Does the maternal vaginal microbiota play a role in seeding the microbiota of neonatal gut and nose?

The acquisition and early maturation of infant microbiota is not well understood despite its likely influence on later health. We investigated the contribution of the maternal microbiota to the microbiota of infant gut and nose in the context of mode of delivery and feeding. Using 16S rRNA sequencing and specific qPCR, we profiled microbiota of 42 mother-infant pairs from the GUSTO birth cohort, at body sites including maternal vagina, rectum and skin; and infant stool and nose. In our study, overlap between maternal vaginal microbiota and infant faecal microbiota was minimal, while the similarity between maternal rectal microbiota and infant microbiota was more pronounced. However, an infant's nasal and gut microbiota were no more similar to that of its own mother, than to that of unrelated mothers. These findings were independent of delivery mode. We conclude that the transfer of maternal vaginal microbes play a minor role in seeding infant stool microbiota. Transfer of maternal rectal microbiota could play a larger role in seeding infant stool microbiota, but approaches other than the generally used analyses of community similarity measures are likely to be needed to quantify bacterial transmission. We confirmed the clear difference between microbiota of infants born by Caesarean section compared to vaginally delivered infants and the impact of feeding mode on infant gut microbiota. Only vaginally delivered, fully breastfed infants had gut microbiota dominated by Bifidobacteria. Our data suggest that reduced transfer of maternal vaginal microbial is not the main mechanism underlying the differential infant microbiota composition associated with Caesarean delivery. The sources of a large proportion of infant microbiota could not be identified in maternal microbiota, and the sources of seeding of infant gut and nasal microbiota remain to be elucidated.

Transcriptional analysis of the genetic elements involved in the lysogeny/lysis switch in the temperate lactococcal bacteriophage phiLC3, and identification of the Cro-like protein ORF76

A transcriptional analysis of the lysogeny-related genes of the temperate bacteriophage Lactococcus lactis phiLC3 was performed using Northern blot hybridization during lysogeny and lytic infection by the phage. The lysogeny-related gene cluster was found to contain four promoters (P(1), P(2), Pint and P(173)), while the P(87) promoter directed transcription of orf80 and the putative gene orf87, which are located between the integrase gene and the cell lysis genes. The start sites of the transcripts were determined by primer extension. The divergently oriented lysogenic P(1) and lytic P(2) promoters located in the genetic switch region are responsible for transcription of orf286 which encodes the phage repressor, and the genes orf63 - orf76 - orf236 - orf110 - orf82 - orf57, respectively, while orf173 is transcribed from P(173). orf76 was identified as the gene encoding the Cro-like protein of phiLC3, and it was shown that ORF76 is able to bind specifically to the genetic switch region, albeit with lower affinity than does the phage repressor ORF286. ORF76 also competed with ORF286 for binding to this region. The functionality of P(1) and P(2), and their regulation by ORF286 and ORF76, was investigated using a reporter gene. In general, P(2) was a stronger promoter than P(1), but expression from both promoters, especially P(2), was regulated and modulated by flanking sequences and the presence of orf286 and orf76. ORF286 and ORF76 were both able to repress transcription from P(1) and P(2), while ORF286 was able to stimulate its own synthesis by tenfold. This work reveals the complex interplay between the regulatory elements that control the genetic switch between lysis and lysogeny in phiLC3 and other temperate phages of Lactococcus.

Comparative genomics reveals close genetic relationships between phages from dairy bacteria and pathogenic Streptococci: evolutionary implications for prophage-host interactions

The genome of the highly pathogenic M1 serotype Streptococcus pyogenes isolate SF370 contains eight prophage elements. Only prophage SF370.1 could be induced by mitomycin C treatment. Prophage SF370.3 showed a 33.5-kb-long genome that closely resembled the genome organization of the cos-site temperate Siphovirus r1t infecting the dairy bacterium Lactococcus lactis. The two-phage genomes shared between 60 and 70% nucleotide sequence identity over the DNA packaging, head and tail genes. Analysis of the SF370.3 genome revealed mutations in the replisome organizer gene that may prevent the induction of the prophage. The mutated phage replication gene was closely related to a virulence marker identified in recently emerged M3 serotype S. pyogenes strains in Japan. This observation suggests that prophage genes confer selective advantage to the lysogenic host. SF370.3 encodes a hyaluronidase and a DNase that may facilitate the spreading of S. pyogenes through tissue planes of its human host. Prophage SF370.2 showed a 43-kb-long genome that closely resembled the genome organization of pac-site temperate Siphoviridae infecting the dairy bacteria S. thermophilus and L. lactis. Over part of the structural genes, the similarity between SF370.2 and S. thermophilus phage O1205 extended to the nucleotide sequence level. SF370.2 showed two probable inactivating mutations: one in the replisome organizer gene and another in the gene encoding the portal protein. Prophage SF370.2 also encodes a hyaluronidase and in addition two very likely virulence factors: prophage-encoded toxins acting as superantigens that may contribute to the immune deregulation observed during invasive streptococcal infections. The superantigens are encoded between the phage lysin and the right attachment site of the prophage genome. The genes were nearly sequence identical with a DNA segment in S. equi, suggesting horizontal gene transfer. The trend for prophage genome inactivation was even more evident for the remaining five prophage sequences that showed massive losses of prophage DNA. In these prophage remnants only 13-0.3 kb of putative prophage DNA was detected. We discuss the genomics data from S. pyogenes strain SF370 within the framework of Darwinian coevolution of prophages and lysogenic bacteria and suggest elements of genetic cooperation and elements of an arms race in this host-parasite relationship.

Comparative genomics of lactococcal phages: insight from the complete genome sequence of Lactococcus lactis phage BK5-T

Lactococcus lactis phage BK5-T and Streptococcus thermophilus phage Sfi21, two cos-site temperate Siphoviridae with 40-kb genomes, share an identical genome organization, sequence similarity at the amino acid level over about half of their genomes, and nucleotide sequence identity of 60% over the DNA packaging and head morphogenesis modules. Siphoviridae with similarly organized genomes and substantial protein sequence similarity were identified in several genera of low-GC-content Gram-positive bacteria. These phages demonstrated a gradient of relatedness ranging from nucleotide sequence similarity to protein sequence similarity to gene map similarity over the DNA packaging and head morphogenesis modules. Interestingly, the degree of relatedness was correlated with the evolutionary distance separating their bacterial hosts. These observations suggest elements of vertical evolution in phages. The structural genes from BK5-T shared no sequence relationships with corresponding genes/proteins from lactococcal phages belonging to distinct lactococcal phage species, including phage sk1 (phage species 936) that showed a closely related gene map. Despite a clearly distinct genome organization, lactococcal phages sk1 and c2 showed nine sequence-related proteins. Over the early gene cluster phage BK5-T shared nine regions of high nucleotide sequence similarity, covering at most two adjacent genes, with lactococcal phage r1t (phage species P335). Over the structural genes, the closest relatives of phage r1t were not lactococcal phages belonging to other phage species, but Siphoviridae from Mycobacteria (high-GC-content Gram-positive bacteria). Evidence for recent horizontal gene transfer between distinct phage species was obtained for dairy phages, but these transfers were limited to phages infecting the same bacterial host species.

