Advances in Molecular Serotyping and Subtyping of Escherichia coli†

Fratamico, Pina M.; DebRoy, Chitrita; Liu, Yanhong; Needleman, David S.; Baranzoni, Gian Marco; Feng, Peter

doi:10.3389/fmicb.2016.00644

Cited by 125 publications

(106 citation statements)

References 93 publications

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“…Different phenotypic and biochemical characteristics have been previously used for the epidemiological investigations of E. coli [3] . However, the limitations of the phenotypically based typing methods (time consuming and lacking sufficient resolution amongst related strains), have led to the development of many DNA-based techniques.…”

Section: Introductionmentioning

confidence: 99%

BOX ve (GTG)5 Parmak izi Metotlarının İran’da Tavuklardan İzole Edilen Escherichia coli’nin Moleküler Tiplendirilmesinde Klonal Heterojenite ve Yeterliliği

Kheiri¹,

Akhtari²

2017

Kafkas Univ Vet Fak Derg

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Citation of This ArticleKheiri R, Akhtari L: Clonal heterogeneity and efficacy of BOX and (GTG)5 fingerprinting methods for molecular typing of Escherichia coli isolated from chickens in IRI. Kafkas Univ Vet Fak Derg, 23 (2): 219-225, 2017. DOI: 10.9775/kvfd.2016 AbstractThis study evaluates the clonal heterogeneity and efficacy of BOX-PCR and (GTG)5-PCR for DNA-based typing of Escherichia coli strains isolated from feces of chickens in IRI. Fecal samples were collected from chicken husbandry followed by E. coli isolation through biochemical tests. Isolates were finger printed by BOX-A1 and (GTG)5 primers. Dendrograms were generated based on 80% similarity and Shannon-Weaver index was calculated. One hundred and six E. coli isolates were obtained from chicken's fecal sample. By (GTG)5 primer, of 106 isolates, two isolates were untypeable, while 104 isolates generated 100 unique, and 2 duplicate profiles. The dendrogram generated six clusters (G1-G6). With BOX-PCR, 106 E. coli isolates revealed 50 unique BOX profiles, in addition to 22 repetitive profiles, while 12 isolates were untypeable. Based on the bands and dendrogram, the 106 strains were grouped into six clusters (B1-B6). Shannon-Weaver index was 4.665 for (GTG)5-PCR and 0.281 for BOX-PCR. (GTG)5-PCR revealed complex clonal heterogeneity, more discriminatory power, less untypeable isolates, higher Shannon-Weaver index, and less isolates with the same profile in comparison to BOX-PCR. Although (GTG)5-PCR proved to be a powerful typing method, it is recommended to combine two or more different typing methods for higher discriminatory power. (GTG)5-PCR; BOX-PCR ile karşılaştırıldığında kompleks klonal heterojenite, daha fazla ayırt edici güç, daha az tiplendirilemeyen izolat, daha yüksek Shannon-Weaver endeksi ve daha az aynı profilli izolat elde edilmesini sağladı. (GTG)5-PCR daha güçlü tiplendirme metodu olmasına rağmen iki veya daha fazla tiplendirme metodunun birlikte kullanılması daha yüksek ayırıcı güç için önerilmektedir. Keywords: BOX-PCR, Chicken, Clonal heterogeneity, Escherichia coli, (GTG)5-PCR, Molecular typing BOX ve (GTG) 5 Parmak izi Metotlarının İran'da Tavuklardan İzole Edilen

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Section: Introductionmentioning

confidence: 99%

BOX ve (GTG)5 Parmak izi Metotlarının İran’da Tavuklardan İzole Edilen Escherichia coli’nin Moleküler Tiplendirilmesinde Klonal Heterojenite ve Yeterliliği

Kheiri¹,

Akhtari²

2017

Kafkas Univ Vet Fak Derg

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“…The detection of virulence genes in E. coli typically has, until recently, relied on phenotypic tests such as hemolysis, the cell culture assay for toxins, or PCR-based amplification of virulence genes (119). Completion of these typing tests (including PFGE, MLST, PCR, and serotyping) would generally take Ͼ5 days, while WGS can provide analogous data in 3 days (120).…”

