic elements, with other intestinal commensals [2]. One important group of antibiotic resistance determinants is beta-lactamases (encoded by bla genes), which hydrolyse the beta-lactam ring in penicillin and first- and second-generation cephalosporins (1GC and 2GC, respectively) [3,4,5,6,7].
Beta-lactamases are divided into the following four classes: the active site serine β-lactamases (Classes A, C, and D) and the zinc-dependent or metallo-β-lactamases (MBLs; Class B) [8]. Extended-spectrum beta-lactamases (ESBLs) are capable of hydrolysing antibiotics, such as aztreonam and fourth-generation cephalosporins (4GCs) [9]. Classification of the cephalosporins into first-, second-, third- (3GCs), fourth- (4GCs), and fifth-generation (5GCs) cephalosporins reflects a mixture of their temporal discovery and their spectrum of activity against Gram-negative and Gram-positive bacteria. Over 400 ESBL genes have been documented within Class A (blaTEM, blaSHV, and blaCTX-M) and Class D (blaOXA) β-lactamases. Class D (blaOXA)-encoded beta-lactamases are frequently encountered in Klebsiella pneumoniae and E. coli, mediating carbapenem (doripenem, meropenem, ertapenem, and imipenem) resistance [10,11].
There is an increase in the incidence of infections caused by ESBL-producing E. coli globally and in sub-Saharan Africa [12,13]. Previous studies in Ghana have indicated high positivity rates (49.3–61.1%) for ESBLs among E. coli isolates recovered from clinical sources [14]. This is of public health concern, particularly because ESBL detection among Gram-negative bacterial species is not routinely performed in the majority of the clinical microbiology laboratories in Ghana. In addition, very little is known about the antimicrobial resistance and virulence gene content of ESBLs in the country, leaving noticeable gaps in antimicrobial resistance surveillance data [15]. This study, therefore, characterised 11 ESBL-producing E. coli using whole-genome sequencing and antimicrobial susceptibility testing to augment existing knowledge.

2. Materials and Methods

2.1. Phenotypic Investigations

Eleven (11) archived E. coli isolates that were recovered from mid-stream urine samples (from two hospitals in Accra, Ghana, during laboratory-based surveillance conducted between April 2017 and March 2018) and were confirmed by colonial morphology, Gram staining and Matrix-assisted Laser Desorption/Ionisation Time of Flight (MALDI-TOF) Mass Spectrometry (Bruker Daltonics, Bremen, Germany) using Biotyper™ system 2.0 software at the genus [log(score) 1.7–2.0)] and species [log(score) ≥ 2.0] levels. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disc diffusion method and interpreted following the Clinical and Laboratory Standards Institute (CLSI) guidelines [16]. E. coli ATCC 25922 and K. pneumoniae ATCC 700603 were used as control strains. ESBL was confirmed by the double-disc method with cefotaxime, ceftazidime, and cefepime, alone and in combination with clavulanic acid [17]. Inhibition zone differences of ≥5 mm between the single and the combination discs for cefotaxime, ceftazidime, or cefepime were regarded as positive for ESBL production.

