Genetic diversity of Escherichia coli isolated from ice cube production sites

Pusparini, Novi; Waturangi, Diana Elizabeth; Usia, Tepy; Nikastri, Eva

doi:10.1186/s13104-018-3737-3

Cited by 7 publications

(3 citation statements)

References 33 publications

(30 reference statements)

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“…3) at 95 per cent similarity cut-off value and exhibited genetic heterogeneity, but Jonas et al [63] reported isolates with similarities above 70-80% which were eventually assigned to the same genotypes. Another study by Pusparini et al [64] reported several unique clusters of ERIC in E. coli strains isolated from ice cube production sites which showed genetic diversity with 50 per cent cut-off value which is in contrary to the similarity cut-off value generated in this present study. On the basis of ERIC-PCR ngerprint, some of the isolates included in our study were genetically diverse.…”

Section: Discussioncontrasting

confidence: 99%

Genetic Characterization Among Carbapenem-resistant Escherichia coli Strains Using Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) Fingerprinting in South Africa

Ebomah¹,

Okoh²

2020

Preprint

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Background Carbapenems belong to beta-lactam class of antibiotics usually considered as the last line of defense because they can be effective against severe infections caused by prevalent multidrug-resistant (MDR) pathogens. However, carbapenems can be deactivated by bacteria that produce carbapenemase (beta-lactamase). This study was conducted to screen for carbapenem-resistance genes (CRGs) harbored by pathogenic strains of Escherichia coli recovered from different environmental samples. We also assessed the genetic relatedness among selected E. coli pathotypes using enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR).Method: Molecular identification and characterization of the presumptive isolates were performed using PCR and isolates that exhibited antimicrobial resistance (AMR) phenotypically were further screened for some relevant CRGs (blaNDM−1, blaKPC and blaOXA−48−like). Furthermore, ERIC-PCR was used to determine the similarity and diversity of 31 E. coli strains which were randomly selected from the different sources analyzed in this study.Result Our findings revealed a total of 238 presumptive E. coli isolates, out of which 192 were confirmed positive for uidA gene. Further screening revealed 77 (40%) isolates belong to six key E. coli pathotypes and 70 of them exhibited phenotypic AMR. Additionally, twenty-nine (41%) of the 70 MDR pathogenic E. coli strains harbored CRGs; with 24 strains harboring blaNDM−1, 8 harboring blaKPC and 2 harboring blaOXA−48−like genes.Conclusion Findings also suggest that the selected E. coli pathotypes belonged to different genomic clusters, while the cluster analysis showed a possible genetic diversity among aquatic and farm isolates. Proper treatment of final effluents before discharge as well as the development of more effective strategies to control and manage the use of antimicrobial agents were strongly recommended.

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Section: Discussioncontrasting

confidence: 99%

Genetic Characterization Among Carbapenem-resistant Escherichia coli Strains Using Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) Fingerprinting in South Africa

Ebomah¹,

Okoh²

2020

Preprint

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“…In the lack of appropriate software, the band patterns generated by REP-PCR were assessed visually. The binary matrix was built based on the absence or presence of each band (coded 0 or 1, respectively) ( Pusparini et al, 2018 ). Phylogenetic tree based on binary matrix was constructed by the free online service at http://insilico.ehu.eus/dice_upgma/ .…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic group, antibiotic resistance, virulence gene, and genetic diversity of Escherichia coli causing bloodstream infections in Iran

Hemati,

Halimi,

Jabalameli

et al. 2024

Front. Microbiol.

