Association of phylogenetic distribution and presence of integrons with multidrug resistance in Escherichia coli clinical isolates from children with diarrhoea

Ahumada-Santos, Yesmi Patricia; Báez-Flores, María Elena; Díaz‐Camacho, Sylvia Páz; Uribe-Beltrán, Magdalena de Jesús; Eslava-Campos, Carlos; Parra‐Unda, Jesús Ricardo; Delgado‐Vargas, Francisco

doi:10.1016/j.jiph.2019.11.019

Cited by 15 publications

(10 citation statements)

References 37 publications

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“…Pathogenic intestinal E. coli (DEC) mainly belong to Phylogenetic groups A, B1, and D, commensals to the groups A and B1, and strains usually belong to the groups B2 and D [13,14]. In our study, phylogenetic analysis predominantly clustered E. coli clinical isolates into B2 followed by A, B1 and D and this corroborates with ndings from previous studies [67][68][69]. However, contradicting results have been reported worldwide where A is the most abundantly isolated phylogroup [70][71][72][73].…”

Section: Discussionsupporting

confidence: 92%

Carbapenem resistance profiles of Pathogenic Escherichia coli in Uganda

Ssekatawa

Byarugaba

Nakavuma

et al. 2020

Preprint

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Background: Escherichia coli has been implicated as one of the main etiological agents of diarrhea, urinary tract infections, meningitis and septicemia worldwide. The ability to cause diseases is potentiated by presence of virulence factors. The virulence factors influence the capacity of E. coli to infect and colonize different body systems. Thus, pathogenic E. coli are grouped into DEC strains that are mainly clustered in phylogenetic group B1 and A; ExPEC belonging to A, B2 and D. Coexistence of virulence and beta-lactamase encoding genes complicates treatment outcomes. Therefore, this study aimed at presenting the CR profiles among pathogenic E. coli. Methods: This was a retrospective cross-sectional study involving use of archived E. coli clinical isolates collected in 2019 from four Ugandan tertiary hospitals. The isolates were subjected to antibiotics sensitivity assays to determine phenotypic resistance. Four sets of multiplex PCR were performed to detect CR genes, DEC pathotypes virulent genes, ExPEC PAI and the E. coli phylogenetic groups. Results:Antibiotic susceptibility revealed that all the 421 E. coli isolates used were MDR as they exhibited 100% resistance to more than one of the first-line antibiotics. The study registered phenotypic and genotypic CR prevalence of 22.8% and 33.0% respectively. The most predominant gene was blaOXA-48 with genotypic frequency of 33.0%, then blaVIM(21.0%), blaIMP(16.5%), blaKPC(14.8%) and blaNDM(14.8%). Spearman’s correlation revealed that presence of CR genes was highly associated with phenotypic resistance. Furthermore, of 421 MDR E. coli isolates, 19.7% harboured DEC virulent genes, where EPEC recorded significantly higher prevalence (10.8%) followed by S-ETEC(3.1%), STEC(2.9%), EIEC (2.0%) and L-ETEC(2.0%). Genetic analysis characterized 46.1% of the isolates as ExPEC and only PAI IV536(33.0%) and PAI IICFT073(13.1%) were detected. Phylogenetic group B2 was predominantly detected (41.1%), followed by A(30.2%), B1(21.6%), and D(7.1%). Furthermore, 38.6% and 23.1% of the DEC and ExPEC respectively expressed phenotypic resistance.Conclusion: Our results exhibited significant level of CR carriage among the MDR DEC and ExPEC clinical isolates belonging to phylogenetic groups B1 and B2 respectively. Virulence and CR genetic factors are mainly located on mobile elements. Thus, constitutes a great threat to the healthcare system as it promotes horizontal gene transfer.

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Section: Discussionsupporting

confidence: 92%

Carbapenem resistance profiles of Pathogenic Escherichia coli in Uganda

Ssekatawa

Byarugaba

Nakavuma

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Pathogenic intestinal E. coli (DEC) mainly belong to Phylogenetic groups A, B1, and D, commensals to the groups A and B1, and strains usually belong to the groups B2 and D [13,14]. In our study, phylogenetic analysis predominantly clustered E. coli clinical isolates into B2 followed by A, B1 and D and this corroborates with findings from previous studies [72,73]. However, contradicting results have been reported worldwide where A is the most abundantly isolated phylogroup [74][75][76][77].…”

