Comparative genomics profiling of clinical isolates of Aeromonas salmonicida using DNA microarrays

Nash, John H. E.; Findlay, Wendy A.; Luebbert, Christian; Mykytczuk, Oksana; Foote, Simon J.; Taboada, Eduardo N.; Carrillo, Catherine D.; Boyd, Jessica M.; Colquhoun, Duncan J.; Reith, Michael; Brown, Laura L.

doi:10.1186/1471-2164-7-43

Cited by 29 publications

(10 citation statements)

References 41 publications

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“…salmonicida isolated since the 1950s and originating from all over the world have very similar patterns, indicating that they form a single clone showing pathoadaptational stability. Altogether, our results confirm those of a previous study comparing genomic profiles of clinical isolates of Aeromonas salmonicida using DNA microarrays [32]. With the origin and intensification of fish farming, genetic rearrangements occurring through IS transposition events could have been responsible for the selection and the emergence of this pathogenic fish specific clone.…”

Section: Discussionsupporting

confidence: 88%

Clustering subspecies of Aeromonas salmonicida using IS630typing

2013

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BackgroundThe insertion element IS630 found in Aeromonas salmonicida belongs to the IS630-Tc1-mariner superfamily of transposons. It is present in multiple copies and represents approximately half of the IS present in the genome of A. salmonicida subsp. salmonicida A449.ResultsBy using High Copy Number IS630 Restriction Fragment Length Polymorphism (HCN-IS630-RFLP), strains of various subspecies of Aeromonas salmonicida showed conserved or clustering patterns, thus allowing their differentiation from each other. Fingerprints of A. salmonicida subsp. salmonicida showed the highest homogeneity while ‘atypical’ A. salmonicida strains were more heterogeneous. IS630 typing also differentiated A. salmonicida from other Aeromonas species. The copy number of IS630 in Aeromonas salmonicida ranges from 8 to 35 and is much lower in other Aeromonas species.ConclusionsHCN-IS630-RFLP is a powerful tool for subtyping of A. salmonicida. The high stability of IS630 insertions in A. salmonicida subsp. salmonicida indicates that it might have played a role in pathoadaptation of A. salmonicida which has reached an optimal configuration in the highly virulent and specific fish pathogen A. salmonicida subsp. salmonicida.

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Section: Discussionsupporting

confidence: 88%

Clustering subspecies of Aeromonas salmonicida using IS630typing

2013

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“…CGH is a comprehensive analytical tool permitting the examination of multiple bacterial strains at the whole-genome level, providing data about the acquisition and loss of genetic information, the potential evolutionary lineages of pathogens, and the identification of virulence-associated and/or strain-specific genes. Recently, a number of important bacterial pathogens of humans and animals have been analyzed using CGH, including Bordetella pertussis (23), Vibrio cholerae (26), Helicobacter pylori (85), Coxiella burnetti (3), Yersinia pestis (42), and Aeromonas salmonicida (67).…”

Section: Discussionmentioning

confidence: 99%

Defining Genomic Islands and Uropathogen-Specific Genes in Uropathogenic Escherichia coli

2007

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Uropathogenic Escherichia coli (UPEC) strains are responsible for the majority of uncomplicated urinary tract infections, which can present clinically as cystitis or pyelonephritis. UPEC strain CFT073, isolated from the blood of a patient with acute pyelonephritis, was most cytotoxic and most virulent in mice among our strain collection. Based on the genome sequence of CFT073, microarrays were utilized in comparative genomic hybridization (CGH) analysis of a panel of uropathogenic and fecal/commensal E. coli isolates. Genomic DNA from seven UPEC (three pyelonephritis and four cystitis) isolates and three fecal/commensal strains, including K-12 MG1655, was hybridized to the CFT073 microarray. The CFT073 genome contains 5,379 genes; CGH analysis revealed that 2,820 (52.4%) of these genes were common to all 11 E. coli strains, yet only 173 UPEC-specific genes were found by CGH to be present in all UPEC strains but in none of the fecal/commensal strains. When the sequences of three additional sequenced UPEC strains (UTI89, 536, and F11) and a commensal strain (HS) were added to the analysis, 131 genes present in all UPEC strains but in no fecal/commensal strains were identified. Seven previously unrecognized genomic islands (>30 kb) were delineated by CGH in addition to the three known pathogenicity islands. These genomic islands comprise 672 kb of the 5,231-kb (12.8%) genome, demonstrating the importance of horizontal transfer for UPEC and the mosaic structure of the genome. UPEC strains contain a greater number of iron acquisition systems than do fecal/commensal strains, which is reflective of the adaptation to the iron-limiting urinary tract environment. Each strain displayed distinct differences in the number and type of known virulence factors. The large number of hypothetical genes in the CFT073 genome, especially those shown to be UPEC specific, strongly suggests that many urovirulence factors remain uncharacterized.Escherichia coli strains capable of causing disease outside the gastrointestinal tract belong to a diverse group of isolates referred to as extraintestinal pathogenic E. coli (ExPEC) (50, 84). ExPEC strains are responsible for a variety of diseases, including urinary tract infections (UTIs), newborn meningitis, septicemia, nosocomial pneumonia, intra-abdominal infections, osteomyelitis and wound infections (22,27,49,84). Uropathogenic E. coli (UPEC), a prominent member of the ExPEC family, is responsible for up to 90% of uncomplicated UTIs in otherwise healthy individuals (108). An infection occurs primarily by the ascending route following the contamination of the periurethral area, presumably via a fecal reservoir. Bacteria ascend the urethra and colonize the bladder, resulting in cystitis, and in severe cases, infection may spread up the ureters to the kidneys, causing pyelonephritis (15). A serious and potentially life-threatening complication of pyelonephritis occurs when bacteria invade the bloodstream and produce a systemic infection. Due to anatomical differences, UTIs are significantly mo...

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“…More recently, DNA microarray was applied in combination with comparative genomic hybridization. Nash et al (2006) investigated 2024 genes belonging to 11 isolates of A. salmonicida subsp. salmonicida alongside 11 atypical isolates.…”

Section: Within the A Salmonicida Speciesmentioning

confidence: 99%

Aeromonas salmonicida: updates on an old acquaintance

Menanteau–Ledouble¹,

Kumar²,

Saleh³

et al. 2016

Dis. Aquat. Org.

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Aeromonas salmonicida is the oldest known infectious agent to be linked to fish disease and constitutes a major bacterial pathogen of fish, in particular of salmonids. This bacterium can be found almost worldwide in both marine and freshwater environments and has been divided into several sub-species. In this review, we present the most recent developments concerning our understanding of this pathogen, including how the characterization of new isolates from non-salmonid hosts suggests a more nuanced picture of the importance of the so-called 'atypical isolates'. We also describe the clinical presentation regarding the infection across several fish species and discuss what is known about the virulence of A. salmonicida and, in particular, the role that the type 3 secretion system might play in suppressing the immune response of its hosts. Finally, isolates have displayed varied levels of antibiotic resistance. Hence, we review a number of solutions that have been developed both to prevent outbreaks and to treat them once they occur, including the application of pre-and probiotic supplements.

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Comparative genomics profiling of clinical isolates of Aeromonas salmonicida using DNA microarrays

Cited by 29 publications

References 41 publications

Clustering subspecies of Aeromonas salmonicida using IS630typing

Clustering subspecies of Aeromonas salmonicida using IS630typing

Defining Genomic Islands and Uropathogen-Specific Genes in Uropathogenic Escherichia coli

Aeromonas salmonicida: updates on an old acquaintance

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