Characterization and rapid identification of phylogroup G inEscherichia coli, a lineage with high virulence and antibiotic resistance potential

Abstract In this study, we examined the association between antimicrobial resistance, CRISPR/Cas systems and virulence with phage susceptibility in Acinetobacter baumannii and investigated draft genomes of phage susceptible multidrug resistant A. baumannii strains from Thailand. We investigated 230 A. baumannii strains using 17 lytic A. baumannii phages and the phage susceptibility was 46.5% (107/230). Phage susceptibility was also associated with resistance to numerous antibiotics (p-value < 0.05). We also found association between biofilm formation and the presence of ompA gene among phage susceptible A. baumannii strains (p-value < 0.05). A. baumannii isolates carrying cas5 or combinations of two or three other cas genes, showed a significant increase in phage resistance. Whole-genome sequences of seven phage susceptible A. baumannii isolates revealed that six groups of antibiotic resistance genes were carried by all seven phage susceptible A. baumannii. All strains carried biofilm associated genes and two strains harbored complete prophages, acquired copper tolerance genes, and CRISPR-associated (cas) genes. In conclusion, our data exhibits an association between virulence determinants and biofilm formation among phage susceptible A. baumannii strains. These data help to understand the bacterial co-evolution with phages.

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Rapid identification of antibiotic resistance using droplet microfluidics

Bioengineered ◽

10.1080/21655979.2016.1156824 ◽

2016 ◽

Vol 7 (2) ◽

pp. 79-87 ◽

Cited By ~ 12

Author(s):

Marie C. Keays ◽

Mark O'Brien ◽

Anam Hussain ◽

Patrick A. Kiely ◽

Tara Dalton

Keyword(s):

Antibiotic Resistance ◽

Rapid Identification ◽

Droplet Microfluidics

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Discovery ofmcr-1-Mediated Colistin Resistance in a Highly VirulentEscherichia coliLineage

mSphere ◽

10.1128/msphere.00486-18 ◽

2018 ◽

Vol 3 (5) ◽

Cited By ~ 12

Author(s):

Brian M. Forde ◽

Hosam M. Zowawi ◽

Patrick N. A. Harris ◽

Leah Roberts ◽

Emad Ibrahim ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Neonatal Meningitis ◽

Colistin Resistance ◽

Content Type ◽

E Coli ◽

Virulence Potential ◽

High Virulence

ABSTRACTResistance to last-line polymyxins mediated by the plasmid-borne mobile colistin resistance gene (mcr-1) represents a new threat to global human health. Here we present the complete genome sequence of anmcr-1-positive multidrug-resistantEscherichia colistrain (MS8345). We show that MS8345 belongs to serotype O2:K1:H4, has a large 241,164-bp IncHI2 plasmid that carries 15 other antibiotic resistance genes (including the extended-spectrum β-lactamaseblaCTX-M-1) and 3 putative multidrug efflux systems, and contains 14 chromosomally encoded antibiotic resistance genes. MS8345 also carries a large ColV-like virulence plasmid that has been associated withE. colibacteremia. Whole-genome phylogeny revealed that MS8345 clusters within a discrete clade in the sequence type 95 (ST95) lineage, and MS8345 is very closely related to the highly virulent O45:K1:H4 clone associated with neonatal meningitis. Overall, the acquisition of a plasmid carrying resistance to colistin and multiple other antibiotics in this virulentE. colilineage is concerning and might herald an era where the empirical treatment of ST95 infections becomes increasingly more difficult.IMPORTANCEEscherichia coliST95 is a globally disseminated clone frequently associated with bloodstream infections and neonatal meningitis. However, the ST95 lineage is defined by low levels of drug resistance amongst clinical isolates, which normally provides for uncomplicated treatment options. Here, we provide the first detailed genomic analysis of anE. coliST95 isolate that has both high virulence potential and resistance to multiple antibiotics. Using the genome, we predicted its virulence and antibiotic resistance mechanisms, which include resistance to last-line antibiotics mediated by the plasmid-bornemcr-1gene. Finding an ST95 isolate resistant to nearly all antibiotics that also has a high virulence potential is of major clinical importance and underscores the need to monitor new and emerging trends in antibiotic resistance development in this important global lineage.

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Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules

Scientific Reports ◽

10.1038/srep30410 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 23

Author(s):

Lena K. Nyberg ◽

Saair Quaderi ◽

Gustav Emilsson ◽

Nahid Karami ◽

Erik Lagerstedt ◽

...

Keyword(s):

Antibiotic Resistance ◽

Bacterial Resistance ◽

Clinical Epidemiology ◽

Rapid Identification ◽

Sequence Information ◽

Dna Molecules ◽

Structural Variations ◽

Mapping Procedure ◽

Single Dna Molecules ◽

Nanofluidic Channels

Abstract The rapid spread of antibiotic resistance – currently one of the greatest threats to human health according to WHO – is to a large extent enabled by plasmid-mediated horizontal transfer of resistance genes. Rapid identification and characterization of plasmids is thus important both for individual clinical outcomes and for epidemiological monitoring of antibiotic resistance. Toward this aim, we have developed an optical DNA mapping procedure where individual intact plasmids are elongated within nanofluidic channels and visualized through fluorescence microscopy, yielding barcodes that reflect the underlying sequence. The assay rapidly identifies plasmids through statistical comparisons with barcodes based on publicly available sequence repositories and also enables detection of structural variations. Since the assay yields holistic sequence information for individual intact plasmids, it is an ideal complement to next generation sequencing efforts which involve reassembly of sequence reads from fragmented DNA molecules. The assay should be applicable in microbiology labs around the world in applications ranging from fundamental plasmid biology to clinical epidemiology and diagnostics.

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Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing

Scientific Reports ◽

10.1038/s41598-020-64616-x ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 3

Author(s):

Arne M. Taxt ◽

Ekaterina Avershina ◽

Stephan A. Frye ◽

Umaer Naseer ◽

Rafi Ahmad

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Rapid Identification ◽

Blood Cultures ◽

Nanopore Sequencing

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Systematic Evaluation of the Accelerate Pheno System for Susceptibility Testing of Gram-Negative Bacteria Isolated from Blood Cultures

Microbiology Spectrum ◽

10.1128/spectrum.01836-21 ◽

2021 ◽

Vol 9 (3) ◽

Author(s):

Yera A. Patel ◽

Thomas J. Kirn ◽

Melvin P. Weinstein ◽

Priyanka Uprety

Keyword(s):

Antibiotic Resistance ◽

Antimicrobial Therapy ◽

Susceptibility Testing ◽

Rapid Identification ◽

Blood Cultures ◽

Morbidity And Mortality ◽

Systematic Evaluation ◽

Gram Negative Bacteria ◽

Gram Negative

Bacteremia is a major cause of morbidity and mortality. Rapid identification of pathogens for early targeted antimicrobial therapy is crucial for detecting emergence of antibiotic resistance and improving outcomes.

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