Sandra Chibani-Chennoufi

Nestlé (Switzerland)

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Harald Brüssow

KU Leuven

Anne Bruttin

Nestlé (Switzerland)

Marie-Lise Dillmann

Nestlé (Switzerland)

Carlos Canchaya

Universidade de Vigo

Elizabeth Kutter

The Evergreen State College

J Sidoti

Nestlé (Switzerland)

Ghislain Fournous

Oslo University Hospital

Sabrina Rami-Shojaei

Nestlé (Switzerland)

Firdausi Qadri

International Centre for Diarrhoeal Disease Research

Laure F. Marvin‐Guy

Nestlé (Switzerland)

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Nestlé (Switzerland)

International Centre for Diarrhoeal Disease Research

Bioanalytica (Switzerland)

Neste Oil (Finland)

Karolinska Institutet

Universidade de Vigo

University of Parma

National University of Ireland

University College Cork

Oslo University Hospital

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Ecology and comparative genomics of SPO1- and T4-like Myoviridae and their use for phage therapy

Sandra Chibani-Chennoufi

Myoviridae

Phage therapy

10.3929/ethz-a-004843287

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Isolation of Escherichia coli Bacteriophages from the Stool of Pediatric Diarrhea Patients in Bangladesh

Journal of Bacteriology (2004)

Sandra Chibani-Chennoufi J Sidoti Anne Bruttin Marie-Lise Dillmann Elizabeth Kutter

A 3-week coliphage survey was conducted in stool samples from 140 Bangladeshi children hospitalized with severe diarrhea. On the Escherichia coli indicator strain K803, all but one phage isolate had 170-kb genomes and the morphology of T4 phage. In spot tests, the individual T4-like phages infected up to 27 out of 40 diarrhea-associated E. coli, representing 22 O serotypes and various virulence factors; only five of them were not infected by any of these new phages. A combination of diagnostic PCR based on g32 (DNA binding) and g23 (major capsid protein) and Southern hybridization revealed that half were T-even phages sensu strictu, while the other half were pseudo-T-even or even more distantly related T4-like phages that failed to cross-hybridize with T4 or between each other. Nineteen percent of the acute stool samples yielded T4-like phages, and the prevalence was lower in convalescent stool samples. T4-like phages were also isolated from environmental and sewage water, but with low frequency and low titers. On the enteropathogenic E. coli strain O127:K63, 14% of the patients yielded phage, all of which were members of the phage family Siphoviridae with 50-kb genomes, showing the morphology of Jersey- and beta-4 like phages and narrow lytic patterns on E. coli O serotypes. Three siphovirus types could be differentiated by lack of cross-hybridization. Only a few stool samples were positive on both indicator strains. Phages with closely related restriction patterns and, in the case of T4-like phages, identical g23 gene sequences were isolated from different patients, suggesting epidemiological links between the patients.

Siphoviridae

Lytic cycle

Coliphage

10.1128/jb.186.24.8287-8294.2004

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Phage-Host Interaction: an Ecological Perspective

Journal of Bacteriology (2004)

Sandra Chibani-Chennoufi Anne Bruttin Marie-Lise Dillmann Harald Brüssow

Nearly 100 years ago, Felix d'Herelle, the codiscoverer of bacteriophages, used bacteria to control insect pests and used phages against bacterial disease.His approaches reflected ecological insights before this branch of biology became an established scientific discipline.In fact, one might have predicted that phage research would become the springboard for biotechnology and ecology.However, d'Herelle was ahead of his time, and the zeitgeist in the 1930s pushed physicists into the question "What is life?"Phages as the simplest biological systems were the logical choice for this question, and phage research became the cradle of molecular biology.Now many researchers speak of a "new age of phage research."It is now realized that phages play an important role in ecology (e.g., phage impact on the cycling of organic matter in the biosphere at a global level) ( 27), that phages influence the evolution of bacterial genomes (most obviously in the development of bacterial pathogenicity) (7), and that phages might provide potential tools to face the antibiotic resistance crisis in medicine (59).With this new trend, we now see a clear shift from the reductionist approach, focusing on a handful of phages in carefully controlled laboratory conditions, towards the study of many different phages in the complexity of real-life situations.In contrast to the molecular biology-oriented phage research where the interaction of molecules took center stage, ecology focuses on the interactions between organisms and their physical environment.Much of ecology is therefore about the evolution of biological diversity in space and time.In contrast to many branches of biology, ecology attributes a great importance to quantitative relationships and numbers and aims at a mathematical formulation of its observations.It is thus appropriate to start this review with an overview of phage titers encountered in the biosphere.Next, we ask how a parasite targets its host if the latter is scarce or not in an appropriate physiological state.Finally, we report on research that tries to bridge phage ecology and genomics and cell biology approaches.It is concluded that the integration of phages into complex networks of interacting biological systems, and analysis by molecular techniques, could give phage research a model character in biology again.