Glycosphingolipid binding specificities of rotavirus: identification of a sialic acid-binding epitope

The glycosphingolipid binding specificities of neuraminidase-sensitive (simian SA11 and bovine NCDV) and neuraminidase-insensitive (bovine UK) rotavirus strains were investigated using the thin-layer chromatogram binding assay. Both triple-layered and double-layered viral particles of SA11, NCDV, and UK bound to nonacid glycosphingolipids, including gangliotetraosylceramide (GA1; also called asialo-GM1) and gangliotriaosylceramide (GA2; also called asialo-GM2). Binding to gangliosides was observed with triple-layered particles but not with double-layered particles. The neuraminidase-sensitive and neuraminidase-insensitive rotavirus strains showed distinct ganglioside binding specificities. All three strains bound to sialylneolactotetraosylceramide and GM2 and GD1a gangliosides. However, NeuAc-GM3 and the GM1 ganglioside were recognized by rotavirus strain UK but not by strains SA11 and NCDV. Conversely, NeuGc-GM3 was bound by rotaviruses SA11 and NCDV but not by rotavirus UK. Thus, neuraminidase-sensitive strains bind to external sialic acid residues in gangliosides, while neuraminidase-insensitive strains recognize gangliosides with internal sialic acids, which are resistant to neuraminidase treatment. By testing a panel of gangliosides with triple-layered particles of SA11 and NCDV, the terminal sequence sialyl-galactose (NeuGc/NeuAcalpha3-Galbeta) was identified as the minimal structural element required for the binding of these strains. The binding of triple-layered particles of SA11 and NCDV to NeuGc-GM3, but not to NeuAc-GM3, suggested that the sequence NeuGcalpha3Galbeta is preferred to NeuAcalpha3Galbeta. Further dissection of this binding epitope showed that the carboxyl group and glycerol side chain of sialic acid played an important role in the binding of such triple-layered particles.

Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages

Comparative phage genomics can retrace part of the evolutionary history of phage modules encoding phage-specific functions such as capsid building or establishment of the lysogenic state. The diagnosis of relatedness is not based exclusively on sequence similarity, but includes topological considerations of genome organization. The gene maps from the lambda-, psiM2-, L5-, Sfi21-, Sfi11-, phiC31-, sk1- and TM4-like phages showed a remarkable synteny of their structural genes defining a lambda supergroup within Siphoviridae (Caudovirales with long non-contractile tails). A hierarchy of relatedness within the lambda supergroup suggested elements of vertical evolution in the capsid module of Siphoviridae. Links to P22-like Podoviridae and P2-like Myoviridae were also detected. Numerous cases of horizontal gene transfer were observed, but recent transfers were limited to interbreeding phage populations. We suggest that tailed phages are the result of both vertical and horizontal evolution and are thus a good model system for web-like phylogenies.

Comparative genomics of the late gene cluster from Lactobacillus phages

Three prophage sequences were identified in the Lactobacillus johnsoni strain NCC533. Prophage Lj965 predicted a gene map very similar to those of pac-site Streptococcus thermophilus phages over its DNA packaging and head and tail morphogenesis modules. Sequence similarity linked the putative DNA packaging and head morphogenesis genes at the protein level. Prophage Lj965/S. thermophilus phage Sfi11/Lactococcus lactis phage TP901-1 on one hand and Lactobacillus delbrueckii phage LL-H/Lactobacillus plantarum phage phig1e/Listeria monocytogenes phage A118 on the other hand defined two sublines of structural gene clusters in pac-site Siphoviridae from low-GC Gram-positive bacteria. Bacillus subtilis phage SPP1 linked both sublines. The putative major head and tail proteins from Lj965 shared weak sequence similarity with phages from Gram-negative bacteria. A clearly independent line of structural genes in Siphoviridae from low-GC Gram-positive bacteria is defined by temperate cos-site phages including Lactobacillus gasseri phage adh, which also shared sequence similarity with phage D3 infecting a Gram-negative bacterium. A phylogenetic tree analysis demonstrated that the ClpP-like protein identified in four cos-site Siphoviridae from Lactobacillus, Lactococcus, Streptococcus, and Pseudomonas showed graded sequence relationships. The tree suggested that the ClpP-like proteins from the phages were not acquired by horizontal gene transfer from their corresponding bacterial hosts.

Broad-range bacteriophage resistance in Streptococcus thermophilus by insertional mutagenesis

Streptococcus thermophilus is a lactic acid bacterium used in industrial milk fermentation. To obtain phage-resistant starters, S. thermophilus strain Sfi1 was submitted to mutagenesis with the thermolabile insertional vector pG(+)host9:ISS1 followed by a challenge with the lytic S. thermophilus phage Sfi19. Vector insertions into four distinct sites led to a phage-resistance phenotype. Three mutants were characterized further. They were protected against the homologous challenging phage and 14 heterologous phages. All three mutants adsorbed phages. No intracellular phage DNA synthesis was observed in mutants R7 and R71, while mutant R24 showed a delayed and diminished phage DNA synthesis compared to the parental Sfi1 strain. In mutant R7 a short deletion occurred next to the insertion site which removed the upstream sequences and the 15 initial codons from orf 394, encoding a likely transmembrane protein. Analogy with other phage systems suggests an involvement of this protein in the phage DNA injection process. In mutant R24 the vector was inserted into orf 269 predicting an oxido-reductase. When the vector sequence was removed via homologous recombination across the duplicated insertion elements, mutant R24 returned to the phage susceptibility of the parental strain. This observation suggested that inactivation of orf 269 was not crucial for the resistance phenotype. A gene encoding a likely restriction subunit of a type I restriction-modification system was located directly downstream of the insertion site in mutant R24. hsdM and hsdS genes encoding the modification and specificity subunits of a type I R-M system and biological evidence for an active R-M system were detected in strain Sfi1, suggesting involvement of a type I R-M system in the resistance phenotype of R24.

Treatment of enterotoxigenic and enteropathogenic Escherichia coli-induced diarrhoea in children with bovine immunoglobulin milk concentrate from hyperimmunized cows: a double-blind, placebo-controlled, clinical trial

BACKGROUND

Enterotoxigenic Escherichia coli (ETEC) and enteropathogenic Escherichia coli (EPEC) are important causes of diarrhoea in young children and are associated with significant mortality rates. Passive immunization with antibodies from immunized cows has previously been shown to be effective as prophylaxis against E. coli-induced diarrhoea and therapeutically against rotavirus and cryptosporidia-induced diarrhoea.

METHODS

We tested the therapeutic efficacy of an oral bovine immunoglobulin milk concentrate (BIC) from cows hyperimmunized with ETEC and EPEC strains, in a randomized, placebo-controlled study in children with E. coli-induced diarrhoea. Eighty-six children between 4-24 months of age attending the International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B) with E. coli-induced diarrhoea (63 EPEC/ETEC and 23 with other diarrhoeagenic E. coli) were randomly assigned to receive orally administered BIC (20 g) containing anti-ETEC/EPEC antibodies or a placebo preparation daily for 4 consecutive days. Daily stool output, intake of oral rehydration solution (ORS), stool frequency, and presence of diarrhoeagenic E. coli strains in the stool were monitored for 4 days.

RESULTS

Children in the treatment group tolerated the BIC with no side effects. There were no significant differences between the two groups with regard to ORS intake, stool output, frequency of diarrhoea, or clearance of pathogen. Nor was there any significant alteration in the duration of diarrhoea.

CONCLUSIONS

In contrast to the prophylactic efficacy of anti-E. coli BIC and the therapeutic efficacy of a similarly prepared anti-rotavirus BIC, antibodies from hyperimmunized cows appear to have no significant therapeutic benefit in the treatment of acute diarrhoea due to EPEC/ETEC.

