Phenotypic Microarrays Suggest Escherichia coli ST131 Is Not a Metabolically Distinct Lineage of Extra-Intestinal Pathogenic E. coli

Alqasim, Abdulaziz; Emes, Richard D.; Clark, Gemma; Newcombe, Jane; Ragione, Roberto M. La; McNally, Alan

doi:10.1371/journal.pone.0088374

Cited by 18 publications

(25 citation statements)

References 43 publications

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“…In this connection, we tested and compared sugar source utilization and found that the ST131 strains were only moderately superior to the other E. coli strains tested in metabolizing the 35 sugars tested. Our data are not in total agreement with those of Gibreel et al (52) or Alqasim et al (49) because our study did not show either a significantly enhanced or a significantly reduced metabolic capacity of ST131 strains in comparison with the metabolic capacity of other non-ST131 E. coli strains. This discrepancy could be due to differences in the types of tests employed, differences in the study populations, and/or comparisons of biased samples.…”

Section: Discussioncontrasting

confidence: 99%

“…The outcome of the zebra fish lethality assay added to our understanding that E. coli ST131 isolates possess an enhanced virulence potential and, thereby, an enhanced ability to cause invasive disease (20,46,47), although this may not consistently corroborate the findings of different studies performed in different settings and with different isolates (48)(49)(50)(51)(52). Nevertheless, the assay provided a much needed in vivo snapshot to establish the virulence attributes of our ST131 strains in adult zebra fish, even though the number of strains in each group was limited.…”

Section: Discussionmentioning

confidence: 99%

“…Studies have reported variations in the virulence-associated gene profile (VAGF) among ST131 strains, which causes one to question the role of VAGF in the current success of ST131 (49,50), and therefore, these studies have proposed other factors, such as an enhanced metabolic potential, that contribute to the fitness of this dominant clone. Also, it is well established that bacterial metabolic potential can enhance fitness, leading to increased pathogenesis.…”

Section: Discussionmentioning

confidence: 99%

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Genotypic and Phenotypic Profiles of Escherichia coli Isolates Belonging to Clinical Sequence Type 131 (ST131), Clinical Non-ST131, and Fecal Non-ST131 Lineages from India

Hussain

Ranjan

Nandanwar

et al. 2014

Antimicrob Agents Chemother

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cIn view of the epidemiological success of CTX-M-15-producing lineages of Escherichia coli and particularly of sequence type 131 (ST131), it is of significant interest to explore its prevalence in countries such as India and to determine if antibiotic resistance, virulence, metabolic potential, and/or the genetic architecture of the ST131 isolates differ from those of non-ST131 isolates. A collection of 126 E. coli isolates comprising 43 ST131 E. coli, 40 non-ST131 E. coli, and 43 fecal E. coli isolates collected from a tertiary care hospital in India was analyzed. These isolates were subjected to enterobacterial repetitive intergenic consensus (ERIC)-based fingerprinting, O typing, phylogenetic grouping, antibiotic sensitivity testing, and virulence and antimicrobial resistance gene (VAG) detection. Representative isolates from this collection were also analyzed by multilocus sequence typing (MLST), conjugation, metabolic profiling, biofilm production assay, and zebra fish lethality assay. All of the 43 ST131 E. coli isolates were exclusively associated with phylogenetic group B2 (100%), while most of the clinical non-ST131 and stool non-ST131 E. coli isolates were affiliated with the B2 (38%) and A (58%) phylogenetic groups, respectively. Significantly greater proportions of ST131 isolates (58%) than non-ST131 isolates (clinical and stool E. coli isolates, 5% each) were technically identified to be extraintestinal pathogenic E. coli (ExPEC). The clinical ST131, clinical non-ST131, and stool non-ST131 E. coli isolates exhibited high rates of multidrug resistance (95%, 91%, and 91%, respectively), extended-spectrum-␤-lactamase (ESBL) production (86%, 83%, and 91%, respectively), and metallo-␤-lactamase (MBL) production (28%, 33%, and 0%, respectively). CTX-M-15 was strongly linked with ESBL production in ST131 isolates (93%), whereas CTX-M-15 plus TEM were present in clinical and stool non-ST131 E. coli isolates. Using MLST, we confirmed the presence of two NDM-1-positive ST131 E. coli isolates. The aggregate bioscores (metabolite utilization) for ST131, clinical non-ST131, and stool non-ST131 E. coli isolates were 53%, 52%, and 49%, respectively. The ST131 isolates were moderate biofilm producers and were more highly virulent in zebra fish than non-ST131 isolates. According to ERIC-based fingerprinting, the ST131 strains were more genetically similar, and this was subsequently followed by the genetic similarity of clinical non-ST131 and stool non-ST131 E. coli strains. In conclusion, our data provide novel insights into aspects of the fitness advantage of E. coli lineage ST131 and suggest that a number of factors are likely involved in the worldwide dissemination of and infections due to ST131 E. coli isolates.

