Two different 16S rRNA genes in a mycobacterial strain.

Sequencing of the gene coding for 16S rRNA (16S rDNA) is a well-established method used to identify bacteria, particularly mycobacteria. Unique sequences allow identification of a particular genus and species. If more than one 16S rDNA is present on one mycobacterial genome, their sequences are assumed to be strictly or almost identical. We have isolated a slowly growing Mycobacterium strain, "X", identified by conventional biochemical tests as Mycobacterium terrae. Identification by amplification and direct sequencing of 16S rDNA yielded ambiguous results in two variable regions, suggesting the presence of different copies of the sequenced gene. Total DNA was digested by restriction enzymes and hybridized after Southern blotting to a probe representing about two-thirds of the 16S rDNA. Two copies of 16S rDNA were identified and cloned. By sequencing, the clones were of two different types, A and B, differing in 18 positions. Oligonucleotides specific to each copy of the 16S rDNA were used to distinguish the positions of the two genes observed in the Southern blot. We conclude that Mycobacterium strain "X" has two different copies of 16S rDNA. Variations in the sequence between two copies of 16S rDNA gene have been described in archaeobacteria, but not in mycobacteria. When placed in a phylogenetic tree together with other slowly growing mycobacteria gene A shows a common root with M. terrae, whereas gene B is placed separately.     

Sequence diversity of Neisseria meningitidis 16S rRNA genes and use of 16S rRNA gene sequencing as a molecular subtyping tool

We investigated the diversity of the primary sequences of 16S rRNA genes among Neisseria meningitidis strains (Men) and evaluated the use of this approach as a molecular subtyping tool. We aligned and compared a 1,417-bp fragment of the 16S rRNA gene from 264 Men strains of serogroups A, B, C, and Y (MenA, MenB, MenC, and MenY, respectively) isolated throughout the world over a 30-year period. Thirty-one positions of difference were found among 49 16S types: differences between types ranged from 1 to 14 positions (0.07 to 0.95%). 16S types and serogroups were highly associated; only 3 out 49 16S types were shared by two or more serogroups. We have identified 16S types that are exclusively associated with strains of certain hypervirulent clones: 16S type 5 with MenA subgroup III, 16S type 4 with the MenB electrophoretic type 5 (ET-5) complex, and 16S types 12 and 13 with MenC of the ET-37 complex. For MenC strains, 16S sequencing provided the highest sensitivity and specificity and the best overall association with the outbreak-related versus sporadic isolates when compared with pulsed-field gel electrophoresis, multilocus enzyme electrophoresis, and multilocus sequence typing. We demonstrated for the first time an unexpected diversity among 16S rRNA genes of Men strains, identified 16S types associated with well-defined hypervirulent clones, and showed the potential of this approach to rapidly identify virulent strains associated with outbreaks and/or an increased incidence of sporadic disease.     

Riemerella anatipestifer extracellular protease S blocks complement activation via the classical and lectin pathways

Riemerella anatipestifer (RA) is the causative agent of infectious serositis in ducklings and other avian species. It is difficult to control the disease due to its 21 serotypes, poor cross-protection, and bacterial resistance to antimicrobial agents. The complement system is an important component of the innate immune system. However, bacterial pathogens exploit several strategies to evade detection by the complement system. Here, we purified and identified a 59-kDa RA extracellular protease S (EcpS) consisting of a gelatinase. In this study, we aimed to determine how EcpS interferes with complement activation and whether it could block complement-dependent neutrophil function. We found that EcpS potently blocked RA phagocytosis and killing by duck neutrophils. Furthermore, EcpS inhibited the opsonization of bacteria by complement 3b. EcpS specifically blocked complement 3b and complement 4b deposition via the classical and lectin pathways, whereas the alternative pathway was not affected. In summary, we show that RA can survive the bactericidal activity of the duck complement system. These results indicate that RA has evolved mechanisms to evade the duck complement system that may increase the efficiency by which this pathogen can gain access and colonize the inner tissues where it may cause severe infections.     

Sequence variation of the 16S to 23S rRNA spacer region in Salmonella enterica

The possibility for identification of Salmonella enterica serotypes by sequence analysis of the 16S to 23S rRNA internal transcribed spacer was investigated by direct sequencing of polymerase chain reaction-amplified DNA from all operons simultaneously in a collection of 25 strains of 18 different serotypes of S. enterica, and by sequencing individual cloned operons from a single strain. It was only possible to determine the first 117 bases upstream from the 23S rRNA gene by direct sequencing because of variation between the rrn operons. Comparison of sequences from this region allowed separation of only 15 out of the 18 serotypes investigated and was not specific even at the subspecies level of S. enterica. To determine the differences between internal transcribed spacers in more detail, the individual rrn operons of strain JEO 197, serotype IV 43:z4,z23:-, were cloned and sequenced. The strain contained four short internal transcribed spacer fragments of 382-384 bases in length, which were 98.4-99.7% similar to each other and three long fragments of 505 bases with 98.0-99.8% similarity. The study demonstrated a higher degree of interbacterial variation than intrabacterial variation between operons for serotypes of S. enterica.     