Genomics, molecular genetics and the food industry

The production of foods for an increasingly informed and selective consumer requires the coordinated activities of the various branches of the food chain in order to provide convenient, wholesome, tasty, safe and affordable foods. Also, the size and complexity of the food sector ensures that no single player can control a single process from seed production, through farming and processing to a final product marketed in a retail outlet. Furthermore, the scientific advances in genome research and their exploitation via biotechnology is leading to a technology driven revolution that will have advantages for the consumer and food industry alike. The segment of food processing aids, namely industrial enzymes which have been enhanced by the use of biotechnology, has proven invaluable in the production of enzymes with greater purity and flexibility while ensuring a sustainable and cheap supply. Such enzymes produced in safe GRAS microorganisms are available today and are being used in the production of foods. A second rapidly evolving segment that is already having an impact on our foods may be found in the new genetically modified crops. While the most notorious examples today were developed by the seed companies for the agro-industry directed at the farming sector for cost saving production of the main agronomical products like soya and maize, its benefits are also being seen in the reduced use of herbicides and pesticides which will have long term benefits for the environment. Technology-driven advances for the food processing industry and the consumer are being developed and may be divided into two separate sectors that will be presented in greater detail: 1. The application of genome research and biotechnology to the breeding and development of improved plants. This may be as an aid for the cataloging of industrially important plant varieties, the rapid identification of key quality traits for enhanced classical breeding programs, or the genetic modification of important plants for improved processing properties or health characteristics. 2. The development of advanced microorganisms for food fermentations with improved flavor production, health or technological characteristics. Both yeasts and bacteria have been developed that fulfill these requirements, but are as yet not used in the production of foods.

Widespread distribution of a group I intron and its three deletion derivatives in the lysin gene of Streptococcus thermophilus bacteriophages

Of 62 Streptococcus thermophilus bacteriophages isolated from various ecological settings, half contain a lysin gene interrupted by a group IA2 intron. Phage mRNA splicing was demonstrated. Five phages possess a variant form of the intron resulting from three distinct deletion events located in the intron-harbored open reading frame (orf 253). The predicted orf 253 gene sequence showed a significantly lower GC content than the surrounding intron and lysin gene sequences, and the predicted protein shared a motif with endonucleases found in phages from both gram-positive and gram-negative bacteria. A comparison of the phage lysin genes revealed a clear division between intron-containing and intron-free alleles, leading to the establishment of a 14-bp consensus sequence associated with intron possession. The conserved intron was not found elsewhere in the phage or S. thermophilus bacterial genomes. Folding of the intron RNA revealed secondary structure elements shared with other phage introns: first, a 38-bp insertion between regions P3 and P4 that can be folded into two stem-loop structures (shared with introns from Bacillus phage SPO1 and relatives); second, a conserved P7.2 region (shared with all phage introns); third, the location of the stop codon from orf 253 in the P8 stem (shared with coliphage T4 and Bacillus phage SPO1 introns); fourth, orf 253, which has sequence similarity with the H-N-H motif of putative endonuclease genes found in introns from Lactococcus, Lactobacillus, and Bacillus phages.

Similarly organized lysogeny modules in temperate Siphoviridae from low GC content gram-positive bacteria

Temperate Siphoviridae from an evolutionarily related branch of low GC content gram-positive bacteria share a common genetic organization of lysogeny-related genes and the predicted proteins are linked by many sequence similarities. Their compact lysogeny modules [integrase/1-2 orfs (phage exclusion? and metalloproteinase motif proteins)/cI-like repressor/cro-like repressor/antirepressor (optional)] differ clearly from that of lambda-like and L5-like viruses, the two currently established genera of temperate Siphoviridae, while they resemble those of the P2-like genus of Myoviridae. In all known temperate Siphoviridae from low GC content gram-positive bacteria the lysogeny module is flanked by the lysis module and the DNA replication module. This modular organization is again distinct from that of the known genera of temperate Siphoviridae. On the basis of comparative sequence analysis we propose a new genus of Siphoviridae: "Sfi21-like" phages. With a larger database of phage sequences it might be possible to establish a genomics-based phage taxonomy and to retrace the evolutionary history of selected phage modules or individual phage genes. The antirepressor of Sfi21-like phages has an unusual widespread distribution since proteins with high aa similarity (40%) were found not only in phages from gram-negative bacteria, but also in insect viruses.

Comparative genomics of Streptococcus thermophilus phage species supports a modular evolution theory

The comparative analysis of five completely sequenced Streptococcus thermophilus bacteriophage genomes demonstrated that their diversification was achieved by a combination of DNA recombination events and an accumulation of point mutations. The five phages included lytic and temperate phages, both pac site and cos site, from three distinct geographical areas. The units of genetic exchange were either large, comprising the entire morphogenesis gene cluster, excluding the putative tail fiber genes, or small, consisting of one or maximally two genes or even segments of a gene. Many indels were flanked by DNA repeats. Differences in a single putative tail fiber gene correlated with the host ranges of the phages. The predicted tail fiber protein consisted of highly conserved domains containing conspicuous glycine repeats interspersed with highly variable domains. As in the T-even coliphage adhesins, the glycine-containing domains were recombinational hot spots. Downstream of a highly conserved DNA replication region, all lytic phages showed a short duplication; in three isolates the origin of replication was repeated. The lytic phages could conceivably be derived from the temperate phages by deletion and multiple rearrangement events in the lysogeny module, giving rise to occasional selfish phages that defy the superinfection control systems of the corresponding temperate phages.

Comparative sequence analysis of the DNA packaging, head, and tail morphogenesis modules in the temperate cos-site Streptococcus thermophilus bacteriophage Sfi21

The temperate Streptococcus thermophilus bacteriophage Sfi21 possesses 15-nucleotide-long cohesive ends with a 3' overhang that reconstitutes a cos-site with twofold hyphenated rotational symmetry. Over the DNA packaging, head and tail morphogenesis modules, the Sfi21 sequence predicts a gene map that is strikingly similar to that of lambdoid coliphages in the absence of any sequence similarity. A nearly one to one gene correlation was found with the phage lambda genes Nu1 to H, except for gene B-to-E complex, where the Sfi21 map resembled that of coliphage HK97. The similarity between Sfi21 and HK97 was striking: both major head proteins showed an N-terminal coiled-coil structure, the mature major head proteins started at amino acid positions 105 and 104, respectively, and both major head genes were preceded by genes encoding a possible protease and portal protein. The purported Sfi21 protease is the first viral member of the ClpP protease family. The prediction of Sfi21 gene functions by reference to the gene map of intensively investigated coliphages was experimentally confirmed for the major head and tail gene. Phage Sfi21 shows nucleotide sequence similarity with Lactococcus phage BK5-T and a lactococcal prophage and amino acid sequence similarity with the Lactobacillus phage A2 and the Staphylococcus phage PVL. PVL is a missing link that connects the portal proteins from Sfi21 and HK97 with respect to sequence similarity. These observations and database searches, which demonstrate sequence similarity between proteins of phage from gram-positive bacteria, proteobacteria, and Archaea, constrain models of phage evolution.

The genetic relationship between virulent and temperate Streptococcus thermophilus bacteriophages: whole genome comparison of cos-site phages Sfi19 and Sfi21

The virulent cos-site Streptococcus thermophilus bacteriophage Sfi19 has a 37,392-bp-long genome consisting of 44 open reading frames all encoded on the same DNA strand. The genome of the temperate cos-site S. thermophilus phage Sfi21 is 3.3 kb longer (40,740 bp, 53 orfs). Both genomes are very similarly organized and differed mainly by gene deletion and DNA rearrangement events in the lysogeny module; gene replacement, duplication, and deletion events in the DNA replication module, and numerous point mutations. The level of point mutations varied from <1% (lysis and DNA replication modules) to >15% (DNA packaging and head morphogenesis modules). A dotplot analysis showed nearly a straight line over the left 25 kb of their genomes. Over the right genome half, a more variable dotplot pattern was observed. The entire lysogeny module from Sfi21 comprising 12 genes was replaced by 7 orfs in Sfi19, six showed similarity with genes from temperate pac-site S. thermophilus phages. None of the genes implicated in the establishment of the lysogenic state (integrase, superinfection immunity, repressor) or remnants of it were conserved in Sfi19, while a Cro-like repressor was detected. Downstream of the highly conserved DNA replication module 11 and 13 orfs were found in Sfi19 and phiSfi21, respectively: Two orfs from Sfi21 were replaced by a different gene and a duplication of the phage origin of replication in Sfi19; a further orf was only found in Sfi21. All other orfs from this region, which included a second putative phage repressor, were closely related between both phages. Two noncoding regions of Sfi19 showed sequence similarity to pST1, a small cryptic plasmid of S. thermophilus.

