Broad range DNA probes for detecting and amplifying eubacterial nucleic acids

Biofilm-Forming Bacteria Implicated in Complex Otitis Media in Children in the Post-Heptavalent Pneumococcal Conjugate Vaccine (PCV7) Era

Background: Chronic media with effusion (COME) and recurrent acute otitis media (RAOM) are closely related clinical entities that affect childhood. The aims of the study were to investigate the microbiological profile of otitis-prone children in the post-PCV7 era and, to examine the biofilm-forming ability in association with clinical history and outcome during a two-year post-operative follow-up. Methods: In this prospective study, pathogens from patients with COME and RAOM were isolated and studied in vitro for their biofilm-forming ability. The minimum inhibitory concentrations (MIC) of both the planktonic and the sessile forms were compared. The outcome of the therapeutic method used in each case and patient history were correlated with the pathogens and their ability to form biofilms. Results: Haemophilus influenzae was the leading pathogen (35% in COME and 40% in RAOM), and Streptococcus pneumoniae ranked second (12% in COME and 24% in RAOM). Polymicrobial infections were identified in 5% of COME and 19% of RAOM cases. Of the isolated otopathogens, 94% were positive for biofilm formation. Conclusions: This is the first Greek research studying biofilm formation in complex otitis media-prone children population in the post-PCV7 era. High rates of polymicrobial infections, along with treatment failure in biofilms, may explain the lack of antimicrobial efficacy in otitis-prone children.

Coping with low pH: molecular strategies in neutralophilic bacteria

As part of their life cycle, neutralophilic bacteria are often exposed to varying environmental stresses, among which fluctuations in pH are the most frequent. In particular, acid environments can be encountered in many situations from fermented food to the gastric compartment of the animal host. Herein, we review the current knowledge of the molecular mechanisms adopted by a range of Gram-positive and Gram-negative bacteria, mostly those affecting human health, for coping with acid stress. Because organic and inorganic acids have deleterious effects on the activity of the biological macromolecules to the point of significantly reducing growth and even threatening their viability, it is not unexpected that neutralophilic bacteria have evolved a number of different protective mechanisms, which provide them with an advantage in otherwise life-threatening conditions. The overall logic of these is to protect the cell from the deleterious effects of a harmful level of protons. Among the most favoured mechanisms are the pumping out of protons, production of ammonia and proton-consuming decarboxylation reactions, as well as modifications of the lipid content in the membrane. Several examples are provided to describe mechanisms adopted to sense the external acidic pH. Particular attention is paid to Escherichia coli extreme acid resistance mechanisms, the activity of which ensure survival and may be directly linked to virulence.

Evaluation of anthropogenic effects on water quality and bacterial diversity in Rawal Lake, Islamabad

Water quality and bacterial diversity in the surface water of Rawal Lake was investigated for a period of 8 months to evaluate the pollution load from anthropogenic effects of surrounding areas. Rawal Lake in Islamabad, Pakistan is an artificial reservoir that provides the water needs for the residents of Rawalpindi and Islamabad. Grabbed water samples were collected according to standard protocols from ten different locations of the lake and tributaries keeping in view the recharge points from adjacent areas. Temperature, pH, electrical conductivity, dissolved oxygen, total dissolved solids, hardness, alkalinity, and turbidity of water samples were determined to study the water quality characteristics. The physicochemical parameters showed higher values at the tributaries as compared to the sampling locations within the lake such as values of hardness and alkalinity were 298 and 244 mg/L, respectively, at the tributary of the Nurpur stream. Bacterial strains were isolated by streaking on differential and selective growth media by observing colony morphology and other biochemical tests such as Gram reaction, oxidase, and catalase test. Template DNA was prepared from pure cultivated bacteria and 16S rRNA gene analysis was performed using universal primers for bacteria. Sequencing was performed by using BigDye terminator cycle sequencing kit. Sequences of nearest relative microbial species were identified by using basic local alignment search tool and used as reference sequences for phylogenetic analysis. Phylogenetic trees were inferred using the neighbor-joining method. Sequencing and phylogenetic characterization of microbes showed various phylotypes, of which Firmicutes, Teobacteria, and Proteobacteria were predominant.

A novel molecular microbiologic technique for the rapid diagnosis of microbial invasion of the amniotic cavity and intra-amniotic infection in preterm labor with intact membranes

PROBLEM

The diagnosis of microbial invasion of the amniotic cavity (MIAC) has been traditionally performed using traditional cultivation techniques, which require growth of microorganisms in the laboratory. Shortcomings of culture methods include the time required (days) for identification of microorganisms, and that many microbes involved in the genesis of human diseases are difficult to culture. A novel technique combines broad-range real-time polymerase chain reaction with electrospray ionization time-of-flight mass spectrometry (PCR/ESI-MS) to identify and quantify genomic material from bacteria and viruses.