2.2. Whole-Genome Sequence Analysis of the Isolates

Whole-genome sequencing was performed at the Noguchi Memorial Institute for Medical Research, University of Ghana, on the eleven E. coli isolates. Genomic DNA was extracted using a standard genomic DNA extraction kit (Qiagen, Hilden, Germany). Extracted DNA was quantified using a Qubit 3.0® Fluorometer with a Qubit high-sensitivity kit (Thermo Fisher Scientific, Toh Tuck, Singapore). Genomic libraries were prepared using the Nextera DNA flex library preparation kit as per the manufacturer’s instructions. Sequencing libraries were quantified using the 2100 bioanalyser system (Agilent, Santa Clara, CA, USA) and Kapa Sybr Fast qPCR kit (Kapa Biosystems, Wilmington, MA, USA). Libraries were sequenced using the MiSeq sequencer (Illumina, San Diego, CA, USA). Raw fastq files were quality-filtered to Phred score ≥20, filtered for a minimum read length of 50 bp, and adaptor-trimmed using BBDuk (BBMap, https://sourceforge.net/projects/bbmap/). The resultant high-quality reads were used for de novo assembly, employing the default settings of SPAdes assembler v 3.13.0. Draft genome multi-fasta files were evaluated using the Quast assessment tool v5.1.0rc1 [18]. Contigs were ordered against a UTI reference E. coli UTI89 (accession CP000432) using ABACAS v1.3.1 [19]. The resulting assemblies were polished using Pilon v1.22 [20] and annotated using Prokka v1.14.6 [21]. MLST (Achtman scheme) was predicted using MLST (Seemann T, mlst, Github https://github.com/tseemann/mlst, v2.19.0, database updated on 1 October 2020) and serotypes using SerotypeFinder 2.0 [22] and abricate --db ecOH (Seemann T, Abricate, Github https://github.com/tseemann/abricate, v1.0.0, database updated on 1 October 2020). AMR genes were identified using Abricate with the ‘CARD’ and ‘ResFinder’ databases, with a minimum identity of 90% and a minimum coverage of 90%. Plasmids were identified using Abricate with the ‘PlasmidFinder’ database with a minimum identity of 80% and a minimum coverage of 90%. Heatmaps and hierarchical clustering were generated using Morpheus (https://software.broadinstitute.org/morpheus/, accessed on 1 October 2021). The data sets presented in this study can be found in the online repository https://www.ncbi.nlm.nih.gov/bioproject/767840 as follows: isolate 0190 (accession number JAIZOE000000000), 0232 (JAIZOC000000000), 0320 (JAIZOB000000000), 0456 (JAIZOA000000000), 0513 (JAIZNZ000000000), 0533 (JAIZNY000000000), 0549 (JAIZNX000000000), 0198 (JAIZOD000000000), 0135 (JAIZNW000000000), 0350 (JAIZNV000000000), and 0492 (JAIZNU000000000).

3. Results

3.1. Antimicrobial Resistance and Serotypes of the Isolates

Antimicrobial susceptibility testing (AST) demonstrated high levels of resistance to β-lactam antibiotics. Only Isolate 0350 was susceptible to ampicillin, cefuroxime (2GCs), and ceftriaxone (a 3GC), and only Isolates 0232 and 0320 were susceptible to ceftazidime (a 3GC) (Table 1). All eleven isolates were resistant to cefotaxime (a 3GC) and cefpodoxime (a 3GC) (Table 1). Three isolates (27%) (0198, 0232, and 0456) were resistant to norfloxacin (a fluoroquinolone), and no isolate was resistant to ertapenem, although Isolate 0232 was classed as intermediate resistant on retesting by Microscan (Renton, WA, USA) (Table 1).
Draft genomes were assembled for each isolate (Table 2), which consisted of an average of 156 contigs (84–271 contigs, SD ± 54), 5,034,761 bp (5,339,158–4,655,431 bp, SD ± 204), 220 bp, and 4696 CDSs (4380–4960, SD ± 202) (Table 2). All the isolates had evidence of plasmids through the presence of plasmid replicon sequences (Supplementary Table S4). The most common plasmid detected was the Col-like small plasmid, which was often also accompanied by an IncFI or IncFII incompatibility group plasmid. Interestingly, both Isolates 0513 and 0533 had replicons from both IncFI and IncFII incompatibility group plasmids (Supplementary Table S4). The genomic data were used to identify 10 different MLSTs (Achtman scheme). Isolates 0513 and 0533 were both ST131 strains (Table 1). Isolate 0190 had a novel gyrB allele along with adk(6), fumC(4), icd(18), mdh(9), purA(26), and recA(7), which are found in STs 99, 1611, 2063, 6401, 10050, and 11138. Three isolates (0198, 0320, and 0135) were from the same MLST clonal complex (CC), CC10 (Table 1), but three isolates (0190, 0456, and 0549) were sporadic and not associated with any specific complex (Table 1).
Serotypes were predicted from the assembly data and were unique to each isolate, with the exception of Isolates 0513 and 0533 (Table 1). SerotypeFinder did not identify an O type for Isolate 0456, although it was predicted to be H8:O8 by Abricate. It also gave an ambiguous O type to 0320 because of the similarity to multiple genes; O62 wzm (100% identity), O68 wzx (99.92%), and O68 wzy (99.91%) (Supplementary Table S1). Analysis using Abrogate identified 0320 as O62:H30 (Supplementary Table S1).

