Transfer of genetic information within a colony of Haemophilus influenzae

FINE-SCALE GENETIC AND PHENOTYPIC STRUCTURE IN NATURAL POPULATIONS OF BACILLUS SUBTILIS AND BACILLUS LICHENIFORMIS: IMPLICATIONS FOR BACTERIAL EVOLUTION AND SPECIATION

The genetic and phenotypic structure of sympatric populations of wild bacteria traditionally identified as Bacillus subtilis and B. licheniformis was analyzed. Small soil samples were taken from a single, tiny site in the Sonoran Desert of Arizona, USA, to provide a true population analysis, in contrast to many analyses of genetic structure using bacterial strain collections of widely heterogeneous origin. Genetic analyses of isolates used multilocus enzyme electrophoresis, mismatches in restriction fragment length polymorphism, and variants from Southern hybridization with B. subtilis DNA probes. Phenotypic analyses of isolates used the API test system for detection of growth and acid production on specific carbon sources. The two species were distinct both phenotypically and genetically, despite their known potential for genetic exchange in laboratory experiments. Genic and genotypic diversity were high in both species, and only 16% of observed allozyme variants might possibly be common to both species. Hence, there is probably modest genetic exchange, if any, between the species in nature. Clear hierarchies of population-genetic structure were found for both species. Different types of genetic data yield concordant population structures for B. subtilis. For both species, two-locus and multilocus statistical analyses of linkage demonstrated modest to strong disequilibrium at the species level but truly panmictic subunits within each species. The evidence for extensive genetic recombination within these fine-scale subdivisions is unequivocal, indicating that the sexuality of these bacteria can be well expressed in nature. The relation of these results to processes of bacterial evolution and speciation is discussed.

GENETIC EXCHANGE BETWEEN BACILLUS SUBTILIS AND BACILLUS LICHENIFORMIS: VARIABLE HYBRID STABILITY AND THE NATURE OF BACTERIAL SPECIES

Experiments employing both broth and soil cultures demonstrated the capacity for bidirectional genetic exchange between the eubacterial species Bacillus subtilis and Bacillus licheniformis. The process was studied using standard laboratory strains and wild isolates of these species. The genetic exchange in soil occurs spontaneously. The interspecific recombination involved markers for antibiotic resistance and for the use of specific carbon sources (API characters). Hybrids frequently had unstable phenotypes, i.e., lacked a consistent expression of foreign genes over repeated transfer and growth. This instability often involved a "correction" back toward the phenotype of one or the other of the parental species for many differentiating characters; the final phenotype was always that of the more probable or actually known recipient species. This "correction" process is reminiscent of phenomena associated with the instability of artificial fusion protoplasts or noncomplementing diploids of B. subtilis, as well as the merodiploids formed by intergeneric crosses with enteric bacteria. The hybrids observed here must also be diploid, in some manner, because they sequentially express traits of both parental species at rates well above the frequency of mutation. Among the unstable changes in hybrids of the wild strains there was a 3:1 bias in favor of "correction." The dynamics of the hybridization process in soil are described. It appears that the hybrids are formed most rapidly following outgrowth from spores and during the early growth of parental vegetative cell populations. Later on, the hybrids are much less frequent in the soil cultures, suggesting that they are competitively inferior to the parental species. It is argued that the capacity for recombination found between B. subtilis and B. licheniformis could locally erase their distinctness, even though they possess only about 15% DNA sequence homology. Yet they remain distinct in the wild. The methods and results of these experiments prepare the way for detailed studies of the nature of species and species boundaries throughout the genus Bacillus.

blaROB-1 presence on pB1000 in Haemophilus influenzae is widespread, and variable cefaclor resistance is associated with altered penicillin-binding proteins

Plasmid pB1000 is a small replicon recently identified as bearing bla(ROB-1) in animal and human Pasteurellaceae in Spain. We identified pB1000 in 11 bla(ROB-1)-positive Australian and North American Haemophilus influenzae isolates, suggesting a wider role for pB1000 in disseminating bla(ROB-1). Native H. influenzae conjugative elements can mobilize plasmids similar to pB1000 at a low frequency of 10(-8), and this might account for the infrequency of bla(ROB-1) compared to the rate of occurrence of bla(TEM-1). Altered penicillin-binding protein 3 was associated with an increased cefaclor MIC in 3 isolates.