METHOD OF STUDY

AF samples obtained by transabdominal amniocentesis from 142 women with preterm labor and intact membranes (PTL) were analyzed using cultivation techniques (aerobic, anaerobic, and genital mycoplasmas) as well as PCR/ESI-MS. The prevalence and relative magnitude of intra-amniotic inflammation [AF interleukin 6 (IL-6) concentration ≥ 2.6 ng/mL], acute histologic chorioamnionitis, spontaneous preterm delivery, and perinatal mortality were examined.

RESULTS

(i) The prevalence of MIAC in patients with PTL was 7% using standard cultivation techniques and 12% using PCR/ESI-MS; (ii) seven of ten patients with positive AF culture also had positive PCR/ESI-MS [≥17 genome equivalents per PCR reaction well (GE/well)]; (iii) patients with positive PCR/ESI-MS (≥17 GE/well) and negative AF cultures had significantly higher rates of intra-amniotic inflammation and acute histologic chorioamnionitis, a shorter interval to delivery [median (interquartile range-IQR)], and offspring at higher risk of perinatal mortality, than women with both tests negative [90% (9/10) versus 32% (39/122) OR: 5.6; 95% CI: 1.4-22; (P < 0.001); 70% (7/10) versus 35% (39/112); (P = 0.04); 1 (IQR: <1-2) days versus 25 (IQR: 5-51) days; (P = 0.002), respectively]; (iv) there were no significant differences in these outcomes between patients with positive PCR/ESI-MS (≥17 GE/well) who had negative AF cultures and those with positive AF cultures; and (v) PCR/ESI-MS detected genomic material from viruses in two patients (1.4%).

CONCLUSION

(i) Rapid diagnosis of intra-amniotic infection is possible using PCR/ESI-MS; (ii) the combined use of biomarkers of inflammation and PCR/ESI-MS allows for the identification of specific bacteria and viruses in women with preterm labor and intra-amniotic infection; and (iii) this approach may allow for administration of timely and specific interventions to reduce morbidity attributed to infection-induced preterm birth.

Enhanced toxicity of Bacillus thuringiensis subspecies kurstaki and aizawai to black cutworm larvae (Lepidoptera: Noctuidae) with Bacillus sp. NFD2 and Pseudomonas sp. FNFD1

Bacillus thuringiensis subspecies kurstaki and aizawai are important control agents for lepidopteran pests. Bioassays were designed to test B. t. kurstaki and aizawai against second- and-fourth instar black cutworm larvae with and without Bacillus sp. NFD2 and Pseudomonas sp. FNFD1 bacteria. B. thuringiensis subsp. aizawai (XenTari) was more toxic to both second- and fourth-instar black cutworm, Agrotis ipsilon (Hufnagel) (Lepidoptera: Noctuidae), larvae than B. t. kurstaki (DiPel) at 7 d after treatment (DAT). When DiPel was combined with NFD2 or FNFD1 versus second instars, the LC50s were 5.0X and 4.7X lower, respectively, than with DiPel alone. DiPel combined with both NFD2 and FNFD1 versus second instars resulted in an LC50 value 7.7X lower than with DiPel alone. When XenTari was combined with NFD2 or FNFD1 versus second instars, the LC50s were 5.2X and 3.8X lower, respectively, than with XenTari alone. XenTari combined with both NFD2 and FNFD1 versus second instars resulted in an LC50 9.7X lower than with XenTari alone. When DiPel was combined with NFD2 or FNFD1 versus fourth instars, the LC50s were 4.4X and 3.4X lower, respectively, than with DiPel alone. DiPel combined with both NFD2 and FNFD1 versus fourth instars resulted in an LC50 5.0X lower than with DiPel alone. When XenTari was combined with NFD2 or FNFD1 versus fourth instars, the LC50s were 5.7X and 3.3X lower, respectively, than with XenTari alone. XenTari combined with both NFD2 and FNFD1 versus fourth instars resulted in an LC50 6.7X lower than with XenTari alone.

Enhanced toxicity of Bacillus thuringiensis japonensis strain Buibui toxin to oriental beetle and northern masked chafer (Coleoptera: Scarabaeidae) larvae with Bacillus sp. NFD2

Bacillus thuringiensisjaponensis strain Buibui (Btj) has the potential to be an important control agent for pest scarabs. Bioassays using autoclaved and nonautoclaved soil showed there were always lower LC, values associated with nonautoclaved soil. We identified five other bacteria found in the hemolymph of insects killed by Btj and used them in bioassays to see whether we could enhance the control achieved with Btj alone. One bacterium, designated NFD2 and later identified as a Bacillus sp., showed the greatest enhancement of Btj in preliminary experiments and was used in bioassays with Btj versus oriental beetle, Anomala orientalis (Waterhouse), and northern masked chafer, Cyclocephala borealis Arrow (Coleoptera: Scarabaeidae), larvae. This bacterium alone was nontoxic to grubs in bioassays. A combination of this bacterium with Btj in nonautoclaved soil resulted in a significantly lower LC50 value (0.23 microg toxin per g soil) from all other treatments for A. orientalis with one exception; the LC50 where NFD2 was added back into autoclaved soil (0.29 microg toxin per g soil). A combination of this bacterium with Btj in nonautoclaved soil resulted in a significantly lower LC50 value (48.29 microg toxin per g soil) from all other treatments for C. borealis with the exception of the treatment where Bacillus sp. NFD2 was added back to autoclaved soil (96.87 microg toxin per g soil) with Btj. This research shows that other soil bacteria can be used to enhance the toxicity of Btj and possibly other Bts.

New methods for selective isolation of bacterial DNA from human clinical specimens

Separation of bacterial DNA from human DNA in clinical samples may have an important impact on downstream applications, involving microbial diagnostic systems. We evaluated two commercially available reagents (MolYsis), Molzym GmbH & Co. KG, Bremen and Pureprove, SIRS-Lab GmbH, Jena, both Germany) for their potential to isolate and purify bacterial DNA from human DNA. We chose oral samples, which usually contain very high amounts of both human and bacterial cells. Three different DNA preparations each were made from eight caries and eight periodontal specimens using the two reagents above and a conventional DNA extraction strategy as reference. Based on target-specific real-time-quantitative PCR assays we compared the reduction of human DNA versus loss of bacterial DNA. Human DNA was monitored by targeting the beta-2-microglobulin gene, while bacteria were monitored by targeting 16S rDNA (total bacteria and Porphyromonas gingivalis) or the glycosyltransferase gene (Streptococcus mutans). We found that in most cases at least 90% of human DNA could successfully be removed, with complete removal in eight of 16 cases using MolYsis, and two (of 16) cases using Pureprove. Conversely, detection of bacterial DNA was possible in all cases with a recovery rate generally ranging from 35% to 50%. In conclusion, both strategies have the potential to reduce background interference from the host DNA which may be of remarkable value for nucleic-acid based microbial diagnostic systems.

Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases

The traditional identification of bacteria on the basis of phenotypic characteristics is generally not as accurate as identification based on genotypic methods. Comparison of the bacterial 16S rRNA gene sequence has emerged as a preferred genetic technique. 16S rRNA gene sequence analysis can better identify poorly described, rarely isolated, or phenotypically aberrant strains, can be routinely used for identification of mycobacteria, and can lead to the recognition of novel pathogens and noncultured bacteria. Problems remain in that the sequences in some databases are not accurate, there is no consensus quantitative definition of genus or species based on 16S rRNA gene sequence data, the proliferation of species names based on minimal genetic and phenotypic differences raises communication difficulties, and microheterogeneity in 16S rRNA gene sequence within a species is common. Despite its accuracy, 16S rRNA gene sequence analysis lacks widespread use beyond the large and reference laboratories because of technical and cost considerations. Thus, a future challenge is to translate information from 16S rRNA gene sequencing into convenient biochemical testing schemes, making the accuracy of the genotypic identification available to the smaller and routine clinical microbiology laboratories.

PCR-based diagnostics for infectious diseases: uses, limitations, and future applications in acute-care settings

Molecular diagnostics are revolutionising the clinical practice of infectious disease. Their effects will be significant in acute-care settings where timely and accurate diagnostic tools are critical for patient treatment decisions and outcomes. PCR is the most well-developed molecular technique up to now, and has a wide range of already fulfilled, and potential, clinical applications, including specific or broad-spectrum pathogen detection, evaluation of emerging novel infections, surveillance, early detection of biothreat agents, and antimicrobial resistance profiling. PCR-based methods may also be cost effective relative to traditional testing procedures. Further advancement of technology is needed to improve automation, optimise detection sensitivity and specificity, and expand the capacity to detect multiple targets simultaneously (multiplexing). This review provides an up-to-date look at the general principles, diagnostic value, and limitations of the most current PCR-based platforms as they evolve from bench to bedside.

