Evaluation of whole-genome sequencing as a genotyping tool for Campylobacter jejuni in comparison with pulsed-field gel electrophoresis and flaA typing

Pendleton, Sean; Hanning, Irene; Biswas, Debabrata; Ricke, Steven C.

doi:10.3382/ps.2012-02695

Cited by 26 publications

(15 citation statements)

References 30 publications

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“…WGS also clarified some of the possible transmission routes suggested by epidemiologic data. In this regard, WGS was superior to PFGE due to its enhanced discriminatory power (Table 2) (0.997 versus 0.892), which has been noted in other studies of bacterial outbreaks (31,79,99,100). In particular, our results are similar to those of Salipante and colleagues (79), who used a different approach to identify SNPs and define outbreak strains but arrived at the same conclusions regarding the deficiencies of PFGE in the context of an A. baumannii outbreak.…”

Section: Figsupporting

confidence: 79%

Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks

2016

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bAcinetobacter baumannii frequently causes nosocomial infections and outbreaks. Whole-genome sequencing (WGS) is a promising technique for strain typing and outbreak investigations. We compared the performance of conventional methods with WGS for strain typing clinical Acinetobacter isolates and analyzing a carbapenem-resistant A. baumannii (CRAB) outbreak. We performed two band-based typing techniques (pulsed-field gel electrophoresis and repetitive extragenic palindromic-PCR), multilocus sequence type (MLST) analysis, and WGS on 148 Acinetobacter calcoaceticus-A. baumannii complex bloodstream isolates collected from a single hospital from 2005 to 2012. Phylogenetic trees inferred from core-genome single nucleotide polymorphisms (SNPs) confirmed three Acinetobacter species within this collection. Four major A. baumannii clonal lineages (as defined by MLST) circulated during the study, three of which are globally distributed and one of which is novel. WGS indicated that a threshold of 2,500 core SNPs accurately distinguished A. baumannii isolates from different clonal lineages. The bandbased techniques performed poorly in assigning isolates to clonal lineages and exhibited little agreement with sequence-based techniques. After applying WGS to a CRAB outbreak that occurred during the study, we identified a threshold of 2.5 core SNPs that distinguished nonoutbreak from outbreak strains. WGS was more discriminatory than the band-based techniques and was used to construct a more accurate transmission map that resolved many of the plausible transmission routes suggested by epidemiologic links. Our study demonstrates that WGS is superior to conventional techniques for A. baumannii strain typing and outbreak analysis. These findings support the incorporation of WGS into health care infection prevention efforts.A n important role of clinical microbiology is to identify relationships between bacterial isolates. At a broad level, phenotypic and genotypic tests are used to categorize bacterial isolates into the same or different species. Within a bacterial species, techniques are used to group isolates into clonal lineages, which are groups of closely related bacteria that share a recent common ancestor but have spread regionally or globally. At a more local level, infection control practitioners must determine whether a group of isolates constitutes a hospital outbreak by ascertaining whether the isolates have a degree of similarity consistent with a common source within the hospital. Once isolates belonging to a hospital outbreak have been identified, similarities and differences between these isolates can be exploited to generate a transmission map to aid in finding the source of the outbreak and in disrupting ongoing pathways of transmission. For some groups of bacteria, such as Acinetobacter, discernment at each level has medically important consequences and therefore must be accomplished by hospital-associated clinical microbiology laboratories.Within the Acinetobacter genus, the Acinetobacter calcoaceticusAcinetobac...

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Section: Figsupporting

confidence: 79%

Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks

2016

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“…WGS can theoretically distinguish strains which differ at only a single nucleotide and, in the limited number of studies where direct comparisons with PFGE have been performed, has provided greater resolution (28,35,36). However, previous work has focused on individual bacterial species, has employed nonuniform validation methodologies, and has utilized heterogeneous library preparation, sequencing, and data analysis methods, making it difficult to integrate and generalize results across studies or to evaluate its suitability for clinical use.…”

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confidence: 99%

Application of Whole-Genome Sequencing for Bacterial Strain Typing in Molecular Epidemiology

et al. 2015

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Nosocomial infections pose a significant threat to patient health; however, the gold standard laboratory method for determining bacterial relatedness (pulsed-field gel electrophoresis [PFGE]) remains essentially unchanged 20 years after its introduction. Here, we explored bacterial whole-genome sequencing (WGS) as an alternative approach for molecular strain typing. We compared WGS to PFGE for investigating presumptive outbreaks involving three important pathogens: vancomycin-resistant Enterococcus faecium (n ‫؍‬ 19), methicillin-resistant Staphylococcus aureus (n ‫؍‬ 17), and Acinetobacter baumannii (n ‫؍‬ 15). WGS was highly reproducible (average < 0.39 differences between technical replicates), which enabled a functional, quantitative definition for determining clonality. Strain relatedness data determined by PFGE and WGS roughly correlated, but the resolution of WGS was superior (P ‫؍‬ 5.6 ؋ 10 ؊8 to 0.016). Several discordant results were noted between the methods. A total of 28.9% of isolates which were indistinguishable by PFGE were nonclonal by WGS. For A. baumannii, a species known to undergo rapid horizontal gene transfer, 16.2% of isolate pairs considered nonidentical by PFGE were clonal by WGS. Sequencing whole bacterial genomes with single-nucleotide resolution demonstrates that PFGE is prone to false-positive and false-negative results and suggests the need for a new gold standard approach for molecular epidemiological strain typing.

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“…Campylobacter jejuni is one of the major food borne disease causing microorganisms that also happens to be very well adapted to the ecological conditions prevalent in the poultry gastrointestinal tract (Pendleton et al, 2013). In an attempt to isolate antibodies that could limit C. jejuni colonization Al-Adwani et al (2013) generated chicken egg-yolk-derived antibodies (IgY) in laying hens against the five different C. jejuni colonization-associated cell surface proteins.…”

Section: Veterinary Applications Of Immunoglobulin Ymentioning

confidence: 99%

The potential application of avian egg antibodies with emphasis on immunotherapeutic and immunodiagnostic purpose

Teshager¹,

Hirigo²,

Fikre³

et al. 2015

J. Vet. Med. Anim. Health

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Avian eggs present an ideal alternative antibody source to mammals as the immunoglobulin (IgY) in the chicken's blood is transported to the egg and accumulates in the egg yolk in large quantities. The existence of an immunoglobulin G (IgG)-like molecule in avian eggs, referred to as IgY, has been well documented, and extensive research has been carried out on its characterization, production and purification. Although it is the functional equivalent of mammalian IgG, the major serum antibody found in mammals IgY is structurally different, and has been found to exhibit several important differences when compared to mammalian antibodies, including its physicochemical properties and immunological capabilities. Recently, considerable research has focus seldom use of IgY as an alternative to mammalian antibodies for several applications, including immunotherapeutic applications, especially for the oral passive immunization against various bacteria and viruses. Much research has also been carried out on the use of IgY as a replacement for IgG in various immunodiagnostic and immunoaffinity purification purposes. The use of IgY offers several advantages over polyclonal antibodies produced in mammals, including providing a much more hygienic, cost efficient, convenient, humane and plentiful source of antigen-specific antibodies.

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Evaluation of whole-genome sequencing as a genotyping tool for Campylobacter jejuni in comparison with pulsed-field gel electrophoresis and flaA typing

Cited by 26 publications

References 30 publications

Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks

Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks

Application of Whole-Genome Sequencing for Bacterial Strain Typing in Molecular Epidemiology

The potential application of avian egg antibodies with emphasis on immunotherapeutic and immunodiagnostic purpose

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