Section: E Colimentioning

confidence: 99%

Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing

et al. 2016

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SUMMARYThe epidemiological investigation of a foodborne outbreak, including identification of related cases, source attribution, and development of intervention strategies, relies heavily on the ability to subtype the etiological agent at a high enough resolution to differentiate related from nonrelated cases. Historically, several different molecular subtyping methods have been used for this purpose; however, emerging techniques, such as single nucleotide polymorphism (SNP)-based techniques, that use whole-genome sequencing (WGS) offer a resolution that was previously not possible. With WGS, unlike traditional subtyping methods that lack complete information, data can be used to elucidate phylogenetic relationships and disease-causing lineages can be tracked and monitored over time. The subtyping resolution and evolutionary context provided by WGS data allow investigators to connect related illnesses that would be missed by traditional techniques. The added advantage of data generated by WGS is that these data can also be used for secondary analyses, such as virulence gene detection, antibiotic resistance gene profiling, synteny comparisons, mobile genetic element identification, and geographic attribution. In addition, several software packages are now available to generatein silicoresults for traditional molecular subtyping methods from the whole-genome sequence, allowing for efficient comparison with historical databases. Metagenomic approaches using next-generation sequencing have also been successful in the detection of nonculturable foodborne pathogens. This review addresses state-of-the-art techniques in microbial WGS and analysis and then discusses how this technology can be used to help support food safety investigations. Retrospective outbreak investigations using WGS are presented to provide organism-specific examples of the benefits, and challenges, associated with WGS in comparison to traditional molecular subtyping techniques.

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“…Inaccuracy due to cross reactivity of the antisera with different serogroups can also be considered a disadvantage (Fratamico et al, 2016a). Traditional serotyping can only be performed in specialised laboratories, although some laboratories are now also using a PCR based typing system (Fratamico et al, 2016a;Iguchi et al, 2015;Lacher et al, 2014).…”

Section: Serological Classificationmentioning

confidence: 99%

“…Overall, serotyping is complex as currently there are 186 different O-groups as well as 53 H-groups among E. coli (Fratamico et al, 2016a). Furthermore, serotyping is labour intensive, time consuming and expensive (Fratamico et al, 2016a).…”

Section: Serological Classificationmentioning

confidence: 99%

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Studies on avian pathogenic Escherichia coli in commercial broiler chicken in South East Queensland

Awawdeh¹,

Turni²,

Henning³

et al.

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Avian pathogenic Escherichia coli (APEC) is the causative agent of avian colibacillosis, a localised or systemic infection resulting in clinical diseases such as colisepticemia, chronic respiratory disease and swollen-head syndrome. Globally, avian colibacillosis is the leading cause of morbidity and mortality in poultry, and it has been associated with massive economic losses and welfare problems.This organism is of public health significance as APEC is communicable to humans. The diagnosis of avian colibacillosis relies on clinical signs, typical pathological lesions and culture of E. coli from affected tissue(s). Antimicrobial therapy is often used both for treatment and control. Previous overseas studies have characterised APEC and identified virulence genes (VGs) that can be used as molecular markers for the identification of APEC. Little is known about APEC in broiler chickens in Australia.The aim of this thesis was to gain a better understanding of the epidemiology of APEC in Australian broiler flocks and how factors including presence of VGs and phylogenetic group can improve the identification of this pathotype in Australia. Firstly, three faecal DNA extraction methods were evaluated. Faeces were collected from healthy chickens and chickens with colibacillosis from commercial broiler farms in South East Queensland (SEQ). The extracted DNA was screened by a pentaplex-PCR for five APEC-associated VGs (iroN, iutA, iss, hlyF and ompT). DNA extracted from E. coli isolates cultured from the cloaca and organs of the birds were screened using the same PCR.Repeated bead beating plus column elution was the preferred DNA extraction method, as it yielded good PCR quality and adequate quantity DNA. However, identifying APEC by direct detection of the five VGs from the faecal material was not feasible as all of these genes were also detected in all of the birds. However, the VGs were more commonly detected in E. coli isolates cultured from birds with colibacillosis.A cross-sectional study was performed to estimate APEC farm-level prevalence in healthy broiler chickens in SEQ and to identify potential risk factors associated with the carriage of APEC. At the farm-level, all of the 40 farms sampled were positive for APEC, that is at least one bird per farm carried APEC, while the within-farm prevalence was 63% (95% Confidence Interval: 55.8, 70.2).Higher APEC within-farm bird-level prevalence was significantly associated with the usage of well water as a source of drinking water, failure to disinfect the water line after each flock, farm visitors not showering before entering the shed, distances greater than 20 metres between the car park and the poultry shed and the presence of wild birds within 50 metres of the shed. Chlorinating the drinking water combined with automatic water filtration reduced within-farm bird-level APEC prevalence. Page | 3Therefore, based on the results concluded from the multivariable model, improving biosecurity and water treatments might reduce APEC prevalence, decrease the risk of co...

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Advances in Molecular Serotyping and Subtyping of Escherichia coli†

Cited by 125 publications

References 93 publications

BOX ve (GTG)5 Parmak izi Metotlarının İran’da Tavuklardan İzole Edilen Escherichia coli’nin Moleküler Tiplendirilmesinde Klonal Heterojenite ve Yeterliliği

BOX ve (GTG)5 Parmak izi Metotlarının İran’da Tavuklardan İzole Edilen Escherichia coli’nin Moleküler Tiplendirilmesinde Klonal Heterojenite ve Yeterliliği

Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing

Studies on avian pathogenic Escherichia coli in commercial broiler chicken in South East Queensland

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