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2. Insular microbiogeography

Author

Kaufman, James H., Elkins, Christopher A., Davis, Matthew, Weis, Allison M, Huang, Bihua C., Mammel, Mark K, Patel, Isha R., Beck, Kristen L., Edlund, Stefan, Chambliss, David, Bianco, Simone, Kunitomi, Mark, and Weimer, Bart C.

Subjects
Quantitative Biology - Genomics, Quantitative Biology - Populations and Evolution
Abstract

The diversity revealed by large scale genomics in microbiology is calling into question long held beliefs about genome stability, evolutionary rate, even the definition of a species. MacArthur and Wilson's theory of insular biogeography provides an explanation for the diversity of macroscopic animal and plant species as a consequence of the associated hierarchical web of species interdependence. We report a large scale study of microbial diversity that reveals that the cumulative number of genes discovered increases with the number of genomes studied as a simple power law. This result is demonstrated for three different genera comparing over 15,000 isolates. We show that this power law is formally related to the MacArthur-Wilson exponent, suggesting the emerging diversity of microbial genotypes arises because the scale independent behavior first reported by MacArthur and Wilson extends down to the scale of microbes and their genes. Assessing the depth of available whole genome sequences implies a dynamically changing core genome, suggesting that traditional taxonomic classifications should be replaced with a quasispecies model that captures the diversity and dynamic exchange of genes. We report Species population "clouds" in a defined microbiome, with scale invariance extending down to the level of single-nucleotide polymorphisms (SNPs)., Comment: 23 pages, 7 figures, including Appendices

Published
2017

14. Insular Microbiogeography: Three Pathogens as Exemplars

Author

Kaufman, James H., primary, Elkins, Christopher A., additional, Davis, Matthew, additional, Weis, Allison M., additional, Huang, Bihua C., additional, Mammel, Mark K., additional, Patel, Isha R., additional, Beck, Kristen L., additional, Edlund, Stefan, additional, Chambliss, David, additional, Douglas, Judith, additional, Bianco, Simone, additional, Kunitomi, Mark, additional, and Weimer, Bart C., additional

Published
2019
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19. Phylogenomic Analysis of Salmonella enterica subsp. enterica Serovar Bovismorbificans from Clinical and Food Samples Using Whole Genome Wide Core Genes and kmer Binning Methods to Identify Two Distinct Polyphyletic Genome Pathotypes

Author

Gopinath, Gopal R; https://orcid.org/0000-0003-2577-7548, Jang, Hyein, Beaubrun, Junia Jean-Gilles, Gangiredla, Jayanthi, Mammel, Mark K, Müller, Andrea, Tamber, Sandeep, Patel, Isha R, Ewing, Laura, Weinstein, Leah M, Wang, Caroline Z, Finkelstein, Samantha, Negrete, Flavia, Muruvanda, Tim, Allard, Marc, Sockett, Donald C, Pagotto, Franco, Tall, Ben D, Stephan, Roger; https://orcid.org/0000-0003-1002-4762, Gopinath, Gopal R; https://orcid.org/0000-0003-2577-7548, Jang, Hyein, Beaubrun, Junia Jean-Gilles, Gangiredla, Jayanthi, Mammel, Mark K, Müller, Andrea, Tamber, Sandeep, Patel, Isha R, Ewing, Laura, Weinstein, Leah M, Wang, Caroline Z, Finkelstein, Samantha, Negrete, Flavia, Muruvanda, Tim, Allard, Marc, Sockett, Donald C, Pagotto, Franco, Tall, Ben D, and Stephan, Roger; https://orcid.org/0000-0003-1002-4762