Molecular methods for diagnosis of infective endocarditis

The culture of viable microorganisms from the blood or from cardiac tissue is currently the most important test for diagnosis of IE. This is followed by phenotypic identification methods used for taxonomic positioning of isolates. However, in those cases where the invading microorganism is difficult or impossible to culture (including instances of prior antimicrobial treatment), molecular methods provide the best means for detection. Molecular identification methods, either nucleic acid target or signal amplification alone or in combination with sequence analysis can offer a more specific and in some cases a more rapid alternative to the phenotypic methods. We propose revised Duke criteria of IE, including positive identification of an organism by molecular biology methods.

The putative haemobartonella that influences Plasmodium falciparum parasitaemia in squirrel monkeys is a haemotrophic mycoplasma

Splenectomised squirrel monkeys (Saimiri sciureus) are increasingly being used as an experimental host for human malaria studies, notably for the assessment of candidate vaccines against Plasmodium falciparum blood-stage infection. Recently, S. sciureus monkeys in our primate-breeding colony were reported to be asymptomatic carriers of a putative Haemobartonella species. Patent haemobartonella infection is frequently activated following splenectomy, and may interfere with studies on the course of P. falciparum parasitaemia in these animals. Here, we show by 16S rRNA gene sequence analysis that this wall-less bacterium is not a rickettsia but, instead, is a haemotrophic mycoplasma. Haemotrophic mycoplasmas are a newly identified group of mycoplasmas that parasitise the surfaces of erythrocytes of a wide variety of vertebrate hosts.

High-density microarray of small-subunit ribosomal DNA probes

Ribosomal DNA sequence analysis, originally conceived as a way to provide a universal phylogeny for life forms, has proven useful in many areas of biological research. Some of the most promising applications of this approach are presently limited by the rate at which sequences can be analyzed. As a step toward overcoming this limitation, we have investigated the use of photolithography chip technology to perform sequence analyses on amplified small-subunit rRNA genes. The GeneChip (Affymetrix Corporation) contained 31,179 20-mer oligonucleotides that were complementary to a subalignment of sequences in the Ribosomal Database Project (RDP) (B. L. Maidak et al., Nucleic Acids Res. 29:173-174, 2001). The chip and standard Affymetrix software were able to correctly match small-subunit ribosomal DNA amplicons with the corresponding sequences in the RDP database for 15 of 17 bacterial species grown in pure culture. When bacteria collected from an air sample were tested, the method compared favorably with cloning and sequencing amplicons in determining the presence of phylogenetic groups. However, the method could not resolve the individual sequences comprising a complex mixed sample. Given these results and the potential for future enhancement of this technology, it may become widely useful.

Endocarditis caused by culture-negative organisms visible by Brown and Brenn staining: utility of PCR and DNA sequencing for diagnosis

Two cases of culture-negative endocarditis with cocci seen in valve vegetations are presented. The organisms were identified by molecular analysis using broad-range PCR primers complementary to the 16S rRNA gene, sequencing, and database search using BLAST software. The results and utility of this method are discussed.

Identification of bacteria using two degenerate 16S rDNA sequencing primers

Two degenerate 16S rDNA primers have been designed for broad-range identification of eubacteria by PCR and automated sequencing. Using a simple method, the primers have proven useful in identification of proteobacteria (Campylobacter, Enterobacter, Escherichia, Helicobacter, Klebsiella), gram-positive bacteria (Mycobacterium, Staphylococcus, Streptococcus) and spirochetes (Borrelia) derived from clinical samples. In several cases, the samples could be identified at the species level.

Comparison of phenotypic and genotypic techniques for identification of unusual aerobic pathogenic gram-negative bacilli

Rapid and accurate identification of bacterial pathogens is a fundamental goal of clinical microbiology, but one that is difficult or impossible for many slow-growing and fastidious organisms. We used identification systems based on cellular fatty acid profiles (Sherlock; MIDI, Inc., Newark, Del.), carbon source utilization (Microlog; Biolog, Inc., Hayward, Calif.), and 16S rRNA gene sequence (MicroSeq; Perkin-Elmer Applied Biosystems Division, Foster City, Calif.) to evaluate 72 unusual aerobic gram-negative bacilli isolated from clinical specimens at the Mayo Clinic. Compared to lengthy conventional methods, Sherlock, Microlog, and MicroSeq were able to identify 56 of 72 (77.8%), 63 of 72 (87.5%), and 70 of 72 (97.2%) isolates to the genus level (P = 0.002) and 44 to 65 (67.7%), 55 of 65 (84.6%), and 58 of 65 (89.2%) isolates to the species level (P = 0.005), respectively. Four Acinetobacter and three Bordetella isolates which could not be identified to the species level by conventional methods were identified by MicroSeq. In comparison to the full 16S rDNA sequences, the first 527 bp provided identical genus information for all 72 isolates and identical species information for 67 (93.1%) isolates. These data show that MicroSeq provides rapid, unambiguous identification of clinical bacterial isolates. The improved turnaround time provided by genotypic identification systems may translate into improved clinical outcomes.