10.1128/jb.186.12.3677-3686.2004

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In Vitro and In Vivo Bacteriolytic Activities of Escherichia coli Phages: Implications for Phage Therapy

Antimicrobial Agents and Chemotherapy (2004)

Sandra Chibani-Chennoufi J Sidoti Anne Bruttin Elizabeth Kutter S. A. Sarker

Four T4-like coliphages with broad host ranges for diarrhea-associated Escherichia coli serotypes were isolated from stool specimens from pediatric diarrhea patients and from environmental water samples. All four phages showed a highly efficient gastrointestinal passage in adult mice when added to drinking water. Viable phages were recovered from the feces in a dose-dependent way. The minimal oral dose for consistent fecal recovery was as low as 10(3) PFU of phage per ml of drinking water. In conventional mice, the orally applied phage remained restricted to the gut lumen, and as expected for a noninvasive phage, no histopathological changes of the gut mucosa were detected in the phage-exposed animals. E. coli strains recently introduced into the intestines of conventional mice and traced as ampicillin-resistant colonies were efficiently lysed in vivo by phage added to the drinking water. Likewise, an in vitro phage-susceptible E. coli strain freshly inoculated into axenic mice was lysed in vivo by an orally applied phage, while an in vitro-resistant E. coli strain was not lysed. In contrast, the normal E. coli gut flora of conventional mice was only minimally affected by oral phage application despite the fact that in vitro the majority of the murine intestinal E. coli colonies were susceptible to the given phage cocktail. Apparently, the resident E. coli gut flora is physically or physiologically protected against phage infection.

Phage therapy

Axenic

10.1128/aac.48.7.2558-2569.2004

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Citations (230)

Phage as agents of lateral gene transfer

Current Opinion in Microbiology (2003)

Carlos Canchaya Ghislain Fournous Sandra Chibani-Chennoufi Marie-Lise Dillmann Harald Brüssow

Prophage

Lysogenic cycle

Horizontal Gene Transfer

Temperateness

Bacterial genome size

Bacterial conjugation

Gene transfer

10.1016/s1369-5274(03)00086-9

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Lactobacillus plantarum Bacteriophage LP65: a New Member of the SPO1-Like Genus of the Family Myoviridae

Journal of Bacteriology (2004)

Sandra Chibani-Chennoufi Marie-Lise Dillmann Laure F. Marvin‐Guy Sabrina Rami-Shojaei Harald Brüssow

The virulent Lactobacillus plantarum myophage LP65 was isolated from industrial meat fermentation. Tail contraction led to reorganization of the tail sheath and the baseplate; a tail tube was extruded. In ultrathin section the phage adsorbed via its baseplate to the exterior of the cell, while the tail tube tunneled through the thick bacterial cell wall. Convoluted membrane structures were induced in the infected cell. Progeny phage was detected 100 min postinfection, and lysis occurred after extensive digestion of the cell wall. Sequence analysis revealed a genome of 131,573 bp of nonredundant DNA. Four major genome regions and a large tRNA gene cluster were observed. One module corresponded to DNA replication genes. Helicase/primase and two replication/recombination enzymes represented the only links to T4-like Myoviridae from gram-negative bacteria. Another module corresponded to the structural genes. Sequence relatedness identified links with Listeria phage A511, Staphylococcus phage K, and Bacillus phage SPO1. LP65 structural proteins were identified by two-dimensional proteome analysis and mass spectrometry. The putative tail sheath protein showed a shear-induced change in electrophoretic migration behavior. The genome organization of the structural module in LP65 resembled that of Siphoviridae from the lambda supergroup.

Myoviridae

Lysin

Siphoviridae

10.1128/jb.186.21.7069-7083.2004

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Citations (96)

Comparative Genomics of the T4-Like Escherichia coli Phage JS98: Implications for the Evolution of T4 Phages

Journal of Bacteriology (2004)

Sandra Chibani-Chennoufi Carlos Canchaya Anne Bruttin Harald Brüssow

ABSTRACT About 130 kb of sequence information was obtained from the coliphage JS98 isolated from the stool of a pediatric diarrhea patient in Bangladesh. The DNA shared up to 81% base pair identity with phage T4. The most conserved regions between JS98 and T4 were the structural genes, but their degree of conservation was not uniform. The head genes showed the highest sequence conservation, followed by the tail, baseplate, and tail fiber genes. Many tail fiber genes shared only protein sequence identity. Except for the insertion of endonuclease genes in T4 and gene 24 duplication in JS98, the structural gene maps of the two phages were colinear. The receptor-recognizing tail fiber proteins gp37 and gp38 were only distantly related to T4, but shared up to 83% amino acid identity to other T6-like phages, suggesting lateral gene transfer. A greater degree of variability was seen between JS98 and T4 over DNA replication and DNA transaction genes. While most of these genes came in the same order and shared up to 76% protein sequence identity, a few rearrangements, insertions, and replacements of genes were observed. Many putative gene insertions in the DNA replication module of T4 were flanked by intron-related endonuclease genes, suggesting mobile DNA elements. A hotspot of genome diversification was located downstream of the DNA polymerase gene 43 and the DNA binding gene 32 . Comparative genomics of 100-kb genome sequence revealed that T4-like phages diversify more by the accumulation of point mutations and occasional gene duplication events than by modular exchanges.

Comparative Genomics

10.1128/jb.186.24.8276-8286.2004

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Citations (44)