16S-23S rRNA Intergenic Region Research Articles

Okeanomitos corallinicola gen. and sp. nov. (Nostocales, Cyanobacteria), a new toxic marine heterocyte-forming Cyanobacterium from a coral reef.

Cyanobacterial mats supplanting coral and spreading coral diseases in tropical reefs, intensified by environmental shifts caused by human-induced pressures, nutrient enrichment, and global climate change, pose grave risks to the survival of coral ecosystems. In this study, we characterized Okeanomitos corallinicola gen. and sp. nov., a newly discovered toxic marine heterocyte-forming cyanobacterium isolated from a coral reef ecosystem of the South China Sea. Phylogenetic analysis, based on the 16S rRNA gene and the secondary structure of the 16S-23S rRNA intergenic region, placed this species in a clade distinct from closely related genera, that is, Sphaerospermopsis stricto sensu, Raphidiopsis, and Amphiheterocytum. The O. corallinicola is a marine benthic species lacking gas vesicles, distinguishing it from other members of the Aphanizomenonaceae family. The genome of O. corallinicola is large and exhibits diverse functional capabilities, potentially contributing to the resilience and adaptability of coral reef ecosystems. Invitro assays revealed that O. corallinicola demonstrates notable cytotoxic activity against various cancer cell lines, suggesting its potential as a source of novel anticancer compounds. Furthermore, the identification of residual saxitoxin biosynthesis function in the genome of O. corallinicola, a marine cyanobacteria, supports the theory that saxitoxin genes in cyanobacteria and dinoflagellates may have been horizontally transferred between them or may have originated from a shared ancestor. Overall, the identification and characterization of O. corallinicola provides valuable contributions to cyanobacterial taxonomy, offering novel perspectives on complex interactions within coral reef ecosystems.

Maize (Zea mays L.): A New Host for Ligustrum witches' Broom Phytoplasma.

In the 2019–2020 growing season, two corn fields located in İmamoğlu town (Adana Province, Turkey) were surveyed following the appearance of phytoplasma-like symptoms on maize plants. A total of 40 samples were collected and tested in first-round and nested PCR using universal primer pairs P1/P7 and R16F2n/R16R2, respectively. All maize-diseased plants reacted positively, whilst no PCR amplifications were obtained from asymptomatic plants. Blast sequence analysis of R16F2n/R16R2-primed amplicons from different maize isolates showed 99.2% to 100% of identity with the 16S rRNA gene of Ligustrum witches’ broom phytoplasma (LiWBP). To gain additional molecular information on the 16S ribosomal RNA and 23S rRNA intergenic spacer region of LiWBP, not identified previously, the P1/P7-primed amplicons were also sequenced and analyzed. The results show that maize isolates from Turkey share 99.6% to 100% of identity among them, whereas the highest identity found (91%) was with members of groups 16SrII and 16SrXXV (peanut and tea witches’ broom groups, respectively). This distant relationship between LiWBP and members of 16SrII and XXV was also confirmed by RFLP and phylogenetic analyses. This is the first finding of LiWBP on maize in nature, where it was found responsible for phyllody disease of corn plants in Turkey. The additional molecular information acquired in this study on the 16S–23S rRNA intergenic spacer region of LiWBP further corroborates its distant relationship to any other phytoplasma groups.

Isolation of atypical wheat-associated xanthomonads in Algeria

Bacterial leaf streak and black chaff are important bacterial diseases of wheat, which have been reported to be caused by Xanthomonas translucens. In 2016, symptoms of bacterial leaf streak and black chaff were observed in Algeria, at experimental wheat breeding stations and in farmers' fields under sprinkler irrigation on two wheat cultivars, 'Hiddab' and 'Simeto'. Yellow Xanthomonas-like bacterial colonies were isolated from plant material, including leaves, spikes and post-harvest crop residues. Initial characterisation using biochemical, physiological and pathogenicity tests identified the bacteria as Xanthomonas. Diagnostic PCR targeting the 16S-23S rRNA intergenic region indicated that the strains were X. translucens, a clade-1 xanthomonad. However, partial DNA sequences of the housekeeping genes gyrB and rpoD revealed that the strains belong to clade 1, but likely represent a new Xanthomonas species that has not been previously described on wheat or other Gramineae. The most closely related strain, NCPPB 2654, was isolated from a bean plant in the United Kingdom in 1974. Further characterization is required to clarify the taxonomic status of the Algerian Xanthomonas isolates from wheat, and to determine their host ranges and impacts on plant cultivation.