3.2. Overview of the Identified Genomes

Genome analysis for genes linked to antibiotic resistance against two curated databases, ResFinder and CARD, identified 28 and 70 genes, respectively (Figure 1A and Figure 1B, respectively). β-lactamase genes from Class A (blaTEM, and blaCTX-M) and Class D (blaOXA) were identified; blaCTX-M-15 was identified in 7/11 isolates, blaCTX-M-3 was identified in an eighth isolate (0232). Additionally, blaTEM was present in 7/11 isolates—while CARD labeled all these as blaTEM-181 (Figure 1B), ResFinder distinguished the blaTEM of Isolate 0232 as blaTEM-35, but those of the other six isolates as blaTEM-1B (Figure 1A). Protein sequence analysis identified blaTEM-35 in Isolate 0232 and blaTEM-1B in Isolates 0190, 0350, 0456, 0320, 0549, and 0492 (Figure 1A); blaTEM-1B differs from blaTEM-181 because of an A182V protein substitution. The blaOXA-1 gene was present in three isolates (0232, 0135, and 0198); however, Isolate 0232 had, in addition, blaOXA-181 (Figure 1); blaOXA-181 belongs to the OXA-48-like family carbapenem-hydrolysing Class D β-lactamases. PlasmidFinder identified putative plasmids through the identification of replicon sequences; however, it was not possible to link the AMR genes with these plasmids.
Analysis of genotypic and phenotypic data revealed a wide diversity within the limited isolate collection with the exception of Isolates 0513 and 0533 (Table 1, Figure 1). Isolate 0513 and 0533 were both predicted to be ST131 and had the same AST profiles (Table 1). Additionally, the AMR genotypes identified were identical (Figure 1).
Isolate 0232 was an outlier from the other E. coli isolates when clustering by AMR genes and was predicted to contain six or seven CDSs (CARD and ResFinder, respectively, Supplementary Tables S2 and S3) that were not found in the other ten isolates (Figure 1A). Isolate 0232 was also the only strain to harbour two blaOXA genes, and was also demonstrated to be intermediately resistant to ertapenem, but sensitive to ceftazidime (Table 1, Figure 1). Additionally, it was the only strain predicted to have blaCTX-M-3, which is only one amino acid different from blaCTX-M-15 (Asp240Gly); however, the difference in the omega loop region of blaCTX-M-15 results in increased ceftazidime hydrolysis and antibiotic resistance compared with blaCTX-M-3. Isolate 0320 was also identified to carry blaCTM-X-15 but was ceftazidime-sensitive.
Isolate 0350 was the only strain susceptible to ampicillin, cefuroxime, and ceftriaxone despite possessing blaTEM-1B, the most common plasmid-mediated β-lactamase of ampicillin resistance. The blaTEM-1B protein sequence was identical in all six strains, with no mutations or frameshifts present in Isolate 0350. Genome analysis suggested that Isolate 0350 had only a few differences in AMR genes from its nearest and resistant neighbor (Figure 1); ResFinder only identified a lack of drfA14 compared with Isolate 0456, and CARD suggested Isolate 0350 was lacking acrS, catI, dfrA14, mdtM, and ugd, but contained a cpxA compared with Isolate 0456. These genes are not involved or targets for β-lactam resistance.
Three strains demonstrated resistance to norfloxacin (a fluroquinolone), which is primarily mediated through non-synonymous mutations in the DNA gyrase (gyrA/B) or topoisomerase (parC) genes. Analysis of the draft genomes demonstrated that compared with norfloxacin-sensitive isolates 0190, 0320, and 0513, resistant isolates 0198 and 0232 have a GyrA A83L and D87N mutation. Isolate 0198 also has an additional GyrA D78E mutation. No mutations were seen in the GyrB of resistant isolates compared to the sensitive consensus sequence. In ParC, Isolates 0198 and 0232 contained an S80I compared with the sensitive consensus sequence. Isolate 0465, which had phenotypic resistance to norfloxacin, did not have non-synonymous mutations within these genes compared to the sensitive strains.