Successful treatment of rotavirus diarrhea in children with immunoglobulin from immunized bovine colostrum

BACKGROUND

Oral ingestion of immunoglobulins in humans has been shown to be effective as prophylaxis against enteric infections. However, its therapeutic effect in children with infectious diarrhea has hitherto not been proven. We treated children with rotavirus diarrhea with immunoglobulins extracted from immunized bovine colostrum (IIBC) containing high titers of antibodies against four rotavirus serotypes.

METHODS

In this double blind placebo-controlled trial, 80 children with rotavirus diarrhea were randomly assigned to receive orally either 10 g of IIBC (containing 3.6 g of antirotavirus antibodies) daily for 4 days or the same amount of a placebo preparation. The daily stool output (grams/kg/day), intake of oral rehydration solution (ml/kg/day), stool frequency (number of stools/day) and presence of rotavirus in stool were monitored for the 4 days during treatment.

RESULTS

Children who received IIBC had significantly less daily and total stool output and stool frequency and required a smaller amount of oral rehydration solution than did children who received placebo (P < 0.05). Clearance of rotavirus from the stool was also earlier in the IIBC group compared with the placebo group (mean day, 1.5 vs. 2.9, P < 0.001). No adverse reactions from the colostrum treatment were observed.

CONCLUSIONS

Treatment with antirotavirus immunoglobulin of bovine colostral origin is effective in the management of children with acute rotavirus diarrhea.

A short noncoding viral DNA element showing characteristics of a replication origin confers bacteriophage resistance to Streptococcus thermophilus

A 302-bp noncoding DNA fragment from the DNA replication module of phage phiSfi21 was shown to protect the Streptococcus thermophilus strain Sfi1 from infection by 17 of 25 phages. The phage-inhibitory DNA possesses two determinants, each of which individually mediated phage resistance. The phage-inhibitory activity was copy number dependent and operates by blocking the accumulation of phage DNA. Furthermore, when cloned on a plasmid, the phiSfi21 DNA acts as an origin of replication driven by phage infection. Protein or proteins in the phiSfi21-infected cells were shown to interact with this phage-inhibitory DNA fragment, forming a retarded protein-DNA complex in gel retardation assays. A model in which phage proteins interact with the inhibitory DNA such that they are no longer available for phage propagation can be used to explain the observed bacteriophage resistance. Genome analysis of phiSfi19, a phage that is insensitive to the inhibitory activity of the phiSfi21-derived DNA, led to the characterisation of a variant putative phage replication origin that differed in 14 of 302 nucleotides from that of phiSfi21. The variant origin was cloned and exhibited an inhibitory activity toward phages that were insensitive to the phiSfi21-derived DNA.

The structural gene module in Streptococcus thermophilus bacteriophage phi Sfi11 shows a hierarchy of relatedness to Siphoviridae from a wide range of bacterial hosts

The structural gene cluster and the lysis module from lytic group II Streptococcus thermophilus bacteriophage phi Sfi11 was compared to the corresponding region from other Siphoviridae. The analysis revealed a hierarchy of relatedness. phi Sfi11 differed from the temperate S. thermophilus bacteriophage phi O1205 by about 10% at the nucleotide level. The majority of the changes were point mutations, mainly at the third base position. Only a single gene (orf 695) differed substantially between the two phages. Over the putative minor tail and lysis genes, phi Sfi11 and the lytic group 1 S. thermophilus phi Sfi19 shared regions with variable degrees of similarity. Orf 1291 from phi Sfi19 was replaced by four genes in phi Sfi11, two of which (orf 1000 and orf 695) showed a complicated pattern of similarity and nonsimilarity compared with phi Sfi19. The predicted orf 695 gp resembles the receptor-recognizing protein of T-even coliphages in its organization, but not its sequence. No sequence similarity was detected between phi Sfi11 and phi Sfi19 in the region covering the major head and tail genes. Comparison of the structural gene map of phi Sfi11 with that of Siphoviridae from gram-positive and -negative bacterial hosts revealed a common genomic organization. Sequence similarity was only found between phi Sfi11 and Siphoviridae from gram-positive hosts and correlated with the evolutionary distance between the bacterial hosts. Our data are compatible with the hypothesis that the structural gene operon from Siphoviridae of the low G + C group of gram-positive bacteria is derived from a common ancestor.

Molecular ecology and evolution of Streptococcus thermophilus bacteriophages--a review

Bacteriophages attacking Streptococcus thermophilus, a lactic acid bacterium used in milk fermentation, are a threat to the dairy industry. These small isometric-headed phages possess double-stranded DNA genomes of 31 to 45 kb. Yoghurt-derived phages exhibit a limited degree of variability, as defined by restriction pattern and host range, while a large diversity of phage types have been isolated from cheese factories. Despite this diversity all S. thermophilus phages, virulent and temperate, belong to a single DNA homology group. Several mechanisms appear to create genetic variability in this phage group. Site-specific deletions, one type possibly mediated by a viral recombinase/integrase, which transformed a temperate into a virulent phage, were observed. Recombination as a result of superinfection of a lysogenic host has been reported. Comparative DNA sequencing identified up to 10% sequence diversity due to point mutations. Genome sequencing of the prototype temperate phage phi Sfi21 revealed many predicted proteins which showed homology with phages from Lactococcus lactis suggesting horizontal gene transfer. Homology with phages from evolutionary unrelated bacteria like E. coli (e.g. lambdoid phage 434 and P1) and Mycobacterium phi L5 was also found. Due to their industrial importance, the existence of large phage collections, and the whole phage genome sequencing projects which are currently underway, the S. thermophilus phages may present an interesting experimental system to study bacteriophage evolution.

Evolution of Streptococcus thermophilus bacteriophage genomes by modular exchanges followed by point mutations and small deletions and insertions

Comparative sequence analysis of 40% of the genomes from two prototype Streptococcus thermophilus bacteriophages (lytic group I phage phi Sfi19 and the cos site containing temperate phage phi Sfi21) suggested two processes in the evolution of their genomes. In a first evolutionarily distant phase the basic genome structure was apparently constituted by modular exchanges. Over the 17-kb-long DNA segment analyzed in the present report, we observed clusters of genes with similarity to genes from Leuconostoc oenos phage L10, Lactococcus lactis phage BK5-T, and Streptococcus pneumoniae phage Dp-1. A chimeric protein was predicted for orf 1291 which showed similarity to both phage BK5-T and phage Dp-1 proteins. The very large orf 1626 gene product showed similarity to two adjacent genes from the Lactobacillus delbrueckii phage LL-H and further phage proteins (Lactococcus lactis, Bacillus subtills). The similarities were localized to distinct parts of this apparently multifunctional protein. The putative phi Sfi19 lysin showed similarity to both lysins of phages and cellular enzymes. In a second, evolutionarily more recent, phase the S, thermophilus phage genomes apparently diversified by point mutations and small deletions/insertions. Over the investigated 17-kb DNA region phi Sfi19 differed from phi Sfi21 by 10% base pair changes, the majority of which were point mutations (mainly at the third codon position), while a third of the base pair differences were contributed by small deletions/insertions. The base pair changes were unevenly distributed. Over the Leuconostoc phage-related DNA the change rate was high, while over the Lactococcus and S. pneumoniae phage-related DNA the change rate was low. We speculate that the degree of base pair change could provide relative time scales for the modular exchange reactions observed in S. thermophilus phages.