Low genetic diversity of Haemophilus influenzae type b compared to nonencapsulated H. influenzae in a population in which H. influenzae is highly endemic

Immunization with Haemophilus influenzae type b (Hib) conjugate polysaccharide vaccines has dramatically reduced Hib disease worldwide. As in other populations, nasopharyngeal carriage of Hib declined markedly in Aboriginal infants following vaccination, although carriage has not been entirely eliminated. In this study, we describe the genetic characteristics and the carriage dynamics of longitudinal isolates of Hib, characterized by using several typing methods. In addition, carriage rates of nonencapsulated H. influenzae (NCHi) are high, and concurrent colonization with Hib and NCHi is common; we also observed NCHi isolates which were genetically similar to Hib. There is a continuing need to promote Hib immunization and monitor H. influenzae carriage in populations in which the organism is highly endemic, not least because of the possibility of genetic exchange between Hib and NCHi strains in such populations.

Molecular cloning of two linked loci that increase the transformability of transformation-deficient mutants of Haemophilus influenzae

A plasmid containing a 13.3-kb insert (pER194) was isolated from an EcoRI genomic library of Haemophilus influenzae on the basis of its ability to increase the transformability of the transformation-deficient mutants Com-78 and Com-101. The plasmid failed to increase the transformability of the Rec-1 and Rec-2 mutants, indicating that the mutations producing the Com-78 and Com-101 phenotypes are distinct from those giving rise to the Rec-1 and Rec-2 phenotypes. The physical mapping of the cloned fragment on the H. influenzae chromosome was found to be consistent with the genetic mapping of the Com-101 trait. A 2.8-kb EcoRI-BglII subfragment, representing one end of the 13.3-kb clone, was found to increase the transformation frequency of the Com-78 and Com-101 mutants when supplied in trans, indicating that the subfragment carries one or more loci required for chromosomal transformation. The corresponding region of the Com-101 chromosome was determined by hybridization analysis to contain a 0.3-kb insertion, suggesting that the Com-101 strain may contain an insertion mutation at this locus. A 3.0-kb EcoRI-MluI subfragment, representing the other end of the 13.3-kb EcoRI fragment, was found to increase the transformation frequency of the Com-101 mutant but not of the Com-78 mutant, suggesting that the Com-101 phenotype results from a complex genotype involving mutations at two or more transformation-related loci. This conclusion is consistent with data indicating that the Com-101 trait can be genetically separated into at least two components.

Cloning and characterization of the Haemophilus influenzae Rd rec-1+ gene

The Haemophilus influenzae Rd rec-1+ gene was cloned from a partial chromosomal digest into a plasmid vector as a 20-kilobase-pair (kbp) BstEII fragment and then subcloned. The smallest subclone with rec-1+ activity carried a 3.1-kbp EcoRI fragment. The identity of the rec-I gene in these clones was confirmed by transforming an Rd strain carrying a leaky rec-1 mutation (recA4) to resistance to methyl methanesulfonate (MMS) by using whole or digested plasmids. It was demonstrated that the Rec+ phenotype of the MMSr transformants was linked to the strA, novAB, and mmsA loci, as expected if the recA4 allele had been replaced by rec-1+. In growing cultures (rec-1 or rec+), all rec-1+-carrying plasmids induced near-maximal levels of transformability when their hosts reached stationary phase; these levels are 100 to 1,000 times higher than the values seen with strains not carrying a Rec plasmid. Transfer of the 3.1-kbp subclone was greatly reduced compared with transfer of similarly sized vector plasmids, and the resulting transformants grew slowly; this suggests an explanation of my failure to directly clone this fragment from chromosomal DNA digests. Transfer of a rec-1+ plasmid to a very poorly genetically transformable H. influenzae Rb strain resulted in greatly increased transformability. Transfer of such plasmids to a noncompetent H. influenzae Rc strain did not render this strain competent. It is suggested that transformability of Rd and Rb strains is limited by rec-1 expression but that the noncompetence of Rc has some other basis.