4. Discussion

In this study, we expanded on the limited knowledge of ESBLs from Ghana. Resistance of isolates to ampicillin, cefuroxime, ceftriaxone, cefotaxime, cefpodoxime, and ceftazidime is consistent with the characteristics of ESBL-producing organisms. Moreover, high levels of resistance (88.9–100%) against ampicillin, cefuroxime, and cefotaxime have been reported among E. coli isolates in previous studies conducted in the country [23]. It is interesting that the proportion of ESBL-producing E. coli resistant to norfloxacin in the current study (3/11, 27%) is comparable to the pooled proportion (6/15, 40%) reported for ESBL-producing and non-producing E. coli isolated from urine samples in a previous study in Ghana [24]. No isolate was resistant to ertapenem despite the presence of carbapenem resistance determinants blaOXA-1 in three strains. A single isolate (0232) carried two blaOXA penemases did show intermediate resistance to ertapenem, and the low level of resistance may be due to this antimicrobial being rarely used in Ghana. However, it is concerning that one strain demonstrated intermediate resistance to ertapenem despite its limited use clinically.
The blaCTX-M and blaTEM genes were common among the ESBL-producing E. coli isolates detected in the study by Donkor et al. [24]. Similarly, in the study by Deku et al. [25] involving a collection of E. coli isolates recovered from a variety of clinical specimens from Ho in Ghana—blood, high vaginal swab, pleural aspirates, sputum, ear swab, wound, and urine—blaTEM-1 and blaCTX-M (blaCTX-M-1, blaCTX-M-825, and blaCTX-M-914) were the predominant genes detected among ESBL isolates. Likewise, in the study by Mahazu et al. [26], which was conducted at two major hospitals in Ghana and involved E. coli from a similar set of specimens, as well as urethral discharge, pus, ascitic fluid, semen, endocervical swabs, stool, and others, blaCTX-M genes (blaCTX-M-14, blaCTX-M-15, and blaCTX-M-27) dominated. These may explain the high proportion of cefotaxime and ampicillin resistance in the current study. The blaCTX-M-15 gene and, to a relatively lesser extent, other blaCTX-M variants, have also been reported to be prevalent in E. coli isolated from locally-bred and imported chicken in the country [27,28]. Hence, it seems that the blaCTX-M genes may be widespread in the country, as confirmed in other previous reports [29,30], and could be harboured by non-typical urine E. coli pathotypes, such as the enteroinvasive, enteroaggregative, enteropathogenic, enteropathogenic, enterotoxigenic, and enterohaemorrhagic E. coli. Dissemination of AMR genes is often associated with plasmid transmission.
In the study by Mahazu et al. [26] involving E. coli isolated from multiple clinical specimens, the predominant sequence type was ST131 (25/102, 24.5%). Similarly, in a recent study in the country, ESBL-producing E. coli isolated from poultry predominantly belonged to ST10 (31/45, 69%) and, in humans, to ST131 (4/34, 12%) [12]. Other studies conducted in the African setting (Nigeria and Tanzania) have also commonly detected ST10 in poultry [31,32], while others conducted in European and Asian countries have additionally identified it in humans at high frequencies (9–11%) [33,34,35]. The detection of CC10 among ESBL-producing E. coli in the current study suggests a link to the livestock production chain. This is especially important as they could cyclically serve as sources of multidrug-resistant E. coli infections and reservoirs for the accumulation of multidrug-resistant E. coli and other Enterobacteriaceae shed by humans. CC131 is known to occur globally, is multidrug-resistant, commonly harbours the blaCTX-M-15 gene, and is associated with pandemics [36]. The two E. coli isolates that belonged to CC131 each harboured the blaCTX-M-15 gene and several other resistant genes, and could be of the same strain. Similarly, STs belonging to CC ST10 were also observed to possess several multidrug-resistant genes that may possibly explain the phenotypic resistances observed.
This study underscores the importance of enhancing antimicrobial stewardship programmes and utilising robust tools like whole-genome sequencing to generate detailed data for informing AMR surveillance efforts in the country. The high level of antimicrobial resistance could be a reflection of the prevalent overuse and misuse of antimicrobials in Ghana.
A limitation of this study was the few isolates from a single time point, which reduces the generalisability of the findings. Subsequent studies that evaluate a higher number of isolates could be helpful in validating the observations in this study.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/microorganisms12061139/s1, Table S1: Prediction of serotypes; Table S2: Identification of antibacterial genes using Abricate and the CARD database; Table S3: Identification of antibacterial genes using Abricate and the ResFinder database. Table S4: Information on plasmids harboured by the E. coli isolates.