Comparison of the lysogeny modules from the temperate Streptococcus thermophilus bacteriophages TP-J34 and Sfi21: implications for the modular theory of phage evolution

A 7.6-kb DNA segment covering the putative lysogeny module of the pac-site-containing temperate Streptococcus thermophilus bacteriophage TP-J34 was sequenced. Sequence alignment with the lysogeny module from the cos-site-containing S. thermophilus bacteriophage phiSfi21 revealed areas of high sequence conservation (e.g., over the int gene), interspersed with regions of low or no sequence similarity (e.g., over the cro gene). Four of the six sharp transition zones from high to low sequence conservation were found within open reading frames coding for the CI repressor, the Anti-repressor, the Immunity protein, and a protein of unknown function. The transition points in the cI and ant genes appear to separate gene segments coding for distinct functional domains of these proteins. In addition, these two transition points were located at or near the deletion sites observed in spontaneous phage phiSfi21 deletion mutants, thus suggesting these transition points as recombinational hotspots. Furthermore, the sequence at the transition point in the cI gene resembles the attachment site of the phage, suggesting the involvement of the phage integrase in at least some of the exchange reactions. Contrary to the initial formulation of the modular theory of phage evolution the unit of the evolutionary exchange in streptococcal phages is not a group of functional genes, but can be as small as a single gene. Exchange reactions can also occur within genes, possibly between gene segments encoding distinct protein domains.

Chicken rotavirus Ch-1 shows a second type of avian VP6 gene

VP6 protein from chicken rotavirus Ch-1 showed more than 13% amino acid differences in comparison with pigeon and turkey VP6 sequences. This difference is greater than that observed between subgroup I and II mammalian rotavirus VP6 sequences. Phylogenetic tree analysis demonstrated that RV Ch-1 VP6 is not a link between avian and mammalian VP6 sequences. RV Ch-1 showed variant aa in 17 positions which were otherwise absolutely conserved in mammalian and avian group A RVs. The 17 replacements were scattered through the entire VP6 sequence except the C-terminal part implicated in the assembly of subviral particles. In RV Ch-1 the proline residue 309, reported to be critical for the trimerization of VP6, was replaced by leucine, but VP6 trimers were still observed. The sequence and hydrophilicity analysis of avian RV VP6 do not explain the anomalous electrophoretic migration behavior of avian VP6 proteins.

The site-specific integration system of the temperate Streptococcus thermophilus bacteriophage phiSfi21

The temperate bacteriophage phiSfi21 integrates its DNA into the chromosome of Streptococcus thermophilus strains via site-specific recombination. Nucleotide sequencing of the attachment sites identified a 40-bp identity region which surprisingly overlaps both the 18-terminal bp of the phage integrase gene and the 11-terminal bp of a host tRNAArg gene. A 2.4-kb phage DNA segment, covering attP, the phage integrase, and a likely immunity gene contained all the genetic information for faithful integration of a nonreplicative plasmid into the attB site. A deletion within the int gene led to the loss of integration proficiency. A number of spontaneous deletions were observed in plasmids containing the 2.4-kb phage DNA segment. The deletion sites were localized to the tRNA side of the identity region and to phage or vector DNA with 3- to 6-bp-long repeats from the border region. A similar type of deletion was previously observed in a spontaneous phage mutant.

A highly conserved DNA replication module from Streptococcus thermophilus phages is similar in sequence and topology to a module from Lactococcus lactis phages

A highly conserved DNA region extending over 5 kb was observed in Streptococcus thermophilus bacteriophages. Comparative sequencing of one temperate and 26 virulent phages demonstrated in the most extreme case an 18% aa difference for a predicted protein, while the majority of the phages showed fewer, if any aa changes. The relative degree of aa conservation was not homogeneous over the DNA segment investigated. Sequence analysis of the conserved segment revealed genes possibly involved in DNA transactions. Three predicted proteins (orf 233, 443, and 382 gene product (gp)) showed nucleoside triphosphate binding motifs. Orf 443 gp showed in addition a DEAH box motif, characteristically found in a subgroup of helicases, and a variant zinc finger motif known from a phage T7 helicase/primase. Tree analysis classified orf 443 gp as a distant member of the helicase superfamily. Orf 382 gp showed similarity to putative plasmid DNA primases. Downstream of orf 382 a noncoding repeat region was identified that showed similarity to a putative minus origin from a cryptic S. thermophilus plasmid. Four predicted proteins showed not only high degrees of aa identity (34 to 63%) with proteins from Lactococcus lactis phages, but their genes showed a similar topological organization. We interpret this as evidence for a horizontal gene transfer event between phages of the two bacterial genera in the distant past.

Molecular ecology of Streptococcus thermophilus bacteriophage infections in a cheese factory

A mozzarella cheese factory using an undefined, milk-derived Streptococcus thermophilus starter system was monitored longitudinally for 2 years to determine whether the diversity of the resident bacteriophage population arose from environmental sources or from genetic changes in the resident phage in the factory. The two hypotheses led to different predictions about the genetic diversity of the phages. With respect to host range, 12 distinct phage types were observed. With two exceptions, phages belonging to different lytic groups showed clearly distinct restriction patterns and multiple isolates of phages showing the same host range exhibited identical or highly related restriction patterns. Sequencing studies in a conserved region of the phage genome revealed no point mutations in multiple isolates of the same phage type, while up to 12% nucleotide sequence diversity was observed between the different phage types. This diversity is as large as that between the most different sequences from phages in our collection. These observations make unlikely a model that postulates a single phage invasion event and diversification of the phage during its residence in the factory. In the second stage of our factory study, a defined starter system was introduced that could not propagate the resident factory phage population. Within a week, three new phage types were observed in the factory while the resident phage population was decreased but not eliminated. Raw milk was the most likely source of these new phages, as phages with identical host ranges and restriction patterns were isolated from raw milk delivered to the factory during the intervention trial. Apparently, all of the genetic diversity observed in the S. thermophilus phages isolated during our survey was already created in their natural environment. A better understanding of the raw-milk ecology of S. thermophilus phages is thus essential for successful practical phage control.

Characterization of the lysogeny DNA module from the temperate Streptococcus thermophilus bacteriophage phi Sfi21

Phage phi Sfi21, the only temperate Streptococcus thermophilus phage from our phage collection, showed extensive DNA homology with virulent phages from lytic group I. Southern blot hybridizations demonstrated that the phi Sfi21-specific DNA was clustered in an approximately 6.6-kb-long region, the putative lysogeny module. Sequence analysis and database research identified an integrase within this module; orf 203 with homology to an anonymous orf 258 from the temperate lactococcal phage BK5-T; orf 127 and orf 122 with weak homology to the N- and C-terminal parts, respectively, of the cl-like repressor from lactococcal phages Tuc2009 and BK5-T; orf 75 with homology to a repressor protein from lambdoid phage 434 and an anti-repressor ant with homology to phage P1. The molecular arrangement of the predicted orfs in phage phi Sfi21 was very similar to that of the lactococcal phage BK5-T. The transition from phi Sfi21-specific DNA into DNA shared with virulent phages was abrupt and flanked at one side by notable DNA repeats. Sequence analysis identified a holin protein to the left of the lysogeny module. A site-specific deletion of 2.4 kb, which reproducibly transformed phi Sfi21 into a lytic phage, was localized in the lysogeny module. It was flanked at both sides by conspicuous DNA repeats. One repeat region reflected the DNA around the attP site, while the other reflected the putative genetic switch region between repressor and anti-repressor genes. S. thermophilus host Sfi1 transformed with a plasmid containing int and orf 203 showed resistance to superinfection by heterologous phages, but not by the homologous phi Sfi21. Part of the int gene could be deleted without loss of this activity, while a deletion in orf 203 resulted in loss of the phage resistance. We speculate on the possibility of a bipartite immunity system for the control of lysogeny in phi Sfi21.

