Draft Genome Sequence Analysis of Multidrug-Resistant Escherichia coli Strains Isolated in 2013 from Humans and Chickens in Nigeria

Sharma, Poonam; Gupta, Sushim K.; Adenipekun, E.; Barrett, John B.; Hiott, Lari M.; Woodley, Tiffanie A.; Iwalokun, BA; Oyedeji, Kolawole S.; Oluwadun, Afolabi; Ramadan, Hazem; Frye, Jonathan G.; Jackson, Charlene R.

doi:10.1128/genomea.01073-17

Cited by 5 publications

(4 citation statements)

References 20 publications

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“…Previously, only a few reports from Nigeria provided draft genome sequence analyses, mainly concerning multidrug-resistant E. coli strains isolated from humans and chicken [52,53]. Whilst three ESBL E. coli poultry isolates belonged to ST6359 [52], the poultry E. coli isolates reported by Sharma et al, were assigned to ST131 and ST162 respectively.…”

Section: Plos Onementioning

confidence: 99%

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Whole genome sequencing of extended-spectrum β-lactamase genes in Enterobacteriaceae isolates from Nigeria

et al. 2020

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Extended Spectrum β-lactamase (ESBL)-producing Enterobacteriaceae are of major concern as they are implicated in multidrug resistant nosocomial infections. They are listed on a recently published global priority list of antibiotic-resistant bacteria by the World Health Organization which raises concern in both healthcare and community settings. This study aimed at determining the frequency of ESBL genes in multidrug resistant human clinical Enterobacteriaceae isolates from Edo state Nigeria and to characterize the resistance mechanisms using whole genome sequencing. A total of 217 consecutive clinical isolates of Enterobacteriaceae, selection based on inclusion criteria, were collected from March-May 2015 from three medical microbiology laboratories of hospitals in Edo state Nigeria. All isolates were analyzed using matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. Antibiotic susceptibility testing was performed by Kirby-Bauer method and minimum inhibitory concentration (MIC) determination by E-test method. Double disc synergy test was used to screen for the production of ESBL. Whole genome sequencing (WGS) was performed for isolate characterization and identification of resistance determinants. Out of 217 consecutive clinical Enterobacteriaceae isolates, 148 (68.2%) were multi-drug resistant. Of these multi-drug resistant isolates, 60 (40.5%) were positive for the ESBL phenotypic test and carried ESBL genes. CTX-M-15 was the predominant ESBL found, among 93.3% (n = 56/60). Thirty-two plasmid incompatibility groups and 28 known and two new sequence types were identified among the ESBL isolates. The high occurrence of CTX-M-15 with associated resistant determinants in multidrug resistant Enterobacteriaceae harboring different plasmid incompatibility groups and sequence types calls for the need of continuous monitoring of this resistance threat to reduce its public health impact. To our knowledge, this study presents the first genomic characterization of ESBL production mediated by bla CTX-M-15 in human clinical isolates of Enterobacter hormaechei, Citrobacter werkmanii and Atlantibacter hermannii from Nigeria.

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Section: Plos Onementioning

confidence: 99%

“…Whilst three ESBL E. coli poultry isolates belonged to ST6359 [52], the poultry E. coli isolates reported by Sharma et al, were assigned to ST131 and ST162 respectively. The human E. coli isolates were assigned to six different STs which included ST131, ST617, ST542, ST398, ST4143 and ST398 [53].…”

Section: Plos Onementioning

confidence: 99%

Whole genome sequencing of extended-spectrum β-lactamase genes in Enterobacteriaceae isolates from Nigeria

et al. 2020

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“…A number of previous Nigerian studies described the detection, frequency/prevalence of resistance to antibiotics in livestock and the environment using phenotypical techniques (Ayandiran et al, 2014;Onuoha, 2017;Otokunefor et al, 2018;Ugwu et al, 2018). Only a few Nigerian studies have been able to explore the genetic mechanisms of antibiotic resistance in bovine animals and the environment (Olowe et al, 2015;Sharma et al, 2017;Adelowo et al, 2018;Ayandiran et al, 2018;Ejikeugwu et al, 2018) which is important to understand the dissemination of resistant isolates. Further studies to characterize prevalent clones and plasmids that harbor antibiotic resistance genes are required.…”