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Section: Discussioncontrasting

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Genotypic and Phenotypic Profiles of Escherichia coli Isolates Belonging to Clinical Sequence Type 131 (ST131), Clinical Non-ST131, and Fecal Non-ST131 Lineages from India

Hussain

Ranjan

Nandanwar

et al. 2014

Antimicrob Agents Chemother

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“…Long branch lengths of the ST 131 cluster reflected ancient origins and high diversity within the ST. Consistent with our findings, a recent study using a phenotypic microarray showed that ST 131 was not a distinct lineage of ExPEC (Alqasim et al, 2014). We observed a similar level of diversity in other sequence types, with substantial variation among strains of the same ST of over 100 pairwise differences.…”

Section: Discussionsupporting

confidence: 93%

Whole-genome sequencing of uropathogenic Escherichia coli reveals long evolutionary history of diversity and virulence

Zhang

Foxman

et al. 2015

Infection, Genetics and Evolution

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Uropathogenic Escherichia coli (UPEC) are phenotypically and genotypically very diverse. This diversity makes it challenging to understand the evolution of UPEC adaptations responsible for causing urinary tract infections (UTI). To gain insight into the relationship between evolutionary divergence and adaptive paths to uropathogenicity, we sequenced at deep coverage (190×) the genomes of 19 E. coli strains from urinary tract infection patients from the same geographic area. Our sample consisted of 14 UPEC isolates and 5 non-UTI-causing (commensal) rectal E. coli isolates. After identifying strain variants using de novo assembly-based methods, we clustered the strains based on pairwise sequence differences using a neighbor-joining algorithm. We examined evolutionary signals on the whole-genome phylogeny and contrasted these signals with those found on gene trees constructed based on specific uropathogenic virulence factors. The whole-genome phylogeny showed that the divergence between UPEC and commensal E. coli strains without known UPEC virulence factors happened over 32 million generations ago. Pairwise diversity between any two strains was also high, suggesting multiple genetic origins of uropathogenic strains in a small geographic region. Constrasting the whole-genome phylogeny with three gene trees constructed from common uropathogenic virulence factors, we detected no selective advantage of these virulence genes over other genomic regions. These results suggest that UPEC acquired uropathogenicity long time ago and used it opportunistically to cause extraintestinal infections.

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“…To increase the number of conditions available for testing, bacterial PMs have been designed to comprehensively screen bacterial strains for unique phenotypes (18). These arrays have been used to assess the fitness cost of antimicrobial resistance (19), to determine whether the increased pathogenicity of sequence type 131 extraintestinal pathogenic Escherichia coli is due to an altered metabolic profile (20), to examine the biological role of two-component systems in E. coli (21), and to identify the physiological functions of genes (22,23). Here, we have optimized growth conditions (culture medium, inoculum size, and incubation time) for N. gonorrhoeae and used them for the first PM analysis of N. gonorrhoeae to assess the physiological functions of vaccine candidate proteins NGO1205, NGO2054, NGO2121, NGO1985, NGO2054, chromosome locus J]); however, in N. gonorrhoeae, it does not contain an invariant cysteine residue, a hallmark feature of all lipoproteins (4).…”