Abstract

Salmonella enterica subsp. enterica serovar Bovismorbificans has caused multiple outbreaks involving the consumption of produce, hummus, and processed meat products worldwide. To elucidate the intra-serovar genomic structure of S. Bovismorbificans, a core-genome analysis with 2690 loci (based on 150 complete genomes representing Salmonella enterica serovars developed as part of this study) and a k-mer-binning based strategy were carried out on 95 whole genome sequencing (WGS) assemblies from Swiss, Canadian, and USA collections of S. Bovismorbificans strains from foodborne infections. Data mining of a digital DNA tiling array of legacy SARA and SARB strains was conducted to identify near-neighbors of S. Bovismorbificans. The core genome analysis and the k-mer-binning methods identified two polyphyletic clusters, each with emerging evolutionary properties. Four STs (2640, 142, 1499, and 377), which constituted the majority of the publicly available WGS datasets from >260 strains analyzed by k-mer-binning based strategy, contained a conserved core genome backbone with a different evolutionary lineage as compared to strains comprising the other cluster (ST150). In addition, the assortment of genotypic features contributing to pathogenesis and persistence, such as antimicrobial resistance, prophage, plasmid, and virulence factor genes, were assessed to understand the emerging characteristics of this serovar that are relevant clinically and for food safety concerns. The phylogenomic profiling of polyphyletic S. Bovismorbificans in this study corresponds to intra-serovar variations observed in S. Napoli and S. Newport serovars using similar high-resolution genomic profiling approaches and contributes to the understanding of the evolution and sequence divergence of foodborne Salmonellae. These intra-serovar differences may have to be thoroughly understood for the accurate classification of foodborne Salmonella strains needed for the uniform development of future food safet

Published
2022

22. Phylogenomic Analysis of Salmonella enterica subsp. enterica Serovar Bovismorbificans from Clinical and Food Samples Using Whole Genome Wide Core Genes and kmer Binning Methods to Identify Two Distinct Polyphyletic Genome Pathotypes

Author

Gopinath, Gopal R., primary, Jang, Hyein, additional, Beaubrun, Junia Jean-Gilles, additional, Gangiredla, Jayanthi, additional, Mammel, Mark K., additional, Müller, Andrea, additional, Tamber, Sandeep, additional, Patel, Isha R., additional, Ewing, Laura, additional, Weinstein, Leah M., additional, Wang, Caroline Z., additional, Finkelstein, Samantha, additional, Negrete, Flavia, additional, Muruvanda, Tim, additional, Allard, Marc, additional, Sockett, Donald C., additional, Pagotto, Franco, additional, Tall, Ben D., additional, and Stephan, Roger, additional

Published
2022
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26. Comparative genomics of the IncA/C multidrug resistance plasmid family

Author

Fricke, W. Florian, Welch, Timothy J., McDermott, Patrick F., Mammel, Mark K., LeClerc, J. Eugene, White, David G., Cebula, Thomas A., and Ravel, Jacques

Subjects
Drug resistance in microorganisms -- Genetic aspects, Plasmids -- Research, Bacterial genetics -- Research, Biological sciences
Abstract

Multidrug resistance (MDR) plasmids belonging to the IncA/C plasmid family are widely distributed among Salmonella and other enterobacterial isolates from agricultural sources and have, at least once, also been identified in a drug-resistant Yersinia pestis isolate (IP275) from Madagascar. Here, we present the complete plasmid sequences of the IncA/C reference plasmid pRA1 (143,963 bp), isolated in 1971 from the fish pathogen Aeromonas hydrophila, and of the cryptic IncA/C plasmid pRAx (49,763 bp), isolated from Escherichia coli transconjugant D7-3, which was obtained through pRA1 transfer in 1980. Using comparative sequence analysis of pRA1 and pRAx with recent members of the IncA/C plasmid family, we show that both plasmids provide novel insights into the evolution of the IncA/C MDR plasmid family and the minimal machinery necessary for stable IncA/C plasmid maintenance. Our results indicate that recent members of the IncA/C plasmid family evolved from a common ancestor, similar in composition to pRA1, through stepwise integration of horizontally acquired resistance gene arrays into a conserved plasmid backbone. Phylogenetic comparisons predict type IV secretion-like conjugative transfer operons encoded on the shared plasmid backbones to be closely related to a group of integrating conjugative elements, which use conjugative transfer for horizontal propagation but stably integrate into the host chromosome during vegetative growth. A hipAB toxin-antitoxin gene cluster found on pRA1, which in Escherichia coli is involved in the formation of persister cell subpopulations, suggests persistence as an early broad-spectrum antimicrobial resistance mechanism in the evolution of IncA/C resistance plasmids.

Published
2009

27. Optical mapping and 454 sequencing of Escherichia coli O157 : H7 isolates linked to the US 2006 spinach-associated outbreak

Author

Kotewicz, Michael L., Mammel, Mark K., LeClerc, J. Eugene, and Cebula, Thomas A.

Subjects
Escherichia coli -- Research, Escherichia coli -- Genetic aspects, Escherichia coli -- Health aspects, Spinach -- Contamination, Food poisoning -- Research, Nucleotide sequencing -- Usage, Single nucleotide polymorphisms -- Research, Biological sciences
Abstract

Optical maps for five representative clinical, food-borne and bovine-derived isolates from the 2006 Escherichia coil O157 : H7 outbreak linked to fresh spinach in the United States showed a common set of 14 distinct chromosomal markers that define the outbreak strain. Partial 454 DNA sequencing was used to characterize the optically mapped chromosomal markers. The markers included insertions, deletions, substitutions and a simple single nucleotide polymorphism creating a BamHI site. The Shiga toxin gene profile of the spinach-associated outbreak isolates ([stx1.sup.-1] [stx2.sup.+] [stx2c.sup.+]) correlated with prophage insertions different from those in the prototypical EDL933 and Sakai reference strains ([stx1.sup.+] [stx2.sup.+] [stx2c.sup.-]). The prophage occupying the yehV chromosomal position in the spinach-associated outbreak isolates was similar to the [stx1.sup.+] EDL933 cryptic prophage V, but it lacked the stx1 gene. In EDL933, the stx2 genes are within prophage BP933-W at the wrbA chromosomal locus; this locus was unoccupied in the spinach outbreak isolates. Instead, the stx2 genes were found within a chimeric BP933-W-like prophage with a different integrase, inserted at the argW locus in the outbreak isolates. An extra set of Shiga toxin genes, stx2c, was found in the outbreak isolates within a prophage integrated at the sbcB locus. The optical maps of two additional clinical isolates from the outbreak showed a single, different prophage variation in each, suggesting that changes occurred in the source strain during the course of this widespread, multi-state outbreak.

Published
2008

28. Altered utilization of n-acetyl-d-galactosamine by Escherichia coli O157:H7 from the 2006 spinach outbreak

Author

Mukherjee, Amit, Mammel, Mark K., LeClerc, J. Eugene, and Cebula, Thomas A.

Subjects
Escherichia coli -- Physiological aspects, Escherichia coli -- Genetic aspects, Spinach -- Diseases and pests, Amines -- Properties, Phenotype -- Properties, Phenotype -- Influence, Glycine -- Properties, Bacterial genetics -- Research, Biological sciences
Abstract

In silico analyses of previously sequenced strains of Escherichia coli O157:H7, EDL933 and Sakai, localized the gene cluster for the utilization of N-acetyl-D-galactosamine (Aga) and D-galactosamine (Gam). This gene cluster encodes the Aga phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) and other catabolic enzymes responsible for transport and catabolism of Aga. As the complete coding sequences for enzyme IIA [(EIIA).sup.Aga/Gam], [EIIB.sup.Aga], [EIID.sup.Aga], and [EIID.sup.Aga] of the Aga PTS are present, E. coli O157:H7 strains normally are able to utilize Aga as a sole carbon source. The Gam PTS complex, in contrast, lacks [EIIC.sup.Gam], and consequently, E. coli O157:H7 strains cannot utilize Gam. Phenotypic analyses of 120 independent isolates of E. coli O157:H7 from our culture collection revealed that the overwhelming majority (118/120) displayed the expected [Aga.sup.+] [Gam.sup.-] phenotype. Yet, when 194 individual isolates, derived from a 2006 spinach-associated E. coli O157:H7 outbreak, were analyzed, all (194/194) displayed an [Aga.sup.-] [Gam.sup.-] phenotype. Comparison of aga/gam sequences from two spinach isolates with those of EDL933 and Sakai revealed a single nucleotide change (G:C[right arrow]A:T) in the agaF gene in the spinach-associated isolates. The base substitution in agaF, which encodes [EILA.sup.Aga/Gam] of the PTS, changes a conserved glycine residue to serine (Gly91Ser). Pyrosequencing of this region showed that all spinach-associated E. coli O157:H7 isolates harbored this same G:C[right arrow]A:T substitution. Notably, when [agaF.sup.+] was cloned into an expression vector and transformed into six spinach isolates, all (6/6) were able to grow on Aga, thus demonstrating that the Gly91Ser substitution underlies the Agaphenotype in these isolates.

Published
2008

30. Analysis of the Molecular Diversity Among Cronobacter Species Isolated From Filth Flies Using Targeted PCR, Pan Genomic DNA Microarray, and Whole Genome Sequencing Analyses

Author

Jang, Hyein, primary, Chase, Hannah R., additional, Gangiredla, Jayanthi, additional, Grim, Christopher J., additional, Patel, Isha R., additional, Kothary, Mahendra H., additional, Jackson, Scott A., additional, Mammel, Mark K., additional, Carter, Laurenda, additional, Negrete, Flavia, additional, Finkelstein, Samantha, additional, Weinstein, Leah, additional, Yan, QiongQiong, additional, Iversen, Carol, additional, Pagotto, Franco, additional, Stephan, Roger, additional, Lehner, Angelika, additional, Eshwar, Athmanya K., additional, Fanning, Seamus, additional, Farber, Jeffery, additional, Gopinath, Gopal R., additional, Tall, Ben D., additional, and Pava-Ripoll, Monica, additional

Published
2020
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34. Analysis of the molecular diversity among cronobacter species isolated from filth flies using targeted PCR, pan genomic DNA microarray, and whole Genome sequencing analyses

Author

Jang, Hyein, Chase, Hannah R, Gangiredla, Jayanthi, Grim, Christopher J, Patel, Isha R, Kothary, Mahendra H, Jackson, Scott A, Mammel, Mark K, Carter, Laurenda, Negrete, Flavia, Finkelstein, Samantha, Weinstein, Leah, Yan, QiongQiong, Iversen, Carol, Pagotto, Franco, Stephan, Roger; https://orcid.org/0000-0003-1002-4762, Lehner, Angelika; https://orcid.org/0000-0003-1863-5090, Eshwar, Athmanya K, Fanning, Séamus; https://orcid.org/0000-0002-1922-8836, Farber, Jeffery, Gopinath, Gopal R, Tall, Ben D, Pava-Ripoll, Monica, Jang, Hyein, Chase, Hannah R, Gangiredla, Jayanthi, Grim, Christopher J, Patel, Isha R, Kothary, Mahendra H, Jackson, Scott A, Mammel, Mark K, Carter, Laurenda, Negrete, Flavia, Finkelstein, Samantha, Weinstein, Leah, Yan, QiongQiong, Iversen, Carol, Pagotto, Franco, Stephan, Roger; https://orcid.org/0000-0003-1002-4762, Lehner, Angelika; https://orcid.org/0000-0003-1863-5090, Eshwar, Athmanya K, Fanning, Séamus; https://orcid.org/0000-0002-1922-8836, Farber, Jeffery, Gopinath, Gopal R, Tall, Ben D, and Pava-Ripoll, Monica

Abstract

Cronobacter species are opportunistic pathogens capable of causing life-threatening infections in humans, with serious complications arising in neonates, infants, immuno-compromised individuals, and elderly adults. The genus is comprised of seven species: Cronobacter sakazakii, Cronobacter malonaticus, Cronobacter turicensis, Cronobacter muytjensii, Cronobacter dublinensis, Cronobacter universalis, and Cronobacter condimenti. Despite a multiplicity of genomic data for the genus, little is known about likely transmission vectors. Using DNA microarray analysis, in parallel with whole genome sequencing, and targeted PCR analyses, the total gene content of two C. malonaticus, three C. turicensis, and 14 C. sakazaki isolated from various filth flies was assessed. Phylogenetic relatedness among these and other strains obtained during surveillance and outbreak investigations were comparatively assessed. Specifically, microarray analysis (MA) demonstrated its utility to cluster strains according to species-specific and sequence type (ST) phylogenetic relatedness, and that the fly strains clustered among strains obtained from clinical, food and environmental sources from United States, Europe, and Southeast Asia. This combinatorial approach was useful in data mining for virulence factor genes, and phage genes and gene clusters. In addition, results of plasmidotyping were in agreement with the species identity for each strain as determined by species-specific PCR assays, MA, and whole genome sequencing. Microarray and BLAST analyses of Cronobacter fly sequence datasets were corroborative and showed that the presence and absence of virulence factors followed species and ST evolutionary lines even though such genes were orthologous. Additionally, zebrafish infectivity studies showed that these pathotypes were as virulent to zebrafish embryos as other clinical strains. In summary, these findings support a striking phylogeny amongst fly, clinical, and surveillance strains isolate

Published
2020

35. Insular Microbiogeography: Three Pathogens as Exemplars

Author

Kaufman, James H., primary, Elkins, Christopher A., additional, Davis, Matthew, additional, Weis, Allison M., additional, Huang, Bihua C., additional, Mammel, Mark K., additional, Patel, Isha R., additional, Beck, Kristen L., additional, Edlund, Stefan, additional, Chambliss, David, additional, Douglas, Judith, additional, Bianco, Simone, additional, Kunitomi, Mark, additional, and Weimer, Bart C., additional

Published
2020
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37. Microbiota of the Hickey Run Tributary of the Anacostia River

Author

Cagle, Robin, primary, Ramachandran, Padmini, additional, Reed, Elizabeth, additional, Commichaux, Seth, additional, Mammel, Mark K., additional, Lacher, David W., additional, Miller, Daniela, additional, Lindley, Sabina, additional, Pop, Mihai, additional, Bazaco, Michael C., additional, Wolpert, Beverly, additional, Strain, Errol A., additional, Aker, Scott, additional, Feely, Joan, additional, and Ottesen, Andrea, additional

Published
2019
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42. Interlaboratory Evaluation of the U.S. Food and Drug Administration Escherichia coli Identification Microarray for Profiling Shiga Toxin–Producing Escherichia coli

Author

Patel, Isha R., primary, Gangiredla, Jayanthi, additional, Lacher, David W., additional, Mammel, Mark K., additional, Bagi, Lori, additional, Baranzoni, Gian Marco, additional, Fratamico, Pina M., additional, Roberts, Elizabeth L., additional, DebRoy, Chitrita, additional, Lindsey, Rebecca L., additional, V. Stoneburg, Devon, additional, Martin, Haley, additional, Smith, Peyton, additional, Strockbine, Nancy A., additional, Elkins, Christopher A., additional, Scheutz, Flemming, additional, and Feng, Peter C.H., additional

Published
2018
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45. Draft Genome Sequences of Escherichia albertii, Escherichia fergusonii, and Strains Belonging to Six Cryptic Lineages of Escherichia spp

Author

Gangiredla, Jayanthi, primary, Mammel, Mark K., additional, Barnaba, Tammy J., additional, Tartera, Carmen, additional, Gebru, Solomon T., additional, Patel, Isha R., additional, Leonard, Susan R., additional, Kotewicz, Michael L., additional, Lampel, Keith A., additional, Elkins, Christopher A., additional, and Lacher, David W., additional

Published
2018
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46. Antimicrobial resistance-conferring plasmids with similarity to virulence plasmids from avian pathogenic Escherichia coli strains in Salmonella enterica serovar Kentucky isolates from poultry

Author

Fricke, W. Florian, McDermott, Patrick F., Mammel, Mark K., Shaohua Zhao, Johnson, Timothy J., Rasko, David A., Fedorka-Cray, Paula J., Pedroso, Adriana, Whichard, Jean M., LeClerec, J. Eugene, White, David G., Cebula, Thomas A., and Ravel, Jacques

Subjects
Drug resistance in microorganisms -- Analysis, Polymerase chain reaction -- Usage, Salmonella -- Genetic aspects, Salmonella -- Environmental aspects, Escherichia coli -- Genetic aspects, Escherichia coli -- Environmental aspects, Biological sciences
Abstract

The plasmid component of the genome of Salmonella Kentucky CVM29188, a multidrug-resistant strain that is isolated from a chicken meat sample with resistance to streptomycin, tetracycline, ampicillin and ceftiofur, is described. A combination of in silico and in vivo approaches, including comparative plasmid transfer, and PCR-based plasmid screenings, is used for providing insights into the genetic basis for multidrug resistance phenotypes of the isolate that provide new clues about virulence evolution and host adaptation in the Salmonella serovar.

Published
2009

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