Investigating the global genomic diversity of Escherichia coli using a multi-genome DNA microarray platform with novel gene prediction strategies

Jackson, Scott A.; Patel, Isha R.; Barnaba, Tammy J.; LeClerc, J. Eugene; Cebula, Thomas A.

doi:10.1186/1471-2164-12-349

Cited by 41 publications

(54 citation statements)

References 28 publications

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“…Thereafter, the absence/presence gene calls similar to binary nucleotide calls for each isolate were generated into Fasta-formatted files, which were then directly uploaded to the MEGA5 software package. Phylogenetic trees were generated using the maximum likelihood method as described by Jackson et al (38).…”

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Comparative Genotypic and Phenotypic Analysis of Cronobacter Species Cultured from Four Powdered Infant Formula Production Facilities: Indication of Pathoadaptation along the Food Chain

Yan

Wang

Gangiredla

et al. 2015

Appl Environ Microbiol

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cCronobacter species are opportunistic pathogens commonly found in the environment. Among the seven Cronobacter species, Cronobacter sakazakii sequence type 4 (ST-4) is predominantly associated with recorded cases of infantile meningitis. This study reports on a 26-month powdered infant formula (PIF) surveillance program in four production facilities located in distinct geographic regions. The objective was to identify the ST(s) in PIF production environments and to investigate the phenotypic features that support their survival. Of all 168 Cronobacter isolates, 133 were recovered from a PIF production environment, 31 were of clinical origin, and 4 were laboratory type strains. Sequence type 1 (n ‫؍‬ 84 isolates; 63.9%) was the dominant type in PIF production environments. The majority of these isolates clustered with an indistinguishable pulsotype and persisted for at least an 18-month period. Moreover, DNA microarray results identified two phylogenetic lineages among ST-4 strains tested. Thereafter, the ST-1 and -4 isolates were phenotypically compared. Differences were noted based on the phenotypes expressed by these isolates. The ST-1 PIF isolates produced stronger biofilms at both 28°C and 37°C, while the ST-4 clinical isolates exhibited greater swimming activity and increased binding to Congo red dye. Given the fact that PIF is a low-moisture environment and that the clinical environment provides for an interaction between the pathogen and its host, these differences may be consistent with a form of pathoadaptation. These findings help to extend our current understanding of the epidemiology and ecology of Cronobacter species in PIF production environments. The epidemiological link between Cronobacter infection in neonates and contaminated powdered infant formula (PIF) has been previously established (4, 5), with C. sakazakii sequence type 4 (ST-4) being linked to cases of meningitis (6). Outbreaks have been associated with contaminated food products and the presence of this bacterium in PIF production environments (5, 7).In order to rapidly and accurately characterize Cronobacter species in PIF and its associated environments, several molecularbased protocols have been developed, which include direct target gene detection and subtyping methods (8-20). Pulsed-field gel electrophoresis (PFGE) is an accepted method for tracking isolates across the food chain, and this approach is generally considered suitable for epidemiological studies (12,(21)(22)(23)(24)(25)(26)(27)(28). A multilocus sequence typing (MLST) scheme for Cronobacter species was developed, which focuses on single nucleotide polymorphisms associated with seven housekeeping genes (including atpD, fusA, glnS, gltB, gyrB, infB, and pps) and identifies their associated alleles (29). This protocol has been used to describe some of the diversity related to the genus (6, 29-31). Both PFGE and MLST have been widely applied to study the genomic diversity of Cronobacter isolated from manufacturing facilities, commercial PIF, and follow-up formula, as we...

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“…Briefly, genomic DNA was purified from all of these bacterial isolates, fragmented by DNase I, and labeled as reported previously (37,38). Hybridization was performed according to the Affymetrix GeneChip expression analysis technical manual for the 49-format array.…”

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confidence: 99%

Comparative Genotypic and Phenotypic Analysis of Cronobacter Species Cultured from Four Powdered Infant Formula Production Facilities: Indication of Pathoadaptation along the Food Chain

Yan

Wang

Gangiredla

et al. 2015

Appl Environ Microbiol

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“…For instance, during the last decade, scientists at the Center of Food Safety and Applied Nutrition (CFSAN), FDA in conjunction with Affymetrix, Inc., have developed several microarray assays [25] for the investigation of genetic diversity and phylogenetic relatedness of Escherichia coli O157:H7 [23,26], STEC [22,27], Salmonella [19], Listeria monocytogenes [21], Cronobacter [28][29][30] and enteric viruses [15,17].…”