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confidence: 99%

Deciphering the Function of New Gonococcal Vaccine Antigens Using Phenotypic Microarrays

et al. 2017

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The function and extracellular location of cell envelope proteins make them attractive candidates for developing vaccines against bacterial diseases, including challenging drug-resistant pathogens, such as Neisseria gonorrhoeae. A proteomicsdriven reverse vaccinology approach has delivered multiple gonorrhea vaccine candidates; however, the biological functions of many of them remain to be elucidated. Herein, the functions of six gonorrhea vaccine candidates-NGO2121, NGO1985, NGO2054, NGO2111, NGO1205, and NGO1344 -in cell envelope homeostasis were probed using phenotype microarrays under 1,056 conditions and a ΔbamE mutant (Δngo1780) as a reference of perturbed outer membrane integrity. Optimal growth conditions for an N. gonorrhoeae phenotype microarray assay in defined liquid medium were developed, which can be useful in other applications, including rapid and thorough antimicrobial susceptibility assessment. Our studies revealed 91 conditions having uniquely positive or negative effects on one of the examined mutants. A cluster analysis of 37 and 57 commonly beneficial and detrimental compounds, respectively, revealed three separate phenotype groups: NGO2121 and NGO1985; NGO1344 and BamE; and the trio of NGO1205, NGO2111, and NGO2054, with the last protein forming an independent branch of this cluster. Similar phenotypes were associated with loss of these vaccine candidates in the highly antibiotic-resistant WHO X strain. Based on their extensive sensitivity phenomes, NGO1985 and NGO2121 appear to be the most promising vaccine candidates. This study establishes the principle that phenotype microarrays can be successfully applied to a fastidious bacterial organism, such as N. gonorrhoeae. IMPORTANCE Innovative approaches are required to develop vaccines against prevalent and neglected sexually transmitted infections, such as gonorrhea. Herein, we have utilized phenotype microarrays in the first such investigation into Neisseria gonorrhoeae to probe the function of proteome-derived vaccine candidates in cell envelope homeostasis. Information gained from this screening can feed the vaccine candidate decision tree by providing insights into the roles these proteins play in membrane permeability, integrity, and overall N. gonorrhoeae physiology. The optimized screening protocol can be applied in investigations into the function of other hypothetical proteins of N. gonorrhoeae discovered in the expanding number of whole-genome sequences, in addition to revealing phenotypic differences between clinical and laboratory strains.KEYWORDS Neisseria gonorrhoeae, vaccine antigens, cell envelope, phenotypic microarrays, antibiotics, Biolog I n Gram-negative bacteria, the cell envelope is composed of the outer membrane, the cell wall, and the cytoplasmic or inner membrane, each of which can be further broken down into its constituents (1). The outer membrane is a bilayer composed of a lipopolysaccharide (LPS) or lipooligosaccharide (LOS) outer leaflet facing the extracel-

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Phenotypic Microarrays Suggest Escherichia coli ST131 Is Not a Metabolically Distinct Lineage of Extra-Intestinal Pathogenic E. coli

Cited by 18 publications

References 43 publications

Genotypic and Phenotypic Profiles of Escherichia coli Isolates Belonging to Clinical Sequence Type 131 (ST131), Clinical Non-ST131, and Fecal Non-ST131 Lineages from India

Genotypic and Phenotypic Profiles of Escherichia coli Isolates Belonging to Clinical Sequence Type 131 (ST131), Clinical Non-ST131, and Fecal Non-ST131 Lineages from India

Whole-genome sequencing of uropathogenic Escherichia coli reveals long evolutionary history of diversity and virulence

Deciphering the Function of New Gonococcal Vaccine Antigens Using Phenotypic Microarrays

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