Genetic diversity of Bartonella taylorii and Bartonella grahamii strains

Bacterial strains are a characteristic feature of many bacterial pathogens, including the species of the genus Bartonella. These bacteria are associated with different vertebrate hosts and vectors and have been detected in North America, Australia, Asia, and Europe. This study presents molecular characterization of Bartonella strains circulating in wild rodents. B. taylorii and B. grahamii are detected with high prevalence in mice, voles, and rats. However, there is a lack of knowledge on the geographical distribution and genetic diversity of B. taylorii and B. grahamii strains in wild rodents. The objectives of this study were to characterize the genetic diversity of B. taylorii and B. grahamii strains by sequence analysis of the housekeeping gene (rpoB) and the 16S-23S rRNA intergenic species region (ITS). Sequence analysis of rpoB gene revealed the presence of 15 B. taylorii genotypes and four B. grahamii genotypes in mice and voles captured in Lithuania. Sequence analysis of the ITS region revealed the presence of six B. taylorii genotypes and four B. grahamii genotypes in Lithuanian voles and mice. Analysis of genetic diversity demonstrated that B. grahamii strains derived from the same geographic region or from regions of close proximity more conservative, while B. grahamii strains from more distant areas are more variable. Genetic diversity of B. taylorii strains seems not to depend on geographic distance.

Phylogenetic connection among close genera of Aphanizomenonaceae (Cyanobacteria): Amphiheterocytum gen. nov., Cylindrospermopsis and Sphaerospermopsis

Aphanizomenonaceae is a recently proposed family of Cyanobacteria encompassing 12 planktic genera. The formation and distribution of heterocytes and akinetes along the trichome are the main morphological characteristics of this family. In this context, Sphaerospermopsis and Cylindrospermopsis are close related genera both molecularly and morphologically differing by 1) rounded akinetes adjacent to the heterocytes disposed along the trichome in Sphaerospermopsis; 2) apical heterocytes and akinetes separated by a few cells (2–3) in Cylindrospermopsis. Recently, during a survey on cyanobacteria from tropical Brazilian eutrophic lakes, strains with similarities to Sphaerospermopsis and Cylindrospermopsis were isolated. Aiming to elucidate the phylogenetic placement of these strains, we performed morphological, physiological and molecular studies. The Brazilian strains were confirmed to be closely related to Sphaerospermopsis and Cylindrospermopsis, but the phylogeny, based on 16S rRNA gene and 16S–23S rRNA intergenic region, clustered them in a well-defined clade separate from these genera. According to these results, we detailed the morphology, physiology, and phylogeny of the proposed new genus Amphiheterocytum, which showed potential to create blooms in tropical shallow lakes.

Genotypic and symbiotic diversity of Rhizobium populations associated with cultivated lentil and pea in sub-humid and semi-arid regions of Eastern Algeria

The genetic structure of rhizobia nodulating pea and lentil in Algeria, Northern Africa was determined. A total of 237 isolates were obtained from root nodules collected on lentil (Lens culinaris), proteaginous and forage pea (Pisum sativum) growing in two eco-climatic zones, sub-humid and semi-arid, in Eastern Algeria. They were characterised by PCR-restriction fragment length polymorphism (RFLP) of the 16S–23S rRNA intergenic region (IGS), and the nodD-F symbiotic region. The combination of these haplotypes allowed the isolates to be clustered into 26 distinct genotypes, and all isolates were classified as Rhizobium leguminosarum. Symbiotic marker variation (nodD-F) was low but with the predominance of one nod haplotype (g), which had been recovered previously at a high frequency in Europe. Sequence analysis of the IGS further confirmed its high variability in the studied strains. An AMOVA analysis showed highly significant differentiation in the IGS haplotype distribution between populations from both eco-climatic zones. This differentiation was reflected by differences in dominant genotype frequencies. Conversely, no host plant effect was detected. The nodD gene sequence-based phylogeny suggested that symbiotic gene diversity in pea and lentil nodulating rhizobial populations in Algeria was low compared to that reported elsewhere in the world.

Ureaplasma urealyticumorUreaplasma parvum: what's the difference?

<i>Ureaplasma urealyticum</i>or<i>Ureaplasma parvum</i>: what's the difference?

First Case of Bartonella henselae Bacteremia in Korea.