Section: Multiple Species Component Arraymentioning

confidence: 99%

“…n=126) and phylogenetically-related strains, which were generated from the gene-difference matrix shown in Table 1 as reported by Tall et al [28]. The microarray experimental protocol as described by Jackson et al [26] was used for the interrogation of the strains and for the analysis. The phylogenetic tree illustrates that the Cronobacter microarray could clearly separate the seven species of Cronobacter, with each species forming their own distinct cluster.…”

Section: Multiple Species Component Arraymentioning

confidence: 99%

Advancements in Microarray Utility for Detection and Tracking of Foodborne Microbes in the Genomic Era

Li¹,

Patel²,

Tall³

et al. 2017

Adv Tech Biol Med

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Outbreaks caused by foodborne microbes pose serious public health and food safety concerns worldwide. There is a great demand for rapid, sensitive and high-throughput methods to detect and track these pathogens in food, water and other environments. Recent advances in DNA genomic technology have enabled high-throughput analyses of strains by capturing total genomic content of strains and with concomitant comparative phylogenies. Microarrays are particularly adept for distilling large amounts of genomic DNA sequence information such as the gene(s) or genetic traits of hundreds of foodborne isolates in a single experiment. Hence, over the past two decades, microarray technology has advanced tremendously due to accessibility to thousands of complete and draft microbial genomes and this progress has led to the design and manufacturing of newer microarrays which can now identify gene sequence variations down to a single nucleotide polymorphism. DNA microarray remains a useful tool for rapid and refined genomic analysis of foodborne microbes. In this review, we will primarily focus our discussion on pathogen detection, serotype identification and tracking the genetic diversity and source of contamination of respective foodborne strains with our first-hand experience in using this technology.

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“…Specifically, the transmission of genotypically related ESBL-producing E. coli isolates may occur between patients and hospitals, as well as between cities and countries, due to the high prevalence of foreign travel (5). Although it has been established that E. coli has a high degree of genomic diversity (14,15), further information on the genotypic and phenotypic changes across time and location is required to better understand the transmission patterns of this organism.…”

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Phenotypic and Genotypic Changes over Time and across Facilities of Serial Colonizing and Infecting Escherichia coli Isolates Recovered from Injured Service Members

et al. 2014

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dEscherichia coli is the most common colonizing and infecting organism isolated from U.S. service members injured during deployment. Our objective was to evaluate the phenotypic and genotypic changes of infecting and colonizing E. coli organisms over time and across facilities to better understand their transmission patterns. E. coli isolates were collected via surveillance cultures and infection workups from U.S. military personnel injured during deployment (June 2009 to May 2011). The isolates underwent antimicrobial susceptibility testing, pulsed-field gel electrophoresis, and multiplex PCR for phylotyping to determine their resistance profiles and clonality. A total of 343 colonizing and 136 infecting E. coli isolates were analyzed, of which 197 (57%) and 109 (80%) isolates, respectively, produced extended-spectrum ␤-lactamases (ESBL). Phylogroup A was predominant among both colonizing (38%) and infecting isolates (43%). Although 188 unique pulsed-field types (PFTs) were identified from the colonizing isolates, and 54 PFTs were identified from the infecting isolates, there was a lack of PFT overlap between study years, combat zones, and military treatment facilities. On a per-subject basis, 26% and 32% of the patients with serial colonizing isolates and 10% and 21% with serial infecting isolates acquired changes in their phylogroup and PFT profiles, respectively, over time. The production of ESBL remained high over time and across facilities, with no substantial changes in antimicrobial susceptibilities. Overall, our results demonstrated an array of genotypic and phenotypic differences for the isolates without large clonal clusters; however, the same PFTs were occasionally observed in the colonizing and infecting isolates, suggesting that the source of infections may be endogenous host organisms.

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Investigating the global genomic diversity of Escherichia coli using a multi-genome DNA microarray platform with novel gene prediction strategies

Cited by 41 publications

References 28 publications

Comparative Genotypic and Phenotypic Analysis of Cronobacter Species Cultured from Four Powdered Infant Formula Production Facilities: Indication of Pathoadaptation along the Food Chain

Comparative Genotypic and Phenotypic Analysis of Cronobacter Species Cultured from Four Powdered Infant Formula Production Facilities: Indication of Pathoadaptation along the Food Chain

Advancements in Microarray Utility for Detection and Tracking of Foodborne Microbes in the Genomic Era

Phenotypic and Genotypic Changes over Time and across Facilities of Serial Colonizing and Infecting Escherichia coli Isolates Recovered from Injured Service Members

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