Bovine rotavirus 993/83 shows a third subtype of avian VP7 protein

VP7 genes of rotavirus (RV) 993/83 isolated from a German calf with diarrhea and of RV PO-13 isolated from a Japanese pigeon were sequenced. Alignment of the deduced VP7 amino acid sequence showed 98.8% sequence identity, while only 70% and 84% identity was seen with VP7 from chicken RV Ch-2 and turkey RV Ty-1, respectively. Over the antigenic regions A, B, and C mammalian RV 993/83 showed more aa identity with mammalian G3 RVs than with chicken RV Ch-2, which could explain the strong one-way cross-neutralization observed between RV 993/83 and G3 RVs. Despite marked VP7 sequence diversity avian RVs could not be differentiated into distinct G types.

Site-specific spontaneous deletions in three genome regions of a temperate Streptococcus thermophilus phage

Site-specific spontaneous deletions were observed with high frequency in three regions of the genome of the temperate Streptococcus thermophilus phage phi SFi21. Deletion sizes were 750 bp (type 1), 2.7 kb (type 2), and 1 kb (type 3). Combinations of types 1 and 3 and 2 and 3 were observed. The mutants grew lytically although with reduced burst sizes. Type 2 mutants lost the capacity to lysogenize host cells. Upon serial passage, the deletion mutants overgrew the wild-type phage. No direct or inverted DNA repeats were associated with type 1 or 2 deletion sites. Several independent phage isolates showed deletions at identical nucleotide positions, suggesting a site-specific recombination system. Sequencing of an Xbal restriction fragment covering the type 1 deletion predicted a single long open reading frame (ORF) showing a high degree of amino acid similarity with two proteins from bacteriophage P1 implicated in its immunity control (KiIA, Ant). Type 1 deletion leads to a loss of the conserved C-terminal part of this ORF.

Effect of malnutrition on serum and milk antibodies in Zairian women

Serum and human milk antimicrobial antibody titers were measured longitudinally in 17 malnourished and 14 control Zairian women during 6 to 18 months of lactation to test whether malnutrition is specifically associated with an impaired secretory antibody response. No decreases in total serum and human milk immunoglobulin concentrations, neutralizing antibody titers against rotavirus, or specific enzyme-linked immunosorbent assay antibody titers against rotavirus, respiratory syncytial virus, Escherichia coli, Streptococcus pneumoniae, and Haemophilus influenzae were detected when malnourished women were compared with control women. Malnutrition had no effect on circulating and secretory antibody concentrations in Zairian women. Daily human milk outputs, however, were about 30% lower in malnourished than in control women, resulting in a correspondingly lower ingestion of immunoglobulins by the children of malnourished women.

Risk factors associated with the recall of respiratory diseases in the Ecuadorian children

Risk factors associated with the recall of a recent episode of acute respiratory infection (ARI) were evaluated in 1,553 Ecuadorian preschool children enrolled into a cross-sectional health and nutrition survey. In a univariate analysis, ARI recall was significantly higher in children living in low altitude regions (Relative Risk, RR = 2.4), in younger children (RR = 1.6), in children from larger families (RR = 1.3), in children with diarrhoea recall (RR = 1.9), in children served with poor quality drinking water (RR = 1.3) and in anaemic children (RR = 1.2) than that in the appropriate control groups. After taking into account the confounding effect of altitude, no association was found between ARI recall and low height-for-age values. Stepwise logistic regression analysis identified living in low altitude regions, diarrhoea recall, and younger age as independent factors associated with a higher recall of ARI. In contrast to the recall of acute diarrhoea, no association between ARI recall and nutritional status was found. The impact of nutritional interventions in children from developing countries may be greater on enteric than on respiratory diseases.

Characterization of a temperate Streptococcus thermophilus bacteriophage and its genetic relationship with lytic phages

The temperate Streptococcus thermophilus bacteriophage phi SFi21 showed an 38-kb-long double-stranded DNA genome with cohesive ends. A single integration site was used in lysogens established in three different S. thermophilus strains. The attP and attB sites were localized on the restriction map of phage DNA and by hybridization on pulsed field separated bacterial DNA. All laboratory-established lysogens showed in addition to integrated prophage DNA unintegrated monomer phage DNA with unligated cos sites. The genetic relatedness of phi SFi21 DNA with DNA from lytic phages was studied in dot blot and Southern blot hybridization by using individual restriction fragments of phiSFi21 DNA as probes. Lytic group I phages hybridized with fragments of the central and the right part of the phiSFi21 genome but failed to hybridize with a fragment joining both parts. Lytic group II phages showed hybridization with the right half of the phiSFi21 genome. In lytic group IV phages, biologically a heterogeneous group, many different combinations of cross hybridization were detected in accordance with the hypothesis of the modular evolution of phage genomes.

Sequence analysis of pigeon, turkey, and chicken rotavirus VP8* identifies rotavirus 993/83, isolated from calf feces, as a pigeon rotavirus

Partial-length gene 4 cDNA encompassing the VP8* portion of VP4 from chicken rotavirus (RV) Ch-1, turkey RV Ty-1 and Ty-3, and pigeon RV PO-13 was sequenced and compared to RV 993/83 isolated from a calf with diarrhea. Ninety-six percent amino acid sequence identity was seen between VP8* from calf RV 993/83 and pigeon RV PO-13, while only 77 to 83% identity was seen in comparison with turkey and chicken RV VP8* sequences. Phylogenetic tree analysis places all avian RV (including calf isolate 993/83) on a branch at the bottom of the VP8* tree. When tested with three neutralizing monoclonal antibodies raised against pigeon RV PO-13, RV 993/83 and Ty-1 share three, Ch-1 shares two, and Ty-3 shares one neutralizing epitope(s) on VP4 with pigeon RV PO-13.

Effect of age on concentrations of serum antibodies to viral, bacterial, and food antigens in elderly Swiss people

Serum antibody concentrations to two viral, five bacterial, and two food antigens were investigated in 307 elderly Swiss subjects, and the hypothesis of whether serum antibody titers decreased with age was tested. The cross-sectional part of the study consisted of 216 unselected consecutive patients hospitalized in one geriatric hospital. The patients were divided into two age groups (65 to 84 and 85 to 102 years old), and their antibody titers were compared. No age-related decreases in antibody titers were observed. The members of the two age groups were well matched for medical diagnosis and nutritional and inflammatory status. The prospective part of the study consisted of 91 healthy elderly subjects living in the community; they were 71 to 76 years old when they were enrolled in the study. Their serum antibody status was measured at the beginning of the study and 4 years later. We observed a significant decrease in diphtheria antitoxin levels and a significant increase in antibody titer to the capsular polysaccharide of Streptococcus pneumoniae. No change in antibody titer to rotavirus, respiratory syncytial virus, lipopolysaccharide of Escherichia coli, C polysaccharide of S. pneumoniae, or the polyribosyl-ribitol phosphate of Haemophilus influenzae was observed. Thus, no signs of B-cell immunosenescence were seen in these two groups of elderly Swiss people.

Effect of malnutrition in Ecuadorian children on titers of serum antibodies to various microbial antigens

The titers of serum antibodies to natural infection with enteric and respiratory pathogens, to a food antigen and to tetanus and diphtheria toxoid were evaluated by enzyme-linked immunosorbent assay in 1,554 Ecuadorian children younger than 5 years of age. The nutritional status of the children was assessed by anthropometry and measurement of biochemical status indicators. The children were enrolled in a representative national nutrition and health survey. Antibody titers were analyzed as a function of the nutritional status of the children. For 12 of 14 antibody concentrations tested, underweight children showed lower antibody titers than did control children. The difference was statistically significant for antibody to both T-cell-dependent antigens (tetanus toxoid, rotavirus, respiratory syncytial virus) and T-cell-independent antigens (lipopolysaccharide, polyribosyl-ribitol phosphate, capsular polysaccharide). When children with a recent episode of diarrhea were excluded, many of the differences remained significant. When these children were further classified by age, only difference in titers of antibodies to respiratory syncytial virus and tetanus toxoid remained significant. No statistically significant difference was detected between underweight and control children with respect to protective antibody levels to four bacterial antigens. Anemic children showed significantly lower antibody levels to both T-cell-dependent and T-cell-independent antigens than did control children, and a higher proportion of anemic children had diphtheria antitoxin below a conservatively defined protective antibody level. No major differences in antibody titers were seen between children with different retinol and zinc concentrations in serum.