Bartonella henselae causes cat-scratch disease, bacteremia, and various focal infections. Despite the worldwide occurrence of B. henselae infections, reports in humans are rare in Korea. The clinical manifestation of all 5 previously reported cases was lymphadenopathy. Herein, we report a case of bacteremia in a woman who presented with prolonged fever. B. henselae was isolated from a blood specimen by cell culture. Conventional polymerase chain reaction amplification and sequencing of the 16S-23S rRNA intergenic space region confirmed the isolate to be B. henselae. The patient had no underlying immunocompromising conditions and no recent exposure to animals. She was successfully managed with a combination of doxycycline and hydroxychloroquine.

Real-time PCR을 이용한 가축생균제용 유산균 정량분석

본 연구는 가축생균제용 유산균을 Real-time PCR정량분석법을 이용하여 분석하였다. SYBR Green1 방법과 Probe 방법을 이용하여 표준곡선을 제작한 결과, SYBR Green1 방법에서는 Slope 값이 -3.346이었고, Y절편은 33.18, $R^2$ 값은 0.993으로 나타났으며, Probe 방법에서는 Slope값이 -3.321이었고, Y절편은 39.10, $R^2$ 값은 0.995로 나타나, 이를 이용한 표준곡선 제작이 가능함을 알 수 있었다. SYBR Green1 방법을 이용한 생균제의 Lactobacilli 정성 정량 분석결과 Real-time PCR값은 4.46~6.56 log copies로 나타났고, 생균수 측정 결과 값은 5.63~7.59 log CFU/g로 나타났으며, Probe 방법을 이용한 생균제의 Lactobacilli 정성 정량 분석결과에서는 Real-time PCR 값은 5.51~7.00 log copies로 나타났으며, 생균수 측정 결과 값은 5.63~7.59 log CFU/g로 나타났다. 본 연구에서 실시한 RT PCR법은 3~4일이 소요되는 기존의 배지법과 비교하여 24시간 이내에 신속하게 검출이 가능하다고 여겨지며, 또한 RT PCR을 이용한 분석방법에서도 dye 사용과 primer 사용에 따라 결과값이 차이가 나타났음을 확인할 수 있었으며, Probe 방법을 이용하여 실험 한 결과가 민감한 결과를 나타내었음을 확인 할 수 있었다. 【This study was conducted using quantitative real-time PCR using Lactobacilli as probiotics. Quantitative real-time PCR (RT PCR) was conducted via a method involving SYBR Green 1 and a probe. Plasmid DNA was cloned using the 16S-23S rRNA intergenic species region. Gene clones were diluted from $10^2$ to $10^{10}$ . Standard curves were constructed via Ct values obtained from the results of Real-time PCR via the aforementioned SYBR Green 1 and probe method. Plasmid DNA was also cloned using the 16S-23S rRNA intergenic species region and the gene clones were diluted from $10^2$ to $10^{10}$ copy numbers via the probe method. Using RT PCR, a standard curve of plasmid DNA copy numbers was also determined. The slope value for the Y-axis intercept and $R^2$ value were measured as -3.346, 33.18, and 0.993, respectively, via the first method. For the second method, the slope value for the Y-axis intercept and $R^2$ were -3.321, 31.10 and 0.995, respectively. The PCR inhibitor could not express the detection curve at a copy number over $10^{10}$ via either method, owing to high DNA density. The DNA extract from probiotics was diluted without pre-culturing, and 16 products were amplified via both methods. The Ct value was 11.06~18.12 in the first method and 16.74~22.11 in the second method. Measured probiotics and log copy values were largely similar among the methods used. It was concluded that both methods are effective for analysis, but further research will be required to verify the optimal method.】

A Report of Cat Scratch Disease in Korea Confirmed by PCR Amplification of the 16S-23S rRNA Intergenic Region ofBartonella henselae

We report a case of cat scratch disease in an 8-yr-old girl who presented with fever and enlargement of both axillary lymph nodes. Both aerobic and anaerobic cultures of the lymph node aspirate were negative for microbial growth. Gram staining and Warthin-Starry silver staining did not reveal any organism. Purified DNA from the PCR-amplicon of the 16S-23S rRNA intergenic region was sequenced and showed 99.7% identity with the corresponding sequence of Bartonella henselae strain Houston-1. Our findings suggest that the internal transcribed spacer is a reliable region for PCR identification of Bartonella species. In patients with lymphadenitis, a history of contact with cats or dogs necessitates the use of diagnostic approaches that employ not only the conventional staining and culture but also molecular methods to detect B. henselae.

First Report of "Candidatus Liberibacter psyllaurous" Associated with Psyllid Yellows of Tomato in Colorado.