Author Contributions

Conceptualisation, N.T.K.D.D., B.E. and R.A.S.; methodology, N.T.K.D.D., R.A.S., B.E. and B.A.; software, R.A.S. and B.A.; validation, N.T.K.D.D., B.E. and R.A.S.; formal analysis, N.T.K.D.D., B.E. and R.A.S.; investigation, N.T.K.D.D., B.E. and R.A.S.; resources, The Fleming Fellowship Fund; data curation, N.T.K.D.D., F.A.-O., C.O.-N. and F.C.N.K.; writing—original draft preparation, N.T.K.D.D., B.E. and R.A.S.; writing—review and editing, N.T.K.D.D., B.E., F.A.-O., F.A.-O., C.O.-N., B.A., F.C.N.K., E.S.D. and R.A.S.; visualisation, N.T.K.D.D., E.S.D. and F.C.N.K.; supervision, R.A.S.; project administration, N.T.K.D.D. and R.A.S.; funding acquisition, R.A.S. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Fleming Fund Fellowship Scheme through the London School of Hygiene and Tropical Medicine and the University of Ghana according to Grant Number RZ07.

Institutional Review Board Statement

The study was conducted in accordance with the Declaration of Helsinki, and approved by the Institutional Review Board of Noguchi Memorial Institute for Medical Research, University of Ghana (FW00001824).

Informed Consent Statement

The archived isolates examined were previously collected and deidentified, so informed consent was not required for this study.

Data Availability Statement

The original contributions presented in the study are included in the article/Supplementary Material; further inquiries can be directed to the corresponding author.

Acknowledgments

N.T.K.D.D. was supported, and the whole-genome sequencing was funded, by the Fleming Fellowship Scheme. The Fleming Fund is a GBP 265 million UKAID investment to tackle antimicrobial resistance in low- and middle-income countries around the world. The Scheme is managed by the U.K. Department of Health and Social Care, in partnership with Mott MacDonald, the Fleming Fund Grants Management Agent. This publication made use of the PubMLST website (https://pubmlst.org/) developed by Keith Jolley (Jolley & Maiden 2010, BMC Bioinformatics, 11:595) and cited at the University of Oxford. The development of that website was funded by the Wellcome Trust.

Conflicts of Interest

The authors declare no conflicts of interest. The funders had no role in the design of this study, in the collection, analyses, or interpretation of data, in the writing of this manuscript, or in the decision to publish the results.