Section: Discussionmentioning

confidence: 99%

Genetic Characterization of Antibiotic Resistant Enterobacteriaceae Isolates From Bovine Animals and the Environment in Nigeria

et al. 2022

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There is a link between antibiotic resistance in humans, livestock and the environment. This study was carried out to characterize antibiotic resistant bovine and environmental Enterobacteriaceae isolates from Edo state, Nigeria. A total of 109 consecutive isolates of Enterobacteriaceae were isolated from March–May 2015 from 150 fecal samples of healthy bovine animals from three farms at slaughter in Edo state Nigeria. Similarly, 43 Enterobacteriaceae isolates were also obtained from a total of 100 environmental samples from different sources. Isolates were recovered and identified from samples using standard microbiological techniques. Recovered isolates were pre-identified by the Microbact Gram-Negative identification system and confirmed with Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and ribosomal multilocus sequence typing (rMLST). Antibiotic susceptibility testing was carried out by Kirby-Bauer method for 14 antibiotics. Whole genome sequencing (WGS) was carried out for isolate characterization and identification of resistance determinants. Out of 109 animal and 43 environmental Enterobacteriaceae isolates, 18 (17%) and 8 (19%) isolates based on selection criteria showed antibiotic resistance and were further investigated by whole genome sequencing (WGS). Resistance genes were detected in all (100%) of the resistant bovine and environmental Enterobacteriaceae isolates. The resistance determinants included β-lactamase genes, aminoglycoside modifying enzymes, qnr genes, sulfonamide, tetracycline and trimethoprim resistance genes, respectively. Out of the 18 and 8 resistant animal and environmental isolates 3 (17%) and 2 (25%) were multidrug resistant (MDR) and had resistance determinants which included efflux genes, regulatory systems modulating antibiotic efflux and antibiotic target alteration genes. Our study shows the dissemination of antibiotic resistance especially MDR strains among Nigerian bovine and environmental Enterobacteriaceae isolates. The presence of these resistant strains in animals and the environment constitute a serious health concern indicated by the difficult treatment options of the infections caused by these organisms. To the best of our knowledge we report the first detailed genomic characterization of antibiotic resistance in bovine and environmental Enterobacteriaceae isolates for Nigeria.

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“…AMR in species of the family Enterobacteriaceae, especially Escherichia coli and Klebsiella pneumoniae, has spread globally causing infections that are difficult to treat [9, 10]. Only a few Nigerian studies have characterized antibiotic resistance genes in poultry isolates [4, 11, 12]. Genetic characterization of AMR genes may give further insight into transmission mechanisms representing a key prerequisite for control of the spread of AMR [13].…”

Section: Introductionmentioning

confidence: 99%

Genetic characterization of Escherichia coli and Klebsiella spp. from humans and poultry in Nigeria

Jesumirhewe

Rosel

Allerberger

et al. 2023

Access Microbiology

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The emergence of antibiotic resistance in livestock, especially food-producing animals, is of major public health importance as a result of the possibility of these bacteria entering the food chain. In this study, the genetic characteristics of antibiotic-resistant Escherichia coli and Klebsiella spp. isolates from humans and poultry in Edo state, Nigeria, were investigated. In April 2017, 45 Klebsiella spp. and 46 E. coli isolates were obtained from urine, clinical wounds, nasal and chicken faecal samples. Isolates were recovered and identified as previously described. Species identification was achieved by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and ribosomal multilocus sequence typing. Antimicrobial susceptibility testing was carried out using the Kirby–Bauer method for 12 antibiotics. A double disc synergy test was used to screen for extended-spectrum beta-lactamse (ESBL) production. Whole genome sequencing was performed for strain characterization of the isolates. Thirteen Klebsiella spp. isolates yielded positive results by the ESBL phenotypic test and harboured ESBL genes. Of the 46 E. coli isolates, 21 human and 13 poultry isolates were resistant to at least one of the tested antibiotics. Four human E. coli isolates harboured ESBL genes and revealed positive results when applying ESBL double disc synergy tests. ESBL genes in the Klebsiella spp. and E. coli isolates include bla CTX-M-15 and bla SHV-28. Whole genome-based core gene multilocus sequence typing of the Klebsiella spp. and E. coli isolates revealed a close relatedness among the isolates. An integrated ‘One Health’ surveillance system is required to monitor transmission of antimicrobial resistance in Nigeria.

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Draft Genome Sequence Analysis of Multidrug-Resistant Escherichia coli Strains Isolated in 2013 from Humans and Chickens in Nigeria

Abstract: Here, we present the draft genome sequences of nine multidrug-resistant Escherichia coli strains isolated from humans (n = 6) and chicken carcasses (n = 3) from Lagos, Nigeria, in 2013. Multiple extended-spectrum β-lactamase (ESBL) genes were identified in these isolates.

Cited by 5 publications

References 20 publications

Whole genome sequencing of extended-spectrum β-lactamase genes in Enterobacteriaceae isolates from Nigeria

Whole genome sequencing of extended-spectrum β-lactamase genes in Enterobacteriaceae isolates from Nigeria

Genetic Characterization of Antibiotic Resistant Enterobacteriaceae Isolates From Bovine Animals and the Environment in Nigeria

Genetic characterization of Escherichia coli and Klebsiella spp. from humans and poultry in Nigeria

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