Differentiation of bacterial 16S rRNA genes and intergenic regions and Mycobacterium tuberculosis katG genes by structure-specific endonuclease cleavage.

We describe here a new approach for analyzing nucleic acid sequences using a structure-specific endonuclease, Cleavase I. We have applied this technique to the detection and localization of mutations associated with isoniazid resistance in Mycobacterium tuberculosis and for differentiating bacterial genera, species and strains. The technique described here is based on the observation that single strands of DNAs can assume defined conformations, which can be detected and cleaved by structure-specific endonucleases such as Cleavase I. The patterns of fragments produced are characteristic of the sequences responsible for the structure, so that each DNA has its own structural fingerprint. Amplicons, containing either a single 5'-fluorescein or 5'-tetramethyl rhodamine label were generated from a 620-bp segment of the katG gene of isoniazid-resistant and -sensitive M. tuberculosis, the 5' 350 bp of the 16S rRNA genes of Escherichia coli O157:H7, Salmonella typhimurium, Salmonella enteritidis, Salmonella arizonae, Shigella sonnei, Shigella dysenteriae, Campylobacter jejuni, staphylococcus, hominis, Staphylococcus warneri, and Staphylococcus aureus and an approximately 550-bp DNA segment comprising the intergenic region between the 16S and 23S rRNA genes of Salmonella typhimurium, Salmonella enteritidis, Salmonella arizonae, Shigella sonnei, and Shigella dysenteriae serotypes 1, 2, and 8. Changes in the structural fingerprints of DNA fragments derived from the katG genes of isoniazid-resistant M. tuberculosis isolates were clearly identified and could be mapped to the site of the actual mutation relative to the labeled end. Bland patterns which clearly differentiated bacteria to the level of genus and, in some cases, species were generated from the 16S genes. Cleavase I analysis of the intergenic regions of Salmonella and Shigella species differentiated genus, species, and serotypes. Structural fingerprinting by digestion with Cleavase I is a rapid, simple, and sensitive method for analyzing nucleic acid sequences and may find wide utility in microbial analysis.     

Genetic identification of cryptic genospecies of Haemophilus causing urogenital and neonatal infections by PCR using specific primers targeting genes coding for 16S rRNA.

Previous genetic analysis of Haemophilus influenzae strains isolated from genital and neonatal infections identified a group of biotype IV that constitutes a cryptic genospecies only distantly related to H. influenzae and H. Haemolyticus. Small-subunit rRNA genes of two representative strains of this genital Haemophilus genospecies (strains 16N and 2406) were sequenced. The analysis indicated that these strains form a monophyletic unit with H. haemolyticus and H. influenzae biogroups Influenzae and Aegyptius and are more closely related to H. haemolyticus than to H. influenzae biogroups Influenzae and Aegyptius. 16S rRNA gene sequences were used to formulate primers for PCR-based identification of cryptic genital Haemophilus organisms. A 242-bp fragment was amplified from strains belonging to the genital Haemophilus genospecies but not from strains of 12 other Haemophilus species, including strains of H. influenzae biotype IV sensu stricto.     

Identification of Aeromonas clinical isolates by restriction fragment length polymorphism of PCR-amplified 16S rRNA genes.

Identification of Aeromonas species, emergent pathogens for humans, has long been controversial due to their phenotypic and genomic heterogeneities. Computer analysis of the published 16S rRNA gene sequences revealed that restriction fragment length polymorphism of the PCR-amplified 16S rRNA gene is a good and rapid way of assessing the identities of all known species of Aeromonas. The method was evaluated with the reference strains of all species (or DNA homology groups) and 76 clinical isolates of diverse origin. Most results from the two approaches were in agreement, but some discrepancies were discerned. Advantages over previous phenotypic and genetic methods are discussed.     