Organization of the Haemophilus influenzae Rd genome

We present the first complete map of the Haemophilus influenzae genome, consisting of a detailed restriction map with a number of genetic loci. All of the ApaI, SmaI, and RsrII restriction sites (total of 45 sites) were mapped by Southern blot hybridization analysis of fragments separated by pulsed-field gel electrophoresis. Cloned genes were placed on the restriction map by Southern hybridization, and antibiotic resistance loci were also located by transformation with purified restriction fragments. The attachment site of the HP1 prophage was mapped. In addition, the number, locations, and orientations of the six rRNA operons in the H. influenzae chromosome were determined. The positions of conserved restriction sites in these rrn operons confirm that the direction of transcription is 16S to 23S, as in most other bacteria. The widely used strain BC200 appears to contain an unexpected 45-kilobase duplication.

Size and physical map of the chromosome of Haemophilus influenzae

A variation of pulse-field electrophoresis, field-inversion gel electrophoresis, was used to determine the size and physical map of the chromosome of Haemophilus influenzae. The DNA of H. influenzae had a low G + C content (39%) and no restriction sites for the enzymes NotI or SfiI. However, a number of restriction enzymes (SmaI, ApaI, NaeI, and SacII) that recognized 6-base-pair sequences containing only G and C nucleotides were found to generate a reasonable number of DNA fragments that were separable in agarose gels by field-inversion gel electrophoresis. The sizes of the DNA fragments were calibrated with a lambda DNA ladder and lambda DNA restriction fragments. The sum of fragment sizes obtained with restriction digests yielded a value for the chromosome of 1,980 kilobase pairs. Hybridization of a labeled fragment with two or more fragments from a digest with a different restriction enzyme provided the information needed to construct a circular map of the H. influenzae chromosome.

Site-specific recombination between cloned attP and attB sites from the Haemophilus influenzae bacteriophage HP1 propagated in recombination-deficient Escherichia coli

Plasmids were constructed which contain both attP and attB DNA segments derived from the insertion sites of the lysogenic bacteriophage HP1 and its host, Haemophilus influenzae. Similar plasmids containing the two junction segments (attL and attR regions) between the phage genome and the lysogenic host chromosome were also prepared. The formation of recombinant dimer plasmids was observed when attP-attB plasmids were propagated in Escherichia coli HB101 (recA), while plasmids containing the junction segments did not form recombinant dimers. Deletion of the phage DNA segment adjacent to the attP site from the attP-attB constructions eliminated detectable recombination, suggesting that this sequence contains the gene encoding the HP1 integrase. No plasmid recombination was observed in strains of E. coli defective in integration host factor. This suggests that integration host factor is important in the expression or activity of the system which produces the site-specific recombination of sequences derived from HP1 and H. influenzae. Further, it suggests that a protein functionally analogous to E. coli integration host factor may be present in H. influenzae.

Mathematical modelling of intercellular regulation causing the formation of spatial structures in bacterial colonies

Bacterial colonies may grow forming stable spatial, particularly circular, structures. For instance, motile bacteria Proteus vulgaris or Escherichia coli grown on agar under certain conditions may form concentric rings with the centre in the inoculation point (Rüss-Münzer, 1935, Bact. Parasit Kde (Abt 1) 7, 214; Budriené, 1985, Dokl. Acad. Nauk SSR, 283, 470). A similar picture can be observed in a different situation, i.e. when a lawn of non-motile Salmonella typhimurium bacteria is cultivated on a solid agar with the locally introduced substrate (Hoppensteadt & Jäger, 1980, Lecture Notes in Biomath. 38, 68). This paper describes a mechanism of bacterial interactions through a hypothetical mediator released by the organisms. A mathematical model has been built. Its analysis has shown that the selected laws of secretion and reception of the mediator can adequately account for the formation of circular structures in the case of both motile and non-motile bacteria.

Sizing of the Haemophilus influenzae Rd genome by pulsed-field agarose gel electrophoresis

The four restriction enzymes ApaI (5'-GGGCCC), EagI (5'-CGGCCG), NaeI (5'-GCCGGC), and SmaI (5'-CCCGGG) were found to produce distributions of DNA fragment sizes useful for mapping of the Haemophilus influenzae Rd genome by pulsed-field agarose gel electrophoresis. ApaI produced 21 fragments (range, 1.6 to 305 kilobases [kb]), EagI yielded 30 fragments (0.6 to 339 kb), NaeI produced 32 fragments (2.3 to 290 kb), and SmaI yielded 16 fragments (6.0 to 377 kb). Summation of the fragment lengths in each digest yielded estimates for the size of the H. influenzae chromosome ranging from 1,834 kb.

Clonal population structure of encapsulated Haemophilus influenzae

Chromosomal genotypes of 2,209 isolates of the six polysaccharide capsule types of Haemophilus influenzae recovered from human hosts worldwide were characterized by an analysis of electrophoretically demonstrable allelic profiles at 17 metabolic enzyme loci. For 222 representative isolates, restriction fragment length polymorphism patterns produced by digestion of cap region DNA were also determined. With few exceptions, isolates belonging to individual phylogenetic lines or groups of allied lineages identified by multilocus enzyme electrophoresis had characteristic cap region restriction fragment length polymorphism patterns and characteristic combinations of cap region patterns and outer membrane protein types. The occurrence of strong associations of characters and the recovery of isolates with identical genetic properties in widely separated geographic regions and over a 40-year period indicated that the population structure of encapsulated H. influenzae is clonal. Recombination of chromosomal genes, including those mediating capsule synthesis, apparently is not a major factor in the short-term evolution of these pathogenic organisms and, therefore, may be of minor clinical significance.

Mobilization of Haemophilus influenzae chromosomal markers by an Escherichia coli F' factor

Filter matings between E. coli K-12 strains carrying an F'::Tn5,Tn9 factor with H. influenzae Rd strains gave rise to kanamycin-chloramphenicol-resistant H. influenzae strains at a frequency of approximately 10(-6). Transfer of the F' factor to H. influenzae was verified by expression of unselected markers in H. influenzae (lac+ or cotransfer of the nonselected antibiotic resistance), physical presence of a high-molecular-weight plasmid in recipient H. influenzae cells, and detection by Southern hybridization analysis of DNA sequences specific for the F' factor replication and partition functions in recipient H. influenzae cells. H. influenzae (F' Tn5,Tn9) strains were capable of transferring kanamycin and chloramphenicol resistances to other H. influenzae strains and were capable of mobilizing H. influenzae chromosomal markers at a low frequency. Insertion of a Tn5 element in the H. influenzae genome near the novobiocin resistance gene increased the frequency of transfer of novobiocin resistance about 30-fold. Transfer of other chromosomal markers also increased, although to a lesser extent, and ordered transfer of chromosomal markers could be demonstrated. Gene transfer was insensitive to DNase I, and transfer of chromosomal (but not F' factor) markers was dependent on the H. influenzae rec-1 and rec-2 gene functions.

Nucleotide sequences and properties of the sites involved in lysogenic insertion of the bacteriophage HP1c1 genome into the Haemophilus influenzae chromosome

Bacteriophage HP1c1 lysogenizes its host Haemophilus influenzae Rd by inserting its genome into the bacterial chromosome. The DNA segments corresponding to the integration regions on the phage and host chromosomes and the two junctions formed between phage and host sequences on lysogenic insertion were isolated and propagated in Escherichia coli HB101 as hybrid plasmids by using pBR322 as the vector. The nucleotide sequences in the vicinity of the point of recombinational insertion were determined. Phage and host DNA shared an extensive, nearly identical, segment that was 183 base pairs long. This segment consisted of 93 identical residues and a 27-residue portion containing 6 mismatches, followed by 63 identical residues. Recombinational insertion occurred within the 63-residue identical segment and involved neither duplication nor deletion of any residues. Short inverted repeats consisting of clustered A-T base pairs were present within the two 27-residue segments. Two additional sites on the host chromosome showed significant hybridization to the phage-host homology region.

Mutations affecting expression and maintenance of genes encoding the serotype b capsule of Haemophilus influenzae

Deletion mutagenesis analysis of a duplicated gene necessary for Haemophilus influenzae serotype b capsule expression showed that only one functional copy of this gene is required for capsule production and for virulence in infant rats. Mutant strains generated in this study differed from each other and from the parental strain in their ability to maintain the large tandem duplication which contains the genes involved in serotype b capsule expression.

Homology-facilitated plasmid transfer in Haemophilus influenzae

The 8 kbp plasmid pAT4 transformed Haemophilus influenzae Rd cells at low frequencies. Transformation was increased up to 100 times, however, when the recipient cells carried a DNA segment in either their chromosome or in a resident plasmid that was homologous to at least part of plasmid pAT4. Linearized plasmid DNA molecules did not transform cells without DNA homology; they efficiently transformed homology recipients, but only when the cuts had been made in the region of shared homology. In most cases examined the circular donor plasmid had been reconstituted from the transforming DNA; in some cases the reconstituted plasmid carried a mutation initially present in the recipient chromosome, provided the transforming plasmid had been linearized in the region of shared homology. Plasmid reconstitution was not observed in recA1 cells. We conclude that homology-facilitated plasmid transformation (transfer) is similar to that reported for Bacillus subtilis and Streptococcus pneumoniae.

Genetic relationships of serologically nontypable and serotype b strains of Haemophilus influenzae

A collection of 242 strains of Haemophilus influenzae, including 65 nontypable (unencapsulated) isolates and 177 encapsulated serotype b isolates recovered largely from children with invasive and noninvasive diseases in the United States, was characterized by the electrophoretic mobilities of 15 metabolic enzymes presumably encoded by chromosomal genes. All enzymes were polymorphic for three to seven electromorphs, and 94 distinctive multilocus genotypes (electrophoretic types [ETs]) were distinguished, among which mean genetic (allelic) diversity was 0.500. Isolates recovered from cases of invasive or noninvasive diseases did not differ significantly in level of genetic variation. The observation that 29 ETs were represented exclusively by serotype b isolates and that each of the 65 nontypable isolates was of a unique ET strongly confirmed the hypothesis that unencapsulated clinical isolates are not merely phenotypic variants of the common serotype b cell lines. Rather, the two types of isolates are distinctive subsets of the multilocus chromosomal genotypes of the species as a whole. Serotype b capsule occurred in three groups of isolates that are distantly related in multilocus enzyme genotype. Isolates of four closely related nontypable biotype IV ETs associated with obstetrical infections or neonatal bacteremia were highly divergent from all others examined and may be specifically distinct. A phylogenetic scenario was proposed in which the ancestor of H. influenzae was encapsulated and the nontypable clones arose by convergent evolutionary loss of the ability to synthesize or extracellularly express a polysaccharide capsule.

Integration of the bacteriophage HP1c1 genome into the Haemophilus influenzae Rd chromosome in the lysogenic state

Restriction fragments hybridizing to phage HP1c1 DNA were identified in digests of DNA from lysogenic strains of Haemophilus influenzae. The results showed that the cohesive ends of the mature phage DNA were joined in lysogens and that the phage genome was covalently linked to the host DNA, indicating that lysogeny involves recombination between specific sites on the phage and host chromosomes. The site on the phage chromosome at which this recombination occurred was between 110 and 750 base pairs of the left end on the mature phage genome.

Major spontaneous genomic rearrangements in Haemophilus influenzae S2 and HP1c1 bacteriophages

Physical maps constructed by the localization of the cleavage site of several restriction endonucleases have shown that the genomes of the Haemophilus bacteriophages S2 and HP1c1 exist in variant forms which differ in the molecular organization of the genomes. At least three regions of different organization of the bacteriophage chromosomes have been identified. The different types of molecular organization can be detected both in the DNA isolated from the mature phage particles and after integration of the phage DNA into the bacterial chromosome.

A population genetic framework for the study of invasive diseases caused by serotype b strains of Haemophilus influenzae

One hundred seventy-seven isolates of serotype b Haemophilus influenzae recovered largely from children with invasive disease in the United States were characterized by the electrophoretic mobilities of 16 metabolic enzymes, the NaDodSO4/PAGE pattern of outer-membrane proteins (OMP), and biotype. Thirty-two distinctive multilocus genotypes (electrophoretic types, ETs) were distinguished on the basis of allele profiles at the enzyme loci. Twenty-eight OMP types and five biotypes were identified, but only 55 distinctive combinations of ET, OMP type, and biotype were represented. The strong nonrandom associations of characters and the recovery of isolates with identical properties in widely separated geographic regions and over a 40-year period suggest that the population structure of H. influenzae is basically clonal. Examination of nonserotype b isolates indicated that clones of serotype b are a restricted subset of the genotypes in the species as a whole. Currently, most of the invasive H. influenzae disease in the United States is caused by serotype b strains of two related ETs, and, more specifically, much of it is attributable to two subclones marked by OMP type. There is evidence that the frequency of the ET-1/OMP 1H/biotype I subclone has increased dramatically in the United States since the 1939-1954 period. The hypothesis that populations of H. influenzae are subject to marked temporal variation in clonal composition is supported by evidence of major differences in the genetic structure of populations in the United States and the Netherlands.