Non-random fragmentation of ribosomal RNA in Helicobacter pylori during conversion to the coccoid form

The integrity of DNA and ribosomal RNAs in exponentially growing (bacillary) and ageing stationary phase (coccoid) cultures of Helicobacter pylori type strain CCUG 17874 was investigated. Extensive non-random fragmentation of rRNAs was observed during the conversion to the coccoid form. Beside a small proportion of full-length 16S and 23S rRNA that was always present, the majority of both 16S and 23S rRNA molecules showed distinct highly specific fragmentation patterns. The 16S rRNA fragmentation was characterised in detail by means of Northern blot and primer extension analysis. One cleavage site was located within the highly conserved U5 region (position about 920). The results could not be attributed to the presence of intervening sequences in the 16S and 23S rRNA genes.

Division of the genus Enterococcus into species groups using PCR-based molecular typing methods

Broad-range 16S rDNA PCR (BR-PCR) applied to DNA from 32 clinical enterococcal isolates and 12 other enterococci from a clinical reference collection followed by species-specific hybridization analysis identified 25 strains of Enterococcus faecalis and 19 Enterococcus species. Randomly amplified polymorphic DNA (RAPD) analysis using UPGMA clustering on the same material revealed four different clusters at a similarity level of 49%. Based on partial 16S rDNA sequence analysis of variable regions V4 and V9, it was possible to divide the 19 type strains specifying the genus Enterococcus into 12 different 16S rDNA species groups. The type strain distribution then served as a template for the analysis of the other 44 strains which were assigned to four different species groups (a-d) based on their 16S rDNA motifs. There was good agreement with the RAPD clusters. Species group a was an individual species line containing 25 strains that were identified as E. faecalis. Group b also represented an individual species line of 12 strains identified as E. faecium. The remaining seven strains that formed species groups c and d could not be fully identified to species by this analysis. It was concluded that BR-PCR of 16S rDNA followed by partial sequence analysis of the PCR products is a reliable technique for the identification and classification of enterococci. Further division of unresolved species groups should be achievable if regions other than V4 and V9 of 16S rDNA are also analysed.

Detection of eubacteria in interstitial cystitis by 16S rDNA amplification

OBJECTIVE

To determine what role non-culturable microorganisms play in the etiology of interstitial cystitis (IC).

MATERIALS AND METHODS

Thirty patients fulfilling NIH criteria for the diagnosis of interstitial cystitis and sixteen control patients with culture negative urine gave written informed consent and underwent bladder biopsy. Polymerase chain reaction (PCR) using two sets of universal primers for bacterial 16S rDNA was performed on urine from the cystoscope and on a cold cup bladder biopsy specimen. Of the PCR positive bladder biopsies, three patients with interstitial cystitis and three controls were randomly selected and cloned. Ten clones from each were sequenced and putative taxonomic assignments made.

RESULTS

12/26 (46%) IC and 5/12 (42%) control urine specimens and 16/30 (53%) and 9/15 (60%) bladder biopsies were PCR positive, respectively. The bacterial populations in the two patient groups tested appeared to be different based upon analysis of the 16S rRNA sequences.

CONCLUSIONS

Both IC and control patients had non-culturable bacteria in their bladders. A random sampling of the two populations revealed that the bacterial populations are different, suggesting a possible link between one or more bacterial species and IC.

The cell wall-less rickettsia Eperythrozoon wenyonii is a Mycoplasma

The 16S rRNA gene of Eperythrozoon (Haemobartonella) wenyonii, a wall-less hemotrophic prokaryote currently classified as a rickettsia, was sequenced to determine the relationship of this organism to other wall-less prokaryotes. Comparison to the GenBank data base showed that this hemotrophic organism is a Mycoplasma (family Mollicutes). Phylogenetic analysis of 16S rRNA genes indicated that this and other recently sequenced 16S rRNA genes of hemotrophic bacteria form a new, separate branch which shares a node in common with the pneumoniae group of mycoplasmas. This result will require that Eperythrozoon wenyonii be reclassified as a Mycoplasma. A main point of this study is that this and related hemotrophic bacteria represent an entirely new group of pathogens among the mycoplasmas.