References

  1. 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]
  2. Aminov, R.I. Horizontal Gene Exchange in Environmental Microbiota. Front. Microbiol. 2011, 2, 158. [Google Scholar] [CrossRef] [PubMed]
  3. 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]
  4. Jacoby, G.A.; Munoz-Price, L.S. The new beta-lactamases. N. Engl. J. Med. 2005, 352, 380–391. [Google Scholar] [CrossRef] [PubMed]
  5. Paterson, D.L.; Bonomo, R.A. Extended-spectrum beta-lactamases: A clinical update. Clin. Microbiol. Rev. 2005, 18, 657–686. [Google Scholar] [CrossRef] [PubMed]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. Nordmann, P.; Dortet, L.; Poirel, L. Carbapenem resistance in Enterobacteriaceae: Here is the storm! Trends Mol. Med. 2012, 18, 263–272. [Google Scholar] [CrossRef]
  11. Poirel, L.; Potron, A.; Nordmann, P. OXA-48-like carbapenemases: The phantom menace. J. Antimicrob. Chemother. 2012, 67, 1597–1606. [Google Scholar] [CrossRef]
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  16. CLSI. Performance Standards for Antimicrobial Susceptibility Testing, 33rd ed.; CLSI Supplement M100: Wayne PA, USA, 2023. [Google Scholar]
  17. 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]
  18. Gurevich, A.; Saveliev, V.; Vyahhi, N.; Tesler, G. QUAST: Quality assessment tool for genome assemblies. Bioinformatics 2013, 29, 1072–1075. [Google Scholar] [CrossRef] [PubMed]
  19. 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]
  20. 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]
  21. Seemann, T. Prokka: Rapid Prokaryotic Genome Annotation. Bioinformatics 2014, 30, 2068–2069. [Google Scholar] [CrossRef]
  22. 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]
  23. 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]
  24. 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]
  25. 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]
  26. 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]
  27. 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]
  28. 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]
  29. 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]
  30. 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]
  31. 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]
  32. 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]
  33. 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]
  34. 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]
  35. 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]
  36. 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]
Microorganisms 12 01139 g001
Figure 1. Presence of genes linked to AMR within the E. coli isolates. Black circles indicate that a gene was identified by Abricate using CARD databases within a draft genome. Isolates were clustered using the Euclidian distance algorithm. (A) Resfinder database. (B) CARD database; in addition, the following genes were conserved in all the 11 isolates: acrA, acrB, acrD, acrF, ampC, ampH, bacA, baeR, baeS, CRP, emrA, emrB, emrK, emrR, emrY, eptA, gadW, gadX, H-NS, kdpE, marA, mdfA, mdtA, mdtB, mdtC, mdtE, mdtF, mdtG, mdtH, mdtN, mdtO, mdtP, msbA, pmrF, tolC, and yojI.
Figure 1. Presence of genes linked to AMR within the E. coli isolates. Black circles indicate that a gene was identified by Abricate using CARD databases within a draft genome. Isolates were clustered using the Euclidian distance algorithm. (A) Resfinder database. (B) CARD database; in addition, the following genes were conserved in all the 11 isolates: acrA, acrB, acrD, acrF, ampC, ampH, bacA, baeR, baeS, CRP, emrA, emrB, emrK, emrR, emrY, eptA, gadW, gadX, H-NS, kdpE, marA, mdfA, mdtA, mdtB, mdtC, mdtE, mdtF, mdtG, mdtH, mdtN, mdtO, mdtP, msbA, pmrF, tolC, and yojI.
Microorganisms 12 01139 g001
Table 1. Antibiotic susceptibility and clonal information of the ESBL E. coli isolates.
Table 1. Antibiotic susceptibility and clonal information of the ESBL E. coli isolates.
IsolateAMPCXMCROCTXCAZCFPNORETPSTCCPredicted
Serotype(s)
0190RRRRRRSS– *– *O96:H19
0198RRRRRRRS61710O101:H10
0232RRRRSRRI205205O100:H12
0320RRRRSRSS3410O62/O68:H30
[O62:H30]
0456RRRRRRRS2522–H8 [O8:H8]
0513RRRRRRSS131131O16:H5
0533RRRRRRSS131131O16:H5
0549 RRRRRRSS1722–O1:H25
0492RRRRRRSS1212O4:H1
0135RRRRRRSS4410O101:H4
0350SSSRRRSS6969O45:H16
AMP = ampicillin; CXM = cefuroxime (2nd-generation cephalosporin [2GC]); CRO = ceftriaxone (3rd generation cephalosporin [3GC]); CTX = cefotaxime (3GC); CAZ = ceftazidime (3GC); CFP = cefpodoxime (3GC), NOR = norfloxacin (fluoroquinolone); ETP = ertapenem (carbapenem). ST = multilocus sequence type; CC = clonal complex. Note, * 0190 had a novel variant of the gyrB(865) allele along with adk(6), fumC(4), icd(18), mdh(9), purA(26), and recA(7). Serotype prediction based on the draft genome using SerotypeFinder. “Oxx:Hyy” indicates additional data using Abricate analysis.
Table 2. Overview of draft genomes.
Table 2. Overview of draft genomes.
AssemblyContigTotal Length (bp)Largest Contig (bp)N50 (bp)GC
(%)		CDS
01351574,909,247363,240110,00550.834567
01902715,238,332677,836147,32050.514960
01981435,061,456433,368138,03050.694710
02322335,131,532332,049154,31550.624877
03201474,655,431312,43984,24250.74380
03501575,339,158355,221131,25650.684957
0456844,810,807484,699199,97850.794465
04921535,189,267626,531317,07450.474808
05131545,086,218338,786172,95150.754727
05331305,104,287575,414212,66950.694747
0549884,856,633656,256279,17650.554461
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.

Share and Cite

MDPI and ACS Style

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

AMA Style

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 Style

Dayie, 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

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop