Genome Sequence and Comparative Pathogenic Determinants of Multidrug Resistant Uropathogenic Escherichia coli O25b:H4, A Clinical Isolate from Saudi Arabia

Essam J. Alyamani, Anamil M. Khiyami, Rayan Y. Booq, Fayez S. Bahwerth, Benjamin Vaisvil, Daniel P. Schmitt and Vinayak Kapatral

Escherichia coli serotype O25b:H4 is involved in human urinary tract infections. In this study, we sequenced and analyzed E. coli O25b:H4 isolated from a patient suffering from recurring UTI infections in an intensive care unit at Hera General Hospital in Makkah, Saudi Arabia. We aimed to determine the virulence genes for pathogenesis and drug resistance of this isolate compared to other E. coli strains. We sequenced and analyzed the E. coli O25b:H4 Saudi strain clinical isolate using next generation sequencing. Using the ERGO genome analysis platform, we performed annotations and identified virulence and antibiotic resistance determinants of this clinical isolate. The E. coli O25b:H4 genome was assembled into four contigs representing a total chromosome size of 5.28 Mb, and three contigs were identified, including a 130.9 kb (virulence plasmid) contig bearing the bla-CTX gene and 32 kb and 29 kb contigs. In comparing this genome to other uropathogenic E. coli genomes, we identified unique drug resistance and pathogenicity factors. In this work, whole-genome sequencing and targeted comparative analysis of a clinical isolate of uropathogenic Escherichia coli O25b:H4 was performed. This strain encodes virulence genes linked with extraintestinal pathogenic E. coli (ExPEC) that are expressed constitutively in E. coli ST131. We identified the genes responsible for pathogenesis and drug resistance and performed comparative analyses of the virulence and antibiotic resistance determinants with those of other E. coli UPEC isolates. This is the first report of genome sequencing and analysis of a UPEC strain from Saudi Arabia.

Published Nov 5. 2016. DOI: 10.22207/JPAM.10.4.01

The genome of Shigella dysenteriae strain Sd1617 comparison to representative strains in evaluating pathogenesis

Ajchara A. Vongsawan , Vinayak Kapatral , Benjamin Vaisvil , Henry Burd , Oralak Serichantalergs , Malabi M. Venkatesan , Carl J. Mason

We sequenced and analyzed Shigella dysenteriae strain Sd1617 serotype 1 that is widely used as model strain for vaccine design, trials and research. A combination of next-generation sequencing platforms and assembly yielded two contigs representing a chromosome size of 4.34 Mb and the large virulence plasmid of 177 kb. This genome sequence is compared with other Shigella genomes in order to understand gene complexity and pathogenic factors.

FEMS Microbiology Letters, 362, 2015, fnv011 doi: 10.1093/femsle/fnv011

Complete Genome Sequence of Flavobacterium psychrophilum Strain CSF259-93, Used To Select Rainbow Trout for Increased Genetic Resistance against Bacterial Cold Water Disease.

Wiens GD, LaPatra SE, Welch TJ, Rexroad C 3rd, Call DR, Cain KD, LaFrentz BR, Vaisvil B, Schmitt DP, Kapatral V.

The genome sequence of Flavobacterium psychrophilum strain CSF259-93, isolated from rainbow trout (Oncorhynchus mykiss), consists of a single circular genome of 2,900,735 bp and 2,701 predicted open reading frames (ORFs). Strain CSF259-93 has been used to select a line of rainbow trout with increased genetic resistance against bacterial cold water disease.

Genome Announc. 2014 Sep 18;2(5). pii: e00889-14. doi: 10.1128/genomeA.00889-14.

Draft Genome Sequence of a New Homofermentative, Lactic AcidProducing Enterococcus faecalis Isolate, CBRD01

Lew P. Christopher, Vinayak Kapatral, Benjamin Vaisvil, Ginger Emel,b and Linda C. DeVeauxc

We report here the draft genome sequence of the novel homofermentative Enterococcus faecalis isolate CBRD01, which is capable of high lactic acid productivity and yields, with minimal nutritional requirements. The genome is 2.8 Mbp, with 37% G+C, and contains genes for two lactate dehydrogenase (LDH) enzymes found in related organisms.

Genome Announc. 2014 Mar-Apr; 2(2): e00147-14.
Published online 2014 Mar 27. doi:  10.1128/genomeA.00147-14

The genome of Syntrophus aciditrophicus: Life at the thermodynamic limit of microbial growth

Michael J. McInerney, Lars Rohlin, Housna Mouttaki, UnMi Kim, Rebecca S. Krupp, Luis Rios-Hernandez, Jessica Sieber, Christopher G. Struchtemeyer, Anamitra Bhattacharyya, John W. Campbell, and Robert P. Gunsalus

Biochemically, the syntrophic bacteria constitute the missing link in our understanding of anaerobic flow of carbon in the biosphere. The completed genome sequence of Syntrophus aciditrophicus SB, a model fatty acid- and aromatic acid-degrading syntrophic bacterium, provides a glimpse of the composition and architecture of the electron transfer and energy-transducing systems needed to exist on marginal energy economies of a syntrophic lifestyle. The genome contains 3,179,300 base pairs and 3,169 genes where 1,618 genes were assigned putative functions. Metabolic reconstruction of the gene inventory revealed that most biosynthetic pathways of a typical Gram-negative microbe were present. A distinctive feature of syntrophic metabolism is the need for reverse electron transport; the presence of a unique Rnf-type ion-translocating electron transfer complex, menaquinone, and membrane-bound Fe-S proteins with associated heterodisulfide reductase domains suggests mechanisms to accomplish this task. Previously undescribed approaches to degrade fatty and aromatic acids, including multiple AMP-forming CoA ligases and acyl-CoA synthetases seem to be present as ways to form and dissipate ion gradients by using a sodium-based energy strategy. Thus, S. aciditrophicus, although nutritionally self-sufficient, seems to be a syntrophic specialist with limited fermentative and respiratory metabolism. Genomic analysis confirms the S. aciditrophicus metabolic and regulatory commitment to a nonconventional mode of life compared with our prevailing understanding of microbiology.

Published online 2007 Apr 18. doi:  10.1073/pnas.0610456104

The cyanobacterial genome core and the origin of photosynthesis.

Armen Y. Mulkidjanian, Eugene V. Koonin, Kira S. Makarova, Sergey L. Mekhedov, Alexander Sorokin, Yuri I. Wolf, Alexis Dufresne, Frédéric Partensky, Henry Burd, Denis Kaznadzey, Robert Haselkorn, and Michael Y. Galperin

Comparative analysis of 15 complete cyanobacterial genome sequences, including “near minimal” genomes of five strains of Prochlorococcus spp., revealed 1,054 protein families [core cyanobacterial clusters of orthologous groups of proteins (core CyOGs)] encoded in at least 14 of them. The majority of the core CyOGs are involved in central cellular functions that are shared with other bacteria; 50 core CyOGs are specific for cyanobacteria, whereas 84 are exclusively shared by cyanobacteria and plants and/or other plastid-carrying eukaryotes, such as diatoms or apicomplexans. The latter group includes 35 families of uncharacterized proteins, which could also be involved in photosynthesis. Only a few components of cyanobacterial photosynthetic machinery are represented in the genomes of the anoxygenic phototrophic bacteria Chlorobium tepidum, Rhodopseudomonas palustris, Chloroflexus aurantiacus, or Heliobacillus mobilis. These observations, coupled with recent geological data on the properties of the ancient phototrophs, suggest that photosynthesis originated in the cyanobacterial lineage under the selective pressures of UV light and depletion of electron donors. We propose that the first phototrophs were anaerobic ancestors of cyanobacteria (“procyanobacteria”) that conducted anoxygenic photosynthesis using a photosystem I-like reaction center, somewhat similar to the heterocysts of modern filamentous cyanobacteria. From procyanobacteria, photosynthesis spread to other phyla by way of lateral gene transfer.

Proc Natl Acad Sci U S A. 2006 Aug 29; 103(35): 13126–13131.
Published online 2006 Aug 21. doi:  10.1073/pnas.0605709103

The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution.

van de Guchte M, Penaud S, Grimaldi C, Barbe V, Bryson K, Nicolas P, Robert C,
Oztas S, Mangenot S, Couloux A, Loux V, Dervyn R, Bossy R, Bolotin A, Batto JM,
Walunas T, Gibrat JF, Bessières P, Weissenbach J, Ehrlich SD, Maguin E.

Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) is a representative of
the group of lactic acid-producing bacteria, mainly known for its worldwide
application in yogurt production. The genome sequence of this bacterium has been
determined and shows the signs of ongoing specialization, with a substantial
number of pseudogenes and incomplete metabolic pathways and relatively few
regulatory functions. Several unique features of the L. bulgaricus genome support
the hypothesis that the genome is in a phase of rapid evolution. (i)
Exceptionally high numbers of rRNA and tRNA genes with regard to genome size may
indicate that the L. bulgaricus genome has known a recent phase of important size
reduction, in agreement with the observed high frequency of gene inactivation and
elimination; (ii) a much higher GC content at codon position 3 than expected on
the basis of the overall GC content suggests that the composition of the genome
is evolving toward a higher GC content; and (iii) the presence of a 47.5-kbp
inverted repeat in the replication termination region, an extremely rare feature
in bacterial genomes, may be interpreted as a transient stage in genome
evolution. The results indicate the adaptation of L. bulgaricus from a
plant-associated habitat to the stable protein and lactose-rich milk environment
through the loss of superfluous functions and protocooperation with Streptococcus
thermophilus.

Proc Natl Acad Sci U S A. 2006 Jun 13;103(24):9274-9. Epub 2006 Jun 5.

The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode.

Foster J, Ganatra M, Kamal I, Ware J, Makarova K, Ivanova N, Bhattacharyya A, Kapatral V, Kumar S, Posfai J, Vincze T, Ingram J, Moran L, Lapidus A, Omelchenko M, Kyrpides N, Ghedin E, Wang S, Goltsman E, Joukov V, Ostrovskaya O, Tsukerman K, Mazur M, Comb D, Koonin E, Slatko B.

Complete genome DNA sequence and analysis is presented for Wolbachia, the obligate alpha-proteobacterial endosymbiont required for fertility and survival of the human filarial parasitic nematode Brugia malayi. Although, quantitatively, the genome is even more degraded than those of closely related Rickettsia species, Wolbachia has retained more intact metabolic pathways. The ability to provide riboflavin, flavin adenine dinucleotide, heme, and nucleotides is likely to be Wolbachia's principal contribution to the mutualistic relationship, whereas the host nematode likely supplies amino acids required for Wolbachia growth. Genome comparison of the Wolbachia endosymbiont of B. malayi (wBm) with the Wolbachia endosymbiont of Drosophila melanogaster (wMel) shows that they share similar metabolic trends, although their genomes show a high degree of genome shuffling. In contrast to wMel, wBm contains no prophage and has a reduced level of repeated DNA. Both Wolbachia have lost a considerable number of membrane biogenesis genes that apparently make them unable to synthesize lipid A, the usual component of proteobacterial membranes. However, differences in their peptidoglycan structures may reflect the mutualistic lifestyle of wBm in contrast to the parasitic lifestyle of wMel. The smaller genome size of wBm, relative to wMel, may reflect the loss of genes required for infecting host cells and avoiding host defense systems. Analysis of this first sequenced endosymbiont genome from a filarial nematode provides insight into endosymbiont evolution and additionally provides new potential targets for elimination of cutaneous and lymphatic human filarial disease.

PLoS Biol. 2005 Apr; 3(4): e121.
Published online 2005 Mar 29. doi:  10.1371/journal.pbio.0030121

Genome Analysis of F. nucleatum sub spp vincentii and Its Comparison With the Genome of F. nucleatum ATCC 25586

Vinayak Kapatral, Natalia Ivanova, Iain Anderson, Gary Reznik, Anamitra Bhattacharyya, Warren L. Gardner, Natalia Mikhailova, Alla Lapidus, Niels Larsen, Mark D'Souza, Theresa Walunas, Robert Haselkorn, Ross Overbeek, and Nikos Kyrpides

We present the draft genome sequence and its analysis for Fusobacterium nucleatum sub spp. vincentii (FNV), and compare that genome with F. nucleatum ATCC 25586 (FN). A total of 441 FNV open reading frames (ORFs) with no orthologs in FN have been identified. Of these, 118 ORFs have no known function and are unique to FNV, whereas 323 ORFs have functional orthologs in other organisms. In addition to the excretion of butyrate, H2S and ammonia-like FN, FNV has the additional capability to excrete lactate and aminobutyrate. Unlike FN, FNV is likely to incorporate galactopyranose, galacturonate, and sialic acid into its O-antigen. It appears to transport ferrous iron by an anaerobic ferrous transporter. Genes for eukaryotic type serine/threonine kinase and phosphatase, transpeptidase E-transglycosylase Pbp1A are found in FNV but not in FN. Unique ABC transporters, cryptic phages, and three types of restriction-modification systems have been identified in FNV. ORFs for ethanolamine utilization, thermostable carboxypeptidase, γ glutamyl-transpeptidase, and deblocking aminopeptidases are absent from FNV. FNV, like FN, lacks the classical catalase-peroxidase system, but thioredoxin/glutaredoxin enzymes might alleviate oxidative stress. Genes for resistance to antibiotics such as acriflavin, bacitracin, bleomycin, daunorubicin, florfenicol, and other general multidrug resistance are present. These capabilities allow Fusobacteria to survive in a mixed culture in the mouth.

Genome Res. 2003 Jun; 13(6a): 1180–1189.
doi:  10.1101/gr.566003

Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis.

Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V,
Bhattacharyya A, Reznik G, Mikhailova N, Lapidus A, Chu L, Mazur M, Goltsman E,
Larsen N, D'Souza M, Walunas T, Grechkin Y, Pusch G, Haselkorn R, Fonstein M,
Ehrlich SD, Overbeek R, Kyrpides N.

Bacillus cereus is an opportunistic pathogen causing food poisoning manifested by
diarrhoeal or emetic syndromes. It is closely related to the animal and human
pathogen Bacillus anthracis and the insect pathogen Bacillus thuringiensis, the
former being used as a biological weapon and the latter as a pesticide. B.
anthracis and B. thuringiensis are readily distinguished from B. cereus by the
presence of plasmid-borne specific toxins (B. anthracis and B. thuringiensis) and
capsule (B. anthracis). But phylogenetic studies based on the analysis of
chromosomal genes bring controversial results, and it is unclear whether B.
cereus, B. anthracis and B. thuringiensis are varieties of the same species or
different species. Here we report the sequencing and analysis of the type strain
B. cereus ATCC 14579. The complete genome sequence of B. cereus ATCC 14579
together with the gapped genome of B. anthracis A2012 enables us to perform
comparative analysis, and hence to identify the genes that are conserved between
B. cereus and B. anthracis, and the genes that are unique for each species. We
use the former to clarify the phylogeny of the cereus group, and the latter to
determine plasmid-independent species-specific markers.

Nature. 2003 May 1;423(6935):87-91.

Discovering lactic acid bacteria by genomics.

Klaenhammer T, Altermann E, Arigoni F, Bolotin A, Breidt F, Broadbent J, Cano R, Chaillou S, Deutscher J, Gasson M, van de Guchte M, Guzzo J, Hartke A, Hawkins T, Hols P, Hutkins R, Kleerebezem M, Kok J, Kuipers O, Lubbers M, Maguin E, McKay L, Mills D, Nauta A, Overbeek R, Pel H, Pridmore D, Saier M, van Sinderen D, Sorokin A, Steele J, O'Sullivan D, de Vos W, Weimer B, Zagorec M, Siezen R.

This review summarizes a collection of lactic acid bacteria that are now undergoing genomic sequencing and analysis. Summaries are presented on twenty different species, with each overview discussing the organisms fundamental and practical significance, environmental habitat, and its role in fermentation, bioprocessing, or probiotics. For those projects where genome sequence data were available by March 2002, summaries include a listing of key statistics and interesting genomic features. These efforts will revolutionize our molecular view of Gram-positive bacteria, as up to 15 genomes from the low GC content lactic acid bacteria are expected to be available in the public domain by the end of 2003. Our collective view of the lactic acid bacteria will be fundamentally changed as we rediscover the relationships and capabilities of these organisms through genomics.