Genotyping of Riemerella anatipestifer by ERIC-PCR and correlation with serotypes

Riemerella anatipestifer (RA) is a widely distributed bacterial pathogen of birds responsible for remarkable losses to poultry production, especially among waterfowl. We characterized the genomic diversity of 166 field isolates of RA, collected from geese and ducks, using enterobacterial repetitive intergenic consensus (ERIC)-polymerase chain reaction (PCR). The field strains and five reference strains showed 17 distinct patterns consisting of five to 12 bands ranging from approximately 150–1800bp. The majority of the strains belonged to two closely related ERIC-PCR types (A and B), while the other types contained only a few isolates each. There was no association between ERIC-PCR type and host species, place, or year of isolation; however the ERIC-PCR pattern was correlated with serotype for most isolates. The majority of serotype 1 strains (101/107) belonged to ERIC-PCR type A while the remaining six strains represented five different ERIC-PCR types (D, G, L, M, and O). Serotypes 1,7 and 7 corresponded to ERIC-PCR types B and C, respectively. Serotypes 2, 4, and 10 could be subdivided by ERIC-PCR revealing two to four patterns within each serotype. These results indicate that ERIC-PCR may be a suitable technique for the molecular identification of RA serotypes, and the detection of subtypes within certain serotypes may aid further epidemiological investigations.

RESEARCH HIGHLIGHTS

• ERIC-PCR analysis of field R. anatipestifer strains revealed 17 distinct patterns

• Most strains belonged to two closely related ERIC-PCR types

• Serotype 1 was the most prevalent serotype representing 64.5% of the strains

• ERIC-PCR may be suitable for molecular identification of R. anatipestifer serotypes

     

Molecular characterization of a plasmid isolated from Riemerella anatipestifer

Sixty strains of Riemerella anatipestifer were isolated from ducks and geese with infectious serositis in Taiwan. Sixty per cent of the isolates (36/60) contained a 3.9 b plasmid, 12% (7/60) contained 6.5 b and 16 b plasmids, 5% (3/60) contained 2.9, 16 and 18 b plasmids and 13% contained no plasmid (14/60). The 3.9 b plasmid (designated as pCFC1) was completely sequenced to determine if it encoded virulence factors. pCFC1 was 27% G-C and had four large open reading frames (ORF). Two of the ORFs (designated as VapD1 and VapD2) encoded proteins that shared 80, 83, 69 and 67 (VapD1) and 50, 48, 21 and 20% (VapD2) identity with virulence-associated proteins of Actinobacillus Actinomycetemcomitans, Dichelobcater nodosus, Haemophilus influenzae and Neisseria gonorrheae, respectively. pCFC1 also had an ORF (designated as RepAl) that encoded a protein with approximately 30% identity to the RepA proteins of Neisseria gonorrhoeae, Campylobactor hyointestinalis and Pseudomonas aeroginosa. The region upstream of the RepA ORF had an A-T-rich region that was followed by four 21 bp perfect and one 20 bp imperfect direct repeat. The fourth ORF (designated as RepA2) encoded a protein with a region that was 44% homologous to the Helicobactor pylori replication protein.     

Identification of ribosomal RNA methyltransferase gene ermF in Riemerella anatipestifer

Riemerella anatipestifer is a major bacterial pathogen of waterfowl, globally responsible for avian septicaemic disease. As chemotherapy is the predominant method for the prevention and treatment of R. anatipestifer infection in poultry, the widespread use of antibiotics has favoured the emergence of antibiotic-resistant strains. However, little is known about R. anatipestifer susceptibility to macrolide antibiotics and its resistance mechanism. We report for the first time the identification of a macrolide resistance mechanism in R. anatipestifer that is mediated by the ribosomal RNA methyltransferase ermF. We identified the presence of the ermF gene in 64/206 (31%) R. anatipestifer isolates from different regions in China. An ermF deletion strain was constructed to investigate the function of the ermF gene on the resistance to high levels of macrolides. The ermF mutant strain showed significantly decreased resistance to macrolide and lincosamide, exhibiting 1024-, 1024-, 4- and >2048-fold reduction in the minimum inhibitory concentrations for erythromycin, azithromycin, tylosin and lincomycin, respectively. Furthermore, functional analysis of ermF expression in E. coli XL1-blue showed that the R. anatipestifer ermF gene was functional in E. coli XL1-blue and conferred resistance to high levels of erythromycin (100 µg/ml), supporting the hypothesis that the ermF gene is associated with high-level macrolide resistance. Our work suggests that ribosomal RNA modification mediated by the ermF methyltransferase is the predominant mechanism of resistance to erythromycin in R. anatipestifer isolates.     

Evaluation of intraspecies genetic variation within the 16S rRNA gene of Mycoplasma hominis and detection by polymerase chain reaction.