Strategy for the detection of Helicobacter species by amplification of 16S rRNA genes and identification of H. felis in a human gastric biopsy

The aim of the present work was to develop polymerase chain reactions (PCRs) based on the conserved nucleotide sequence of the 16S rRNA gene for detection of bacteria of the Helicobacter genus in human antral biopsy samples. The assay for Helicobacter spp was developed by amplifying a 399-bp 16S rRNA gene sequence specific to the genus Helicobacter. The identity of the amplicon was confirmed by hybridization with an internal probe and by restriction by endonuclease VspI showing two expected fragments of 295 and 104 base pairs. A total of 65 dyspeptic patients from France and New Caledonia were screened for Helicobacter spp infection through the use of the following diagnostic assays on biopsy specimens collected through endoscopy: direct detection of bacteria in histological sections by Giemsa and Warthin Starry staining, urease test and bacterial isolation, PCR for Helicobacter pylori ureC/glmM gene, and PCR targeted to 16S rRNA genes. The 16S rRNA gene PCR assay was able to detect down to 680 bacterial cells, as assessed by agarose gel electrophoresis, and down to 4 bacterial cells by hybridization of amplicon with the internal probe. The 16S rRNA PCR test was 100% specific and sensitive; results obtained with this test were in agreement with the visualization of bacteria by histology. Urease test and culture were 86.4% and 22.7% sensitive, and 96.5 and 100% specific, respectively. The H. pylori ureC/glmM gene-based PCR was 100% specific and only 95.4% sensitive, since one biopsy from a Melanesian patient contained a Helicobacter strain other than H. pylori. For this Melanesian patient, a branch-specific PCR targeting the epsilon branch of Proteobacteria was used to amplify a 967-bp amplicon. This amplicon was sequenced and matched with the H. felis sequence. This was confirmed using an H. felis-specific urease PCR test.

Detection of bacteria in equine synovial fluid by use of the polymerase chain reaction

Equine synovial fluid aliquots were inoculated with Salmonella enteritidis, Escherichia coli, Actinobacillus equuli, Staphylococcus aureus, and Streptococcus zooepidemicus to obtain approximate concentrations of 1000, 100, 10, and 1 colony forming U/mL. Synovial fluid aliquots were also inoculated with an unquantitated inoculum of Bacteroides fragilis and Clostridium perfringens. Inoculated synovial fluid was incubated in trypticase-soy broth or Columbia broth for approximately 12 hours. Then aliquots were removed for DNA extraction and polymerase chain reaction (PCR) analysis for detection of a 531 base-pair segment of bacterial DNA corresponding to a region of the 16S ribosomal gene. Duplicate samples of inoculated synovial fluid were prepared for microbial culture. Bacteria were detected in all samples inoculated with bacteria but not in control synovial fluid samples. Under experimental conditions there was no difference between microbial culture and PCR analyses for detection of bacteria. Experimentally, PCR was able to detect bacteria in synovial fluid within 24 hours of inoculation.

Broad-range PCR amplification and DNA sequence analysis reveals variable motifs in 16S rRNA genes of Mobiluncus species

Using DNA primers based on highly conserved regions of bacterial 16S ribosomal RNA genes, a technique was established for detection of Mobiluncus species by polymerase chain reaction (PCR) and hybridization analysis. Part of the 16S rRNA genes of Mobiluncus mulieris, Mobiluncus curtisii and uncharacterized Mobiluncus strains were analyzed by broad-range PCR amplification and direct DNA sequencing analysis. Sequence comparison of the partial 16S rRNA genes of Mobiluncus curtisii, Mobiluncus mulieris and atypical Mobiluncus strains studied indicated genus and species-specific motifs within the variable regions V3, V4 and V9 of 16S ribosomal DNAs. A Mobiluncus curtisii-specific primer, located within the variable region V3 of the 16S rRNA gene, was designed for Southern blot hybridization analysis of broad-range PCR products. Broad-range amplification combined with a M. curtisii-specific hybridization probe, Mob V3, distinguished between Mobiluncus curtisii, Mobiluncus mulieris, and atypical Mobiluncus strains.

Molecular methods: applications for clinical infectious diseases

The application of molecular biology to microbiology has led to a surge of new information about most infectious microorganisms, the pathogenesis of the infections they cause, and the specific microbial antigens involved in the immune response to these infections. The simultaneous application of the same techniques to diagnosis and epidemiology has also shown great promise, but these developments have not yet had a major effect on the routine practice of medicine. For some purposes, direct probe tests perform as well as other available methods. However, for most infections, these methods have not been proven sufficiently sensitive. The latest generation of highly sensitive diagnostics based on the polymerase chain reaction will overcome this technical obstacle and may revolutionize the management of many infections. Difficulties inherent in performing these tests will require special procedures and training in clinical laboratories to ensure that they are performed reliably. Nucleic acid-based methods for epidemiologic typing of microorganisms and for identification of noncultivatable pathogens are particularly useful for analysis of poorly cultivatable, dangerous, or otherwise untypeable microorganisms.