Bovine rotavirus V1005 a P5, not a P12, type like all viruses in a German survey

Bovine rotavirus (BRV) V1005, like 34 further cell culture-adapted strains in a 6-year survey in Upper Bavaria, Germany, is not a P12 but a P5 P-type rotavirus. The conclusion is based on dot blot hybridization with P1-, P5-, and P11-specific cDNAs, encompassing the VP8* region of major sequence diversity, and on PCR using P1-, P5-, and P11-specific primer pairs derived from the VP5* region of VP4 (VP5* and VP8*, respectively, are the larger and smaller tryptic cleavage products of VP4). Sequencing of the hyperdivergent region of VP4 confirmed the close relatedness of BRV V1005 to BRV UK, the P5 prototype virus.

Coproantibodies to rotavirus serotype 1 infection in German children

One hundred and ninety-eight serial stool samples were collected from 27 infants and children hospitalized in Bochum, Germany with gastroenteritis due to serotype 1 rotavirus (RV). RV antigen and RV-specific antibodies (Ab) (IgA ELISA and RV Wa-neutralizing Ab) were measured. The prevalence of RV-Ab positive stool samples in RV patients did not differ from that in stool samples from 80 control patients (40% and 42% for ELISA Ab and 11% and 6% for neutralizing Ab, respectively). None of the patients was breastfed in the week preceding stool collection. No significant increase in the prevalence of RV-Ab was observed between stool samples obtained during the early and late phase of hospitalization. We observed patients that continued to excrete RV antigen in the presence of neutralizing stool activities, and patients that showed cessation of RV stool excretion and resolution of clinical symptoms in the absence of RV-neutralizing activity in the stool samples.

Distinct Streptococcus thermophilus bacteriophages share an extremely conserved DNA fragment

A cross-hybridizing 2.2-kb EcoRI fragment was cloned from two lytic Streptococcus thermophilus bacteriophages with distinct phenotypes. The DNA fragments, which contained two unidentified open reading frames, differed at only 3 of 2207 nucleotide positions. Partial sequencing of a temperate S. thermophilus phage and of a further lytic phage belonging to a different lytic group isolated 20 years earlier from a different geographical area confirmed this extreme sequence conservation. Hybridization of this phage DNA with bacterial host DNA was not observed. The evolutionary implications of these observations are briefly discussed.

Antibody response to polyribosyl-ribitol phosphate antigen of Haemophilus influenzae in Ecuadorian and German children

Serum samples from 1,221 Ecuadorian children 0 to 5 years of age and from 236 German subjects were tested by enzyme-linked immunosorbent assay for class-specific antibodies to the capsular polysaccharide of Haemophilus influenzae type b (PRP antigen). A gradual prevalence increase of and mean titer increase in immunoglobulin M (IgM) antibody was seen in Ecuadorian but not in German children older than 6 months. At the end of the first year of life, about 50% of the Ecuadorian children showed IgM and IgG antibody to PRP. Seroepidemiological analysis revealed that living at a low altitude and lower calorie intake (a proxy measure of breast-feeding) were factors associated with earlier acquisition of PRP antibody. Children from low-altitude areas of Ecuador also experienced significantly more episodes of significant respiratory infections. The acquisition of PRP-reactive antibodies in Ecuadorian children might thus reflect exposure to encapsulated H. influenzae type b in lower respiratory tract infections.

A unique VP4 gene allele carried by an unusual bovine rotavirus strain, 993/83

The VP4 protein of an unusual group A calf rotavirus strain, 993/83 (serotype G7 and subgroup non-I and non-II), was determined to contain 770 amino acids, shorter than any other VP4 proteins sequenced to date. The 993/83 VP4 exhibited only 55-62% amino acid identity to the VP4s of the representatives of 12 distinct P serotypes, suggesting that 993/83 VP4 represents a new P serotype.

Nutritional and environmental risk factors for diarrhoeal diseases in Ecuadorian children

Risk factors associated with diarrhoea, based on the recall of a recent episode were evaluated from a cross-sectional national nutrition and health study in 1,620 Ecuadorian children less than 5 years old. Prevalence of diarrhoea varied with the age of the children; 6- to 23-months-old children showed the highest prevalence. In this age range the prevalence of diarrhoea was significantly associated with hygienic factors (quality of drinking water, sanitation and refuse system), but not with demographic factors (sex, altitude, population density, family size). The nutritional status of the children was determined by anthropometry and blood chemistry. After stratification for sanitation levels, a low weight-for-age Z-score and low serum retinol and zinc concentrations showed a statistically significant (p < or = 0.06) association with diarrhoea prevalence only in children living under better hygienic conditions. Multivariate analysis revealed significant associations between both sanitation levels and nutritional level as defined by anthropometry, but not by blood chemistry, and diarrhoea prevalence.

Tetanus and diphtheria immunization coverage in Ecuadorian children after a national vaccination campaign

Between October 1985 and June 1986, a national vaccination campaign was launched in Ecuador. Between March and November 1986, 7798 Ecuadorian children < 5 years old were enrolled in a representative health survey. According to their vaccination cards, 65% of children had a complete series of three doses of diphtheria-tetanus-pertussis (DTP) vaccination. Serum samples were obtained from a subset of 1400 children; by ELISA, 80% had serologic evidence of recent DTP vaccination and > 80% of the newborns had tetanus antitoxin titers, indicating recent tetanus vaccination of their mothers. For all 1400 children, median tetanus and diphtheria antitoxin titers were 1.0 and 0.6 IU/mL, respectively. These data indicate the possibility of success of such vaccination campaigns if supported by the government.

Nucleotide sequence of gene 6 of avian-like group A rotavirus 993/83

Two cDNA clones, which hybridized in Northern blots to RNA segment 6 of the homologous avian-like group A rotavirus (RV) 993/83 and pigeon RV PO-13, but not to mammalian group A rotaviruses, were sequenced. The gene 6 sequence contained a single long open reading frame encoding a protein of 397 amino acids (total MW 44,460). Comparison of the deduced amino acid sequence with VP6 protein from mammalian group A RV revealed 72 to 74.3% of amino acid identity. These values are surprisingly low in view of the high homology levels described up to now for group A RV. Avian-like RV 993/83 is however not a missing link between group A and C RV as it is as distantly related to group C RV as group A mammalian RV to group C RV. The evolutionary implications of these observations are briefly discussed.

Rotavirus-inhibitory activity in serial milk samples from Mexican women and rotavirus infections in their children during their first year of life

A total of 75 children born in rural Mexico were followed for diarrheal diseases and rotavirus (RV) excretion during the first year of life. For 18 children, an average of 14 serial breast milk samples were obtained between days 2 and 360 after delivery and were tested for RV-inhibitory activity. Of these samples, 70, 62, and 85% showed inhibitory activity against serotype (ST) 1 human RV, ST4 human RV, and ST3 simian RV, respectively; the median titers were 10, 10, and 20, respectively. Some 89% of the milk samples showed RV-specific antibodies in an enzyme-linked immunosorbent assay (median titer, 20). Surprisingly, 98% of the milk samples inhibited ST6 bovine RV. ST6, but not ST1, RV-inhibitory activity survived heat treatment (10 min at 80 degrees C). Of the 18 children tested, 13 children experienced 23 episodes of diarrhea (enterotoxigenic [n = 8] and enteropathogenic [n = 3] Escherichia coli, Campylobacter jejuni [n = 4], Shigella flexneri [n = 2], RV [n = 1]) and 5 children experienced 6 RV infections. Only one RV infection was associated with diarrhea. The five RV excretors did not differ from the nonexcretors with respect to the RV-inhibitory activity in the breast milk fed to them. The RV-inhibitory titers were too low in the majority of the studied Mexican milk samples to indicate an important effect of breast-feeding on the take rate of oral human, simian, or reassortant RV vaccines. Breast-feeding might, however, inhibit the take rate of a bovine RV vaccine.