Mycoplasma hominis is a heterogeneous species with DNA-DNA hybridization values ranging from 51 to 100%. We report here the sequencing of the 16S rRNA gene of a strain (183) that greatly differs from the type strain (PG21) of this species. Comparison of 16S rDNA sequences from these two strains showed limited differences, indicating that the two strains belong to the same rRNA species complex. Using these nucleotide sequence data, we established a rapid method for the detection of M. hominis by using polymerase chain reaction. This method was shown to be sensitive and specific when tested with reference strains and clinical isolates.     

Evaluation of different diagnostic tools for the detection and identification of Riemerella anatipestifer

Riemerella anatipestifer (RA) is an important avian pathogen with considerable impact on poultry production worldwide. However, the diagnosis of RA infections may be difficult, mainly due to problems with unequivocal differentiation of RA from other Flavobacteriaceae and a lack of standardized methods and reagents. The aim of the present study was therefore to complement the routine diagnostic strategies for RA by design and evaluation of alternative diagnostic tools. We designed and validated a new RA-specific polymerase chain reaction assay, which proved to be a valuable tool for the identification of RA isolates as well as for rapid and sensitive RA detection directly from diagnostic samples. Matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry fingerprinting of whole bacterial cells was also demonstrated to identify RA isolates efficiently. Furthermore, this method may also provide opportunities for RA subtyping. In our study, a stable subcluster was formed by the mass spectroscopy profiles of a group of RA isolates originating from turkey flocks in northern Germany, suggesting an epidemiological relationship of these isolates. Serotyping is a further important measure to characterize RA isolates. We tested a set of commercially available anti-RA sera with RA serotype reference strains and field isolates to allow comparison between these sera and reference sera. In summary, this report contributes to the improvement of present microbiological and molecular strategies for the diagnosis of RA infections by providing new tools as well as enhanced knowledge on existing methods.     

Electron microscopical localisation of the 23S and 16S rRNA genes within an inverted repeat for two chromoplast DNAs

Summary Circular plastid DNA molecules, isolated from flower chromoplasts of the daffodil (a monocotyledon), and the nasturtium (a dicotyledon), have been shown by electron microscopy to contain inverted repeat sequences of 28.5 ± 0.7 kbp and 27.1 ± 1.0 kbp, respectively. The regions separating the repeats have lengths of 16.6 ± 0.8 kb for the shorter region, and 87.8 ± 4.8 kb for the longer in the daffodil, and 18.5 ± 0.5 kb and 82.3 ± 3.1 kb for the corresponding regions in the nasturtium. Further, in both cases, the 23S and 16S ribosomal RNA genes have been located by hybridisation (R-Loop technique) within this inverted repeat. Although the distance between the 16S and 23S genes is comparable, the position of the rRNA gene blocks within the repeats is different in these two chromoplast DNAs, with a shift of 1,500 bp.     

New serotypes of Riemerella anatipestifer isolated from ducks in Thailand

Thirty-two Riemerella anatipestifer isolates from ducks were serotyped by agar gel precepitin test using chicken antisera against serotypes 1 to 19 R. anatipestifer reference strains. The heat stable saline extracts from 29 field isolates reacted with the antisera of serotypes 1, 6, 7, 10, 11, 14, or 19. The isolates belonging to serotype 1 were the most prevalent (56.3%). Antigens from the remaining three isolates did not react with any of the available antisera. Additional investigations showed that they represent two new serotypes, serotypes 20 and 21.     

Touchdown enzyme time release-PCR for detection and identification of Chlamydia trachomatis, C. pneumoniae, and C. psittaci using the 16S and 16S-23S spacer rRNA genes

Three touchdown enzyme time release (TETR)-PCR assays were used to amplify different DNA sequences in the variable regions of the 16S and 16S-23S spacer rRNA genes specific for Chlamydia trachomatis, Chlamydia pneumoniae, and Chlamydia psittaci as improved tests for sensitive diagnosis and rapid species differentiation. The TETR-PCR protocol used 60 cycles of amplification, which provided improved analytical sensitivity (0.004 to 0.063 inclusion-forming unit of Chlamydia species per PCR). The sensitivity of TETR-PCR with primer set CTR 70-CTR 71 was 96.7%, and the specificity was 99.6%, compared to those of the AMPLICOR PCR for the detection of C. trachomatis in vaginal swab samples. TETR-PCR for C. pneumoniae with primer set CPN 90-CPN 91 was 90% sensitive and 93.3% specific compared with a nested PCR with primer set CP1/2-CPC/D for clinical respiratory samples. TETR-PCR for C. psittaci with primer set CPS 100-CPS 101 showed substantial agreement with cell culturing (kappa, 0.78) for animal tissue samples. Primer sets were then combined into a single multiplex TETR-PCR test. The respective 315-, 195-, and 111-bp DNA target products were precisely amplified when DNA from each of the respective Chlamydia species or combinations of them was used. Multiplex chlamydia TETR-PCR correctly identified one strain of each of the 15 serovars of C. trachomatis, 22 isolates of C. pneumoniae, and 20 isolates of C. psittaci. The primer sets were specific for each species. No target products were amplified when DNA from C. pecorum or a variety of other microorganisms was tested for specificity. TETR-PCR with primers selected for specific sequences in the 16S and 16S-23S spacer rRNA genes is a valuable test that could be used either with individual primers or in a multiplex assay for the identification and differentiation of Chlamydia species from culture isolates or for the detection of chlamydiae in clinical samples.     