Use of the polymerase chain reaction to study arthritis due to Neisseria gonorrhoeae

OBJECTIVE

To explore the utility of the polymerase chain reaction (PCR) in the diagnosis, management, and investigation of arthritis due to Neisseria gonorrhoeae.

METHODS

The PCR was used to detect DNA from N gonorrhoeae in model systems and in extracts of synovial fluid (SF) from patients with systemic gonococcal infections and objective evidence of arthritis.

RESULTS

One N gonorrhoeae organism or its equivalent was detectable in human SF from inflamed joints. Five of 8 patients with systemic N gonorrhoeae infection and arthritis had N gonorrhoeae DNA demonstrated by PCR in at least 1 pretreatment SF specimen that was N gonorrhoeae culture positive. Thirty-seven of 38 control specimens were negative, the exception probably being due to cross-contamination from a positive specimen. All specimens that were positive for N gonorrhoeae by other methods were also positive by PCR. Two others were positive by PCR but negative by other methods. Four pretreatment specimens were negative by all methods, including PCR. This suggests that, for these patients, negative cultures reflected true absence of N gonorrhoeae, and not the presence of unculturable organisms. This group also had a significantly shorter duration of disease than did the patients with N gonorrhoeae DNA found in their SF. All patients had a prompt response to antibiotic treatment. Two of 3 patients whose specimens were previously positive showed marked decreases in SF N gonorrhoeae DNA after treatment.

CONCLUSION

The PCR using these or similar oligonucleotide primers can be a useful adjunct in the diagnosis of gonococcal arthritis and can be of value in assessing its response to therapy. In some N gonorrhoeae-associated arthritides, there appears to be a lack of both viable and nonviable N gonorrhoeae organisms in the SF. These observations may have implications regarding the pathogenesis of this form of arthritis.

Construction of a DNA amplification assay for detection of Legionella species in clinical samples

A polymerase chain reaction (PCR) assay for the detection of Legionella spp. in clinical bronchial fluid samples was constructed. The assay could detect a 375 bp fragment of the 16S RNA gene, equivalent to 10 cfu in simulated clinical bronchial fluid and blood samples. Seven clinically relevant Legionella spp. involving 12 serogroups produced a positive signal, whereas three Legionella spp. and none of a panel of 26 bacterial strains produced a signal in the constructed assay. Investigation of bronchial fluid from 51 patients with clinically suspected Legionnaire's disease revealed the presence of Legionella DNA by PCR in seven patients. The results were verified by Southern blot analysis of the amplified DNA fragment. None of 37 control patients produced a positive signal. Only one of the seven bronchial fluid samples positive for Legionella by PCR was positive by conventional culture, thus indicating the increased sensitivity of PCR compared to culture.

Isolation and characterization of full-length chromosomes from non-culturable plant-pathogenic Mycoplasma-like organisms

We describe the isolation and characterization of full-length chromosomes from non-culturable plant-pathogenic, mycoplasma-like organisms (MLOs). MLO chromosomes are circular and their sizes (640 to 1185 kbp) are heterogeneous. Divergence in the range of chromosome sizes is apparent between MLOs in the two major MLO disease groups, and chromosome size polymorphism occurs among some related agents. MLO chromosome sizes overlap those of culturable mycoplasmas; consequently, small genome size alone cannot explain MLO non-culturability. Hybridization with cloned MLO-specific chromosomal and 16S rRNA probes detected two separate chromosomes in some MLO 'type' strains. Large DNA molecules that appear to be MLO megaplasmids were also demonstrated. The ability to characterize full-length chromosomes from virtually any non-culturable prokaryote should greatly facilitate the molecular and genetic analysis of these difficult bacteria.

Geometric differences allow differential enzymatic inactivation of PCR product and genomic targets

The value of the polymerase chain reaction (PCR) is markedly limited by the ease of carry-over contamination. We predicted that the location of the target sequence which spans the linear center of the molecule in PCR products, but not in genomic molecules, would allow digestion by certain exonucleases (Exo). This would eliminate amplifiable targets specifically from PCR products and do so without the need to control either the size of the genomic molecules or the extent of the digestion reaction. Testing with T7 Exo and model targets in phage lambda DNA yielded results consistent with those predicted. By heat inactivating the Exo, complete reaction mixtures could be decontaminated and then amplified in an automatic thermal cycler without reopening the reaction tubes and risking recontamination.