Greenhouse tomato growers from Fort Lupton, CO contacted the USDA-ARS-USHRL in 2002 regarding plant symptoms resembling "psyllid yellows" associated with Bactericera cockerelli (Sulc) infestations that initially begin as retarded growth, erectness of new growth, chlorosis, and purpling of leaves followed by widespread chlorosis and production of many small, poor-quality fruit (1). Symptoms appeared ≈6 weeks after psyllids were observed and were generally restricted to the top half of the plant. Leaf cuttings from beefsteak tomatoes cv. Quest were immediately placed in RNAlater (Applied Biosystems, Austin, TX). Samples from symptomatic and asymptomatic plants were collected in September and December of 2002. At each date, leaves were sampled from multiple plants and placed in separate RNAlater bottles. September samples exhibited initial "psyllid yellows" symptoms and December samples exhibited severe symptoms. Samples remained at 4°C in RNAlater for 6 years until recent findings suggested that a new species of bacteria, named either "Candidatus Liberibacter psyllaurous" (2) or "Ca. L. solanacearum" (3), may be the causal agent of "psyllid yellows". The Qiagen (Valencia, CA) DNeasy Plant Kit and recommended protocols were used for four separate DNA isolations from each of the four tomato samples that had previously remained unopened. Five PCR primer pairs designed to amplify three distinct genetic regions within the "Ca L. psyllaurous" rrn operon (16S rRNA, 16S-23S rRNA intergenic region, and 23S rRNA) were used and one primer pair specific to the tomato DNA (18S rRNA gene) that successfully amplified from all samples was used as a positive control. Bacterial primers included one pair designed specifically for 16S rRNA sequences of 'Ca. L. asiaticus', 'americanus', and 'africanus' species (USHRL-CL1) and four sets, Lp-1 through Lp-4, previously described (2) that amplify nonoverlapping regions of the 16S-23S rRNA operon. The USHRL-CL1 primers (USHRL-CL1f: 5'-CTTACCAGCCCTTGACATGTATAGGA-3', and USHRL-CL1r: 5'-TCCCTATAAAGTACCCAACATCTAGGTAAA-3') amplify a 195-bp fragment from bp 895 to 1,089 of the 'Ca. Liberibacter' sp. 16S rRNA Genbank Accession No. L22532. Only samples from severe symptomatic plants collected in December 2002 yielded amplicons that were purified and sequenced (Genbank: USHRL-CL1, FJ871062; Lp-1, FJ871058; Lp-2, FJ871059; Lp-3, FJ871060; Lp-4, FJ871061). For each bacterial primer pair, the fragment amplified was highly homologous (98 to 100% identity) to "Ca. L. psyllaurous" rRNA gene/intergenic space sequences. The 16S rRNA coding region was identical to two GenBank 'Ca. Liberibacter' sp. entries: EU921627 and EU921626 from B. cockerelli samples collected in Dalhart, TX and zebra chip potato samples from Garden City, KS, respectively; however, the whole 2,500 bp amplified and sequenced from our sample contained 11 to 14 polymorphisms when compared to nine "Ca. L. psyllaurous" sequences. Our results clearly indicate that "Ca. L. psyllaurous" isolates were associated with tomato "psyllid yellows" symptoms in Colorado as early as 2002 and significant sequence variation exists within the 16S/23S rRNA intergenic region and 23S rRNA coding region to allow analysis of genetic diversity among "Ca. L. psyllaurous" isolates.

Isolates of ‘Candidatus Nostocoida limicola’ Blackall et al. 2000 should be described as three novel species of the genus Tetrasphaera, as Tetrasphaera jenkinsii sp. nov., Tetrasphaera vanveenii sp. nov. and Tetrasphaera veronensis sp. nov.

Despite differences in their morphologies, comparative analyses of 16S rRNA gene sequences revealed high levels of similarity (>94 %) between strains of the filamentous bacterium 'Candidatus Nostocoida limicola' and the cocci Tetrasphaera australiensis and Tetrasphaera japonica and the rod Tetrasphaera elongata, all isolated from activated sludge. These sequence data and their chemotaxonomic characters, including cell wall, menaquinone and lipid compositions and fingerprints of their 16S-23S rRNA intergenic regions, support the proposition that these isolates should be combined into a single genus containing six species, in the family Intrasporangiaceae in the Actinobacteria. This suggestion receives additional support from DNA-DNA hybridization data and when partial sequences of the rpoC1 gene are compared between these strains. Even though few phenotypic characterization data were obtained for these slowly growing isolates, it is proposed, on the basis of the extensive chemotaxonomic and molecular evidence presented here, that 'Candidatus N. limicola' strains Ben 17, Ben 18, Ben 67, Ben 68 and Ben 74 all be placed into the species Tetrasphaera jenkinsii sp. nov. (type strain Ben 74(T)=DSM 17519(T)=NCIMB 14128(T)), 'Candidatus N. limicola' strain Ben 70 into Tetrasphaera vanveenii sp. nov. (type strain Ben 70(T)=DSM 17518(T)=NCIMB 14127(T)) and 'Candidatus N. limicola' strains Ver 1 and Ver 2 into Tetrasphaera veronensis sp. nov. (type strain Ver 1(T)=DSM 17520(T)=NCIMB 14129(T)).

