Genotypic characterization of multiple drug resistant Escherichia coli isolates from a pediatric cancer hospital in Egypt

Hassan, Reem; Tantawy, M.; Gouda, Nouran A.; Elzayat, Mariam G; Gabra, Sara; Nabih, Amena; Diab, Aya A.; El-Hadidi, Mohamed; Bakry, Usama; Shoeb, Mohamed R.; Elanany, Mervat; Shalaby, Lobna; Sayed, Ahmed

doi:10.1038/s41598-020-61159-z

Cited by 15 publications

(18 citation statements)

References 55 publications

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“…In particular, the E. coli O104:H4 outbreak in Germany in 2011 was caused by a strain that had acquired characteristics of two previously described pathotypes (Burger, 2012). The emergence of antibiotic-resistant Shigella with the absence of an effective vaccine highlights the importance of detailed studies of this pathogen (Hassan et al, 2020). Our results contribute to the understanding of genomic properties associated with adàptation to the intracellular lifestyle of Shigella and EIEC and the developed approaches should be broadly applicable to other young bacterial pathogens.…”

Section: Discussionmentioning

confidence: 80%

High Rates of Genome Rearrangements and Pathogenicity of Shigella spp.

et al. 2021

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Shigella are pathogens originating within the Escherichia lineage but frequently classified as a separate genus. Shigella genomes contain numerous insertion sequences (ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous recombination. Here, we study 414 genomes of E. coli and Shigella strains to assess the contribution of genomic rearrangements to Shigella evolution. We found that Shigella experienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic E. coli. The high rearrangement rate resulted in independent disruption of syntenic regions and parallel rearrangements in different Shigella lineages. Specifically, we identified two types of chromosomally encoded E3 ubiquitin-protein ligases acquired independently by all Shigella strains that also showed a high level of sequence conservation in the promoter and further in the 5′-intergenic region. In the only available enteroinvasive E. coli (EIEC) strain, which is a pathogenic E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli, we found a rate of genome rearrangements comparable to those in other E. coli and no functional copies of the two Shigella-specific E3 ubiquitin ligases. These data indicate that the accumulation of ISs influenced many aspects of genome evolution and played an important role in the evolution of intracellular pathogens. Our research demonstrates the power of comparative genomics-based on synteny block composition and an important role of non-coding regions in the evolution of genomic islands.

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Section: Discussionmentioning

confidence: 80%

High Rates of Genome Rearrangements and Pathogenicity of Shigella spp.

et al. 2021

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“…Genes aadA1 and aadA2 confer resistance to Aminoglycosides (e.g., Spectinomycin and Streptomycin) [ 42 ] and they were also found in a study on birds from Australia [ 43 ]. The gene aph (6)-Id was reported as the most commonly detected gene in E. coli clinical isolates from Egypt [ 44 ].…”

Section: Discussionmentioning

confidence: 99%

Occurrence and Antimicrobial Resistance Traits of Escherichia coli from Wild Birds and Rodents in Singapore

Ong

Khor²,

Quek

et al. 2020

IJERPH

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Antimicrobial resistance (AMR) in Escherichia coli (E. coli) poses a public health concern worldwide. Wild birds and rodents, due to their mobility, are potential vehicles for transmission of AMR bacteria to humans. Ninety-six wild birds’ faecal samples and 135 rodents’ droppings samples were collected and analysed in 2017. Forty-six E. coli isolates from wild birds and rodents were subjected to AMR phenotypic and genotypic characterisation. The proportion of E. coli isolates resistant to at least one of the antimicrobials tested from wild birds (80.8%) was significantly higher than that of isolates from rodents (40.0%). The proportion of E. coli isolates resistant to each antimicrobial class for wild birds was 3.8% to 73.1% and that for rodents was 5.0% to 35.0%. Six out of 26 E. coli isolates from wild birds (23.1%) and two out of 20 (10.0%) isolates from rodents were multi-drug resistant (MDR) strains. These MDR E. coli isolates were detected with various antimicrobial resistance genes such as blaTEM-1B and qnrS1 and could be considered as part of the environmental resistome. Findings in this study suggested that wild birds and rodents could play a role in disseminating antimicrobial resistant E. coli, and this underscores the necessity of environment management and close monitoring on AMR bacteria in wild birds and rodents to prevent spreading of resistant organisms to other wildlife animals and humans.

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“…In particular, the E. coli O104:H4 outbreak in Germany in 2011 was caused by a strain that had acquired characteristics of two previously described pathotypes (59). The emergence of antibiotic-resistant Shigella with the absence of an effective vaccine highlights the importance of a detailed investigation of this pathogen (60). Our results contribute to the understanding of genomic properties associated with adаptation to intracellularptation to intracellular lifestyle of Shigella and EIEC and the developed approaches should be broadly applicable to other young bacterial pathogens.…”

Section: Discussionmentioning

confidence: 99%

High rates of genome rearrangements and pathogenicity ofShigellaspp

Seferbekova

Zabelkin

Yakovleva

et al. 2020

Preprint

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KeywordShigella, Escherichia coli, genomic rearrangements, pathogens, recombination, IS, ipaH AbstractThe genus Shigella comprises a polyphyletic group of facultative intracellular pathogens that evolved from Escherichia coli. Shigella genomes have accumulated mobile elements, which may have been caused by decreased effective population size and concomitant reduction of purifying selection that allowed their proliferation. Here, we investigated the interplay of the accumulation of genomic repeats with genomic rearrangements and their impact on adaptation in bacterial evolution. We studied 414 genomes of E. coli and Shigella strains to assess the contribution of genomic rearrangements to Shigella pathoadaptation. We show that Shigella accumulated a variety of insertion sequences (ISs), experienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination. IS families differ in the expansion rates in Shigella lineages, as expected given their independent origin. In contrast, the number of IS elements and, consequently, the rate of genome rearrangements in the enteroinvasive E. coli strain (EIEC) strain are comparable to those in other E. coli. We found two chromosomal E3 ubiquitin-protein ligases (putative IpaH family proteins) that are functional in all Shigella strains, while only one pseudogenised copy is found in the EIEC strain and none in other E. coli. Taken together, our data indicate that ISs played an important role in the adaptation of Shigella strains to a intracellular lifestyle and that the composition of functional types of ubiquitinprotein ligases may explain the differences in the infectious dose and disease severity between Shigella and EIEC pathotypes. Impact statementPathogenic Escherichia coli frequently cause infections in humans. Many E. coli exist in nature and their ability to cause disease is fueled by their ability to incorporate novel genetic information by extensive horizontal gene transfer of plasmids and pathogenicity islands. The emergence of antibiotic-resistant Shigella, which is a pathogenic form of E. coli, coupled with the absence of an effective vaccine against them, highlights the importance of continued study of these pathogenic bacteria. Our study contributes to the understanding of genomic properties associated with molecular mechanisms underpinning the pathogenic nature of Shigella. We show the contribution of insertion sequences in adaptation of these intracellular pathogens and indicate a role of chromosomal ipaH genes in Shigella pathogenesis. The approaches developed in our study are broadly applicable to investigation of genotype-phenotype correlation in historically young bacterial pathogens. Data summary

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Genotypic characterization of multiple drug resistant Escherichia coli isolates from a pediatric cancer hospital in Egypt

Cited by 15 publications

References 55 publications

High Rates of Genome Rearrangements and Pathogenicity of Shigella spp.

High Rates of Genome Rearrangements and Pathogenicity of Shigella spp.

Occurrence and Antimicrobial Resistance Traits of Escherichia coli from Wild Birds and Rodents in Singapore

High rates of genome rearrangements and pathogenicity ofShigellaspp

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