Seroprevalence of immunoglobulin M (IgM) and IgG antibodies to polysaccharides of Streptococcus pneumoniae in different age groups of Ecuadorian and German children

The age-specific prevalence of serum immunoglobulin M (IgM) antibody to capsular polysaccharides of Streptococcus pneumoniae, as detected by enzyme-linked immunosorbent assay, was studied in 1,301 Ecuadorian children enrolled in a national nutrition and health survey. This prevalence was 6% in infants < 6 months old and increased to 28% in children 6 to 11 months old, 49% in those 12 to 17 months old, and 58% in those 18 to 23 months old. About 80% of the 5-year-old children had this antibody. When tested separately against six different capsular polysaccharides, serum IgM antibody reacted with decreasing frequency with serotype 3, 8, 19, 6, 23, and 1 capsular polysaccharides. We did not observe a broadening of the antibody response with increasing age in the sense that more and more serotypes were recognized. A similar age-related prevalence was found for IgM antibody to the species-specific C-polysaccharide of S. pneumoniae and for IgG antibody to capsular polysaccharides of S. pneumoniae. A smaller German serum collection showed a comparable age-related prevalence of pneumococcus-specific serum IgG and IgM antibodies. The highest incidence of respiratory diseases was observed in 1- and 2-year-old Ecuadorian children. It thus seems that acquisition of serum antibody to S. pneumoniae reflects more the developmental maturation of an immune response than an actual exposure to different pneumococcal serotypes.

Field trial of an infant formula containing anti-rotavirus and anti-Escherichia coli milk antibodies from hyperimmunized cows

Two groups of 124 and 108 children, respectively, living in urban Santiago, Chile in low socioeconomic conditions were prospectively followed for 6 months for their incidence of diarrhea. Each cohort was divided into two subgroups receiving either a commercial milk formula or the same formula containing 1% (wt/wt) bovine milk immunoglobulin concentrate from cows hyperimmunized with human rotaviruses and the major enteropathogenic Escherichia coli (EPEC) serogroups. Neither group differed with respect to incidence of diarrhea (98 episodes in 117 treated children versus 95 episodes in 115 control children), duration and clinical symptoms of diarrhea, and weight gain. Furthermore, neither group differed with respect to isolation of rotavirus (14 and 13 isolates in treatment and control groups, respectively) and isolation of enteropathogenic E. coli (14 and 15 isolates in treatment and control groups, respectively). The treatment but not the control formula contained neutralizing antibody against all human rotavirus serotypes. Titers were comparable to human breast milk samples. All isolated EPEC serogroups were included in the vaccine used for the immunization of the cows. The treatment, but not the control formula, protected mice against a lethal challenge with an EPEC strain. In conclusion, feeding an antibody-supplemented formula had no positive effect on diarrheal diseases under the conditions of a fairly well-controlled small-scale field trial.

Rotavirus 993/83, isolated from calf faeces, closely resembles an avian rotavirus

Polypeptides from purified virions of the calf rotavirus (RV) isolate 993/83 and those from the pigeon RV isolate PO-13 comigrated on SDS-polyacrylamide gels. Two polypeptides of 45K and 47K were detected at the position of VP6. Both proteins behaved like authentic VP6 protein with EDTA and heat treatment. RV 993/83 and PO-13 showed identical one-dimensional peptide maps for VP2, and the 45K and 47K proteins. More than 70% of sera from German cattle older than 1 year showed neutralizing serum antibodies to RV 993/83 and RV PO-13.

Epidemiological analysis of serologically determined rotavirus and enterotoxigenic Escherichia coli infections in Ecuadorian children

The statistical association of rotavirus- and enterotoxigenic Escherichia coli-specific serum antibody with demographic and hygienic factors was tested in Ecuadorian children enrolled in a cross-sectional survey. In 7- to 10-month-old children, enterotoxigenic E. coli-specific antibody was associated (P less than 0.05) with poor drinking water quality, lack of a sewage system, and feeding of supplementary food. In 7- to 14-month-old children, rotavirus-specific antibody was associated only with family size but notably not with hygienic factors.

Neutralizing serum antibodies to serotype 6 human rotaviruses PA151 and PA169 in Ecuadorian and German children

Serum samples from 726 Ecuadorian children who underwent natural rotavirus (RV) exposure were tested for neutralizing serum antibodies against two serotype 6 (ST6) human RV (HRV) isolates from Italy, PA151 and PA169, and two ST6 bovine RV (BRV) isolates, NCDV and UK. Gene 4 was distinct in all four ST6 strains. Ninety-one, 56, 67, and 65 serum samples neutralized HRV PA151 (13%), HRV PA169 (8%), BRV NCDV (9%), and BRV UK (9%), respectively. A total of 44 of the 91 serum samples which neutralized HRV PA151 did not neutralize the other three ST6 RV strains. In addition, we identified three serum samples that neutralized HRV PA151 but none of the six human or four animal RV STs. However, we failed to identify serum samples that neutralized HRV PA169 without neutralizing at least one of the major HRV STs. With a hospital-based serum collection from German children (excluding gastroenteritis patients), we identified 3 out of 197 serum samples tested that neutralized HRV PA151 specifically, whereas none neutralized HRV PA169 exclusively. None of the 71 German infants hospitalized with primary RV gastroenteritis showed a PA151- or a PA169-specific antibody response.

Reactivity of human serum antibody with lipopolysaccharide O 78 antigen from enterotoxigenic Escherichia coli

Fifteen and five of 20 volunteers challenged with the enterotoxigenic Escherichia coli strain O 78.H11 showed a fourfold titre increase of serum ELISA antibody to the homologous O 78 and the heterologous O 8 lipopolysaccharide antigen, respectively. Sixty-three of 191 sera from 1- to 48-month-old German children showed serum antibody reactive with O 78 antigen, all but two of these O 78-positive sera also showed reactivity with at least one further O antigen. Only 14 of the O 78 reactive sera also showed antibody to heat-labile enterotoxin. In addition, soluble O 8 antigen could inhibit the binding of serum antibody to absorbed O 78 in 68% of the German children. Antibody reactive with O 78 antigen is thus not a reliable serological marker for enterotoxigenic E. coli infection in German children.

Isolation of an avianlike group A rotavirus from a calf with diarrhea

An atypical group A rotavirus (993/83) was isolated from a 3-day-old German calf with diarrhea. It differed from 35 conventional German bovine rotavirus isolates analyzed previously with respect to subgroup (strain 993/83 was non-subgroup I and non-subgroup II), serotype (strain 993/83 showed a two-way cross-reaction with serotype 7 and a one-way cross-reaction with serotype 3), and electropherotype (strain 993/83 showed comigrating gene segments 10 and 11). Isolate 993/83 reacted with only one of four monoclonal antibodies that recognized a common VP6 epitope(s). In addition, VP6 and VP2 of isolate 993/83 showed one-dimensional peptide maps that differed substantially from the peptide maps of VP6 and VP2 from all bovine rotavirus isolates. By RNA-RNA hybridization, the 993/83 probe failed to react with a panel of mammalian rotavirus strains, including bovine rotaviruses. It hybridized, however, to genomic RNA of an avian rotavirus strain. Isolate 993/83 could thus represent a candidate for a natural interspecies transmission of rotavirus between different classes of vertebrates.