Differentiation of Streptococcus uberis from Streptococcus parauberis by polymerase chain reaction and restriction fragment length polymorphism analysis of 16S ribosomal DNA

Streptococcus uberis type II has been proposed recently as a separate species designated Streptococcus parauberis (A. M. Williams and M. D. Collins, J. Appl. Bacteriol. 68:485-490, 1990). Differentiation of S. parauberis from S. uberis has been possible only by DNA-DNA hybridization or 16S rRNA sequencing, since the biochemical and serological characteristics of the two species are indistinguishable. A simple and reliable technique was developed for differentiating S. parauberis (S. uberis type II [ATCC 13386]) from S. uberis (S. uberis type I [ATCC 9927, ATCC 13387, and ATCC 27958]) by restriction fragment length polymorphism (RFLP) analysis of 1.4-kb 16S ribosomal DNA (rDNA). Oligonucleotide primers complementary to 16S rRNA genes were used to amplify 16S ribosomal gene fragments from genomic DNA by polymerase chain reaction. The 1.4-kb 16S rDNA fragment was digested with ScaI, NspI, DdeI, and AvaII restriction endonucleases. Restriction fragments produced by all four restriction endonucleases were characteristic for each species. RFLP analysis of 16S rDNA from 24 "S. uberis" isolates obtained from mammary secretions of dairy cows indicated that all 24 isolates were indeed S. uberis.

Construction of a DNA probe and detection of Actinobacillus pleuropneumoniae by using polymerase chain reaction

A 1.5-kb Actinobacillus pleuropneumoniae 4074 DNA fragment from a genomic library was found to hybridization. No cross-hybridization hybridization. No cross-hybridization was detected with DNAs from hemolytic members of the family Pasteurellaceae. From the nucleotide sequence of the putative genomic probe, three primers were synthesized for use in polymerase chain reactions (PCRs), with 31 strains tested by using purified and crude DNA targets. PCR amplification products of 610 and 985 bp were observed in nucleic acids extracted from the 12 known serotypes and a biotype 2 strain. Template DNAs from other gram-negative and gram-positive bacteria, some of them found in the normal flora of swine and the upper respiratory tract, were not amplified by PCR. The only exception was an amplification of a similar 610- or 985-bp sequence in Actinobacillus lignieresii, a species that is closely related to A. pleuropneumoniae but that has never been isolated from swine. Amplification of specific A. pleuropneumoniae sequences by PCR directly from clinical specimens may find applications in the identification of asymptomatic carriers as well as in efforts to eradicate porcine pleuropneumonia.

Amplification of nucleic acids by polymerase chain reaction (PCR) and other methods and their applications

The in vitro replication of DNA, principally using the polymerase chain reaction (PCR), permits the amplification of defined sequences of DNA. By exponentially amplifying a target sequence, PCR significantly enhances the probability of detecting target gene sequences in complex mixtures of DNA. It also facilitates the cloning and sequencing of genes. Amplification of DNA by PCR and other newly developed methods has been applied in many areas of biological research, including molecular biology, biotechnology, and medicine, permitting studies that were not possible before. Nucleic acid amplification has added a new and revolutionary dimension to molecular biology. This review examines PCR and other in vitro nucleic acid amplification methodologies--examining the critical parameters and variations and their widespread applications--giving the strengths and limitations of these methodologies.

The agent of bacillary angiomatosis. An approach to the identification of uncultured pathogens

BACKGROUND

Bacillary angiomatosis is an infectious disease causing proliferation of small blood vessels in the skin and visceral organs of patients with human immunodeficiency virus infection and other immunocompromised hosts. The agent is often visualized in tissue sections of lesions with Warthin-Starry staining, but the bacillus has not been successfully cultured or identified. This bacillus may also cause cat scratch disease.

METHODS

In attempting to identify this organism, we used the polymerase chain reaction. We used oligonucleotide primers complementary to the 16S ribosomal RNA genes of eubacteria to amplify 16S ribosomal gene fragments directly from tissue samples of bacillary angiomatosis. The DNA sequence of these fragments was determined and analyzed for phylogenetic relatedness to other known organisms. Normal tissues were studied in parallel.

RESULTS

Tissue from three unrelated patients with bacillary angiomatosis yielded a unique 16S gene sequence. A sequence obtained from a fourth patient with bacillary angiomatosis differed from the sequence found in the other three patients at only 4 of 241 base positions. No related 16S gene fragment was detected in the normal tissues. These 16S sequences associated with bacillary angiomatosis belong to a previously uncharacterized microorganism, most closely related to Rochalimaea quintana.

CONCLUSIONS

The cause of bacillary angiomatosis is a previously uncharacterized rickettsia-like organism, closely related to R. quintana. This method for the identification of an uncultured pathogen may be applicable to other infectious diseases of unknown cause.