Section: Extraintestinal Pathogenic Escherichia Coli (Expec)supporting

confidence: 91%

Carbapenem Resistance Profiles of Pathogenic Escherichia coli in Uganda

Ssekatawa

Byarugaba

Nakavuma

et al. 2021

EJBIO

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Escherichia coli has been implicated as one of the main etiological agents of diarrhea, urinary tract infections, meningitis and septicemia worldwide. The ability to cause diseases is potentiated by presence of virulence factors. The virulence factors influence the capacity of E. coli to infect and colonize different body systems. Thus, pathogenic E. coli are grouped into DEC strains that are mainly clustered in phylogenetic group B1 and A; ExPEC belonging to A, B2 and D. Coexistence of virulence and beta-lactamase encoding genes complicates treatment outcomes. Therefore, this study aimed at presenting the carbapenem resistance (CR) profiles among pathogenic E. coli. This was a retrospective cross-sectional study involving use of 421 archived E. coli clinical isolates collected in 2019 from four Uganda tertiary hospitals. The isolates were subjected to antibiotics sensitivity assays to determine phenotypic resistance. Four sets of multiplex PCR were performed to detect CR genes, DEC pathotypes virulence genes, ExPEC PAI and the E. coli phylogenetic groups. Antibiotic susceptibility revealed that all the 421 E. coli isolates used were MDR as they exhibited 100% resistance to more than one of the first-line antibiotics. The study registered phenotypic and genotypic CR prevalence of 22.8% and 33.0% respectively. The most predominant gene was blaOXA-48 with genotypic frequency of 33.0%, then blaVIM (21.0%), blaIMP (16.5%), blaKPC (14.8%) and blaNDM (14.8%). Spearman’s correlation revealed that presence of CR genes was highly associated with phenotypic resistance. Furthermore, of 421 MDR E. coli isolates, 19.7% harboured DEC virulence genes, where EPEC recorded significantly higher prevalence (10.8%) followed by S-ETEC (3.1%), STEC (2.9%), EIEC (2.0%) and L-ETEC (2.0%). Genetic analysis characterized 46.1% of the isolates as ExPEC and only PAI IV536 (33.0%) and PAI IICFT073 (13.1%) were detected. Phylogenetic group B2 was predominantly detected (41.1%), followed by A (30.2%), B1(21.6%), and D (7.1%). Furthermore, 38.6% and 23.1% of the DEC and ExPEC respectively expressed phenotypic resistance. Our results exhibited significant level of CR carriage among the MDR DEC and ExPEC clinical isolates belonging to phylogenetic groups B1 and B2 respectively. Virulence and CR genetic factors are mainly located on mobile elements. Thus, constitutes a great threat to the healthcare system as this promotes horizontal gene transfer.

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“…Clermont and colleagues developed a new polymerase chain reaction (PCR)-based method to classify the eight phylogenetic groups of E. coli, of which seven are clustered in E. coli sensu stricto (A, B1, B2, C, D, E, and F) and one belongs to Escherichia Clade 1 (Clermont et al, 2013). Several studies have reported that phylogenetic groups B2 and D are associated with extraintestinal infection, while the other groups are more prevalent among diarrheagenic and commensal bacteria (Picard et al, 1999;Kumar, Nahid & Zahra, 2017;Ahumada-Santos et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Distribution of phylogenetic groups, adhesin genes, biofilm formation, and antimicrobial resistance of uropathogenic Escherichia coli isolated from hospitalized patients in Thailand

Tewawong

Kowaboot

Pimainog

et al. 2020

PeerJ

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Background Urinary tract infections (UTIs) are the most common bacterial infections and are often caused by uropathogenic Escherichia coli (UPEC). We investigated the distribution of phylogenetic groups, adhesin genes, antimicrobial resistance, and biofilm formation in E. coli isolated from patients with UTIs. Methods In the present study, 208 UPEC isolated from Thai patients were classified into phylogenetic groups and adhesin genes were detected using multiplex PCR. Antimicrobial susceptibility testing was performed using agar disk diffusion. The Congo red agar method was used to determine the ability of the UPEC to form biofilm. Results The most prevalent UPEC strains in this study belonged to phylogenetic group B2 (58.7%), followed by group C (12.5%), group E (12.0%), and the other groups (16.8%). Among adhesin genes, the prevalence of fimH (91.8%) was highest, followed by pap (79.3%), sfa (12.0%), and afa (7.7%). The rates of resistance to fluoroquinolones, trimethoprim-sulfamethoxazole, and amoxicillin-clavulanate were 65%, 54.3%, and 36.5%, respectively. The presence of adhesin genes and antibiotic resistance were more frequent in groups B2 and C compared to the other groups. Of the 129 multidrug-resistant UPEC strains, 54% were biofilm producers. Our findings further indicated that biofilm production was significantly correlated with the pap adhesin gene (p ≤ 0.05). Conclusion These findings provide molecular epidemiologic data, antibiotic resistance profiles, and the potential for biofilm formation among UPEC strains that can inform further development of the appropriate prevention and control strategies for UTIs in this region.

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Association of phylogenetic distribution and presence of integrons with multidrug resistance in Escherichia coli clinical isolates from children with diarrhoea

Cited by 15 publications

References 37 publications

Carbapenem resistance profiles of Pathogenic Escherichia coli in Uganda

Carbapenem resistance profiles of Pathogenic Escherichia coli in Uganda

Carbapenem Resistance Profiles of Pathogenic Escherichia coli in Uganda

Distribution of phylogenetic groups, adhesin genes, biofilm formation, and antimicrobial resistance of uropathogenic Escherichia coli isolated from hospitalized patients in Thailand

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