Prevalence of 16S rRNA methylase genes in Enterobacteriaceae isolates from a Greek University Hospital

16S ribosomal RNA methylase-mediated high-level resistance to 4-,6-aminoglycosides has been reported in clinical isolates of gram-negative bacilli from several countries. Three of 1534 (0.2%) isolates of Klebsiella pneumoniae and three of 734 (0.4%) Proteus mirabilis isolates from a university hospital in Athens, Greece, were positive for rmtB and highly resistant to all aminoglycosides tested (MICs ≥256 mg/L). Two of the K. pneumoniae rmtB-bearing isolates, were KPC-2 and OXA-10 producers and the third was a DHA-1 producer. One of the P. mirabilis isolates was a VIM-1 and OXA-10 producer and one was an OXA-10 producer. All rmtB-harbouring isolates were clonally unrelated. None of the E. coli (n = 1398) and Enterobacter spp. (n = 414) isolates were positive for armA, rmtA, rmtB, rmtC or rmtD.     

Characterization of a predominant immunogenic outer membrane protein of Riemerella anatipestifer

The ompA gene, encoding the 42-kDa major antigenic outer membrane protein OmpA of Riemerella anatipestifer, the etiololgical agent of septicemia anserum exsudativa, was cloned and expressed in Escherichia coli. Recombinant OmpA displayed a molecular mass similar to that predicted from the nucleotide sequence of the ompA gene but lower than that observed in total cell lysates of R. anatipestifer. The ompA gene showed a conserved C-terminal region comprising the OmpA-like domain and a variable N-terminal region. This structure is similar to those of the analogous outer membrane proteins of several gram-negative bacteria. However, OmpA of R. anatipestifer contains six EF-hand calcium-binding domains and two PEST regions, which distinguish it from other outer membrane proteins. The occurrence of these motifs in OmpA suggests a possible role in virulence for this protein. The ompA gene is present in the R. anatipestifer type strain and in all serotype reference strains. However, it exhibits some minor genetic heterogeneity among different serotypes, which seems not to affect the strong antigenic characteristics of the protein. OmpA is a conserved and strong antigenic determinant of R. anatipestifer and hence is suggested to be a valuable protein for the serodetection of R. anatipestifer infections, independent of their serotype.     

Amplification of 16S rRNA sequences to detect Mycobacterium paratuberculosis.

A probe based on 16S ribosomal RNA (rRNA) sequences was developed to detect Mycobacterium paratuberculosis, the causative agent of Johne's disease in cattle. Three universal primers were used to sequence the amplified fragments of the 16S rRNA gene of various species of mycobacteria. When the nucleotide sequences were analysed, a deletion was detected in the sequence of the fast-growing species. An oligonucleotide probe (P) directed to this region was synthesised and hybridised directly with total RNA of various mycobacterial strains in a dot-spot assay. The probe detected M. paratuberculosis, some other slow-growing mycobacteria of the M. avium-intracellulare (MAI) complex, and one atypical strain, M. gordonae. To increase the sensitivity of the probe, a 413-bp fragment of the 16S rRNA gene of M. paratuberculosis between P and a second oligonucleotide primer was amplified and hybridised with a M. paratuberculosis/M. avium-specific probe. When faecal samples of cattle were tested, all culture-positive samples were positive in the PCR assay.     

Aspergillus nidulans 5S rRNA genes and pseudogenes

Summary The sequence of four Aspergillus nidulans 5S rRNA genes and of two pseudogenes has been determined. A conserved sequence about 100 by upstream of the 5S rRNA coding sequences has been found in three genes and one pseudogene. The two pseudogenes correspond to the 5 half of the 5S rRNA coding sequence and their 3 flanking sequences which are not homologous to 5S rRNA are strongly conserved.