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Escherichia coli is one of the most important pathogens causing bloodstream infections (BSIs) throughout the world. We sought to characterize the phylogroup classification, major human sequence types (STs), antimicrobial resistance, presence of selected antimicrobial resistance and virulence genes, and genetic diversity of E. coli isolated from patients with BSIs at the University Hospital in Iran. A total of 100 E. coli bloodstream isolates were collected between December 2020 and June 2022. This study used PCR to investigate phylogenetic groups (A, B1, B2, C, D, E, and F), four major STs (ST69, ST73, ST95, and ST131), antibiotic resistance genes (ARGs), virulence-associated genes (VAGs), and pathogenicity islands (PAIs). Antimicrobial susceptibility testing was done by disk diffusion method. Genetic diversity was analyzed by repetitive element sequence-based PCR (REP-PCR). The phylogenetic group B2 (32%) predominated, followed by phylogenetic group E (25%). ST131 (28%) was the most prevalent ST and the majority of these isolates (89.3%) were of serotype O25b. Most of E. coli isolates (75%) were categorized as multidrug resistant (MDR) with high rates of resistance (>55%) to ampicillin, trimethoprim-sulfamethoxazole, ciprofloxacin, cefazolin, and ceftriaxone. The most frequent ARGs were blaTEM (66%), sul1 (57%), and sul2 (51%). The most prevalent VAGs and PAIs were fimH (type 1 fimbriae adhesin; 85%), aer (iucC) (aerobactin; 79%), traT (serum resistance; 77%), iutA (aerobactin siderophore receptor; 69%), and PAI IV536 (75%), respectively. The highest rate of ARGs and VAGs was observed in the ST131 isolates. REP-PCR analysis showed high diversity among the studied isolates. The high prevalence of MDR septicemic E. coli with different types of ARGs, VAGs and genotypes is an extremely worrisome sign of BSIs treatment and poses a major threat for hospitalized patients. Active surveillance, stringent prescribing policies, increasing the awareness of ARGs among clinicians and re-defining the infection control measures are essential to curb the dissemination of these strains.

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“…Pohon filogenetik hasil ERIC PCR menunjukkan kekerabatan isolat Vibrio dari air, feses, hepatopankreas, udang sehat dan udang EHP. Clustering pada pohon filogenetik dilakukan berdasarkan tingkat kemiripan 50% (0.5 similarity) (Pusparini et al, 2018).…”

Section: Tabelunclassified

Diversity Analysis of Genus Vibrio in Enterocytozoon Hepatopenaei (EHP) Infected Shrimp with Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC PCR) Method

Amelia

Halalludin²,

Naim

et al. 2020

JAFH

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Udang merupakan salah satu komoditas unggulan nasional dan memiliki nilai ekonomi yang tinggi. Produksi udang budidaya di Indonesia tahun 2012-2017 mengalami kenaikan secara signifikan. Meski mengalami kenaikan, masih terdapat masalah yang harus diatasi, salah satunya adalah penyakit yang disebabkan oleh parasit Enterocytozoon Hepatopenaei (EHP). Infeksi EHP mengganggu sel tubulus hepatopankreas. Lesi yang disebabkan oleh EHP dapat menjadi tempat pertumbuhan koloni Vibrio sehingga meningkatkan kemungkinan munculnya penyakit lain. Penelitian ini bertujuan untuk mengetahui keanekaragaman Vibrio pada udang terinfeksi EHP yang dianalisis dengan Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC PCR). ERIC PCR dapat membedakan strain bakteri yang berkerabat dekat, prosedur kerja yang sederhana, cepat dan murah. Bakteri Vibrio diisolasi dari hepatopankreas, feses dan air udang terinfeksi EHP dan udang sehat (kontrol), dilanjutkan dengan ekstraksi DNA, ERIC PCR, elektroforesis dan konstruksi pohon filogenetik. Hasil penelitian menunjukkan bahwa jumlah bakteri Vibrio pada hepatopankreas, air dan feses udang terinfeksi EHP lebih tinggi dibandingkan dengan udang sehat. Udang terinfeksi EHP memiliki keanekaragaman Vibrio yang lebih rendah dari pada udang sehat. Hal ini menunjukkan adanya spesies Vibrio spesifik yang mendominasi pada udang terinfeksi EHP.

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Genetic diversity of Escherichia coli isolated from ice cube production sites

Cited by 7 publications

References 33 publications

Genetic Characterization Among Carbapenem-resistant Escherichia coli Strains Using Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) Fingerprinting in South Africa

Genetic Characterization Among Carbapenem-resistant Escherichia coli Strains Using Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) Fingerprinting in South Africa

Phylogenetic group, antibiotic resistance, virulence gene, and genetic diversity of Escherichia coli causing bloodstream infections in Iran

Diversity Analysis of Genus Vibrio in Enterocytozoon Hepatopenaei (EHP) Infected Shrimp with Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC PCR) Method

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