Cat-scratch disease in veterinary-associated populations and in its cat reservoir in Taiwan

In Taiwan, the first human case of cat-scratch disease (CSD) was diagnosed by a serologic test in 1998. Since then, no studies have been conducted to understand the epidemiology of the infection in Taiwan. Therefore, this study is the first epidemiologic survey of CSD in cats and humans in this country. Using veterinary-associated individuals as the study population, it was identified that 1.7% of them were seropositive for B. henselae, and residence was the only factor associated with seropositivity. Bartonella species were successfully isolated from 25 (19.1%) of the 131 cats tested. Only B. henselae and B. clarridgeiae were obtained from bacteremic cats. Furthermore, 9.2% of 131 cats were dually-infected with genotypes I and II of B. henselae. It is the highest prevalence of co-infection that has ever been reported worldwide. In cats, the seroprevalence was 23.7% by indirect immunofluorescence antibody assay with B. henselae Houston-1 (type I) as the antigen. When 12 bacteremic but seronegative cats were re-tested by IFA slides coated with B. henselae U-4 antigen (type II), 9 cats were identified to be seropositive. Our study further suggested that using only direct PCR of 16S-23S rRNA intergenic region or the combination of the PCR method and indirect immuno-fluorescence test will be useful to diagnose Bartonella-free cats.

Nested-PCR法による猫血液からの&lt;I&gt;Bartonella&lt;/I&gt;遺伝子の検出

Three different nested-PCR assays were evaluated in terms of their ability to detect Bartonella DNA in catblood samples. The primer pairs used were parts of the citrate synthase (gltA) gene, heat shock protein (htrA) gene and 16S-23S rRNA intergenic region (ITS) gene, respectively. Of the 29 culture-positive cats-blood samples, Bartonella DNA was detected in 20 (68.9%) by the gltA nested-PCR and htrA nested-PCR. The ITS nested- PCR detected Bartonella DNA in 26 of 29 (89.7%). In two of 29 specimens, none of the gene examined was detected. These results indicate that the nested-PCR is a useful tool for the detection of Bartonella DNA in cat-blood samples.

Identification of waterborne bacteria by the analysis of 16S-23S rRNA intergenic spacer region.

In this study, we evaluated, the use of universal primers, specific for the 16S-23S rRNA intergenic region, to detect and identify nine species that are of high interest for the microbiological control of water. The analysis of the fragments was carried out using a High Resolution acrylamide/bisacrylamide gels in a fluorescent automated DNA sequencer. The results showed specific profiles for each of the nine species but this technique failed to detect simultaneously micro-organisms in samples containing a mixed population. Nevertheless, the electrophoretic profiles obtained provided a very useful tool for the rapid and specific identification of water isolates. A possible new methodology for a rapid identification of pathogens in water.

Development of a sensitive DNA microarray suitable for rapid detection of Campylobacter spp.

Campylobacter is the most common cause of human acute bacterial gastroenteritis worldwide, widely distributed and isolated from human clinical samples as well as from many other different sources. To comply with the demands of consumers for food safety, there is a need for development of a rapid, sensitive and specific detection method for Campylobacter. In this study, we present the development of a novel sensitive DNA-microarray based detection method, evaluated on Campylobacter and non- Campylobacter reference strains, to detect Campylobacter directly from the faecal cloacal swabs. The DNA-microarray method consists of two steps: first, both universal bacterial sequences and specific Campylobacter sequences (size range: 149–307 bp) are amplified and fluorescently labeled using multiplex-PCR, targeting the 16S rRNA, the 16S-23S rRNA intergenic region and specific Campylobacter genes. Secondly, the Cy5 labeled PCR-amplicons are hybridised to immobilised capture probes on the microarray. The method allows detection of three to thirty genome equivalents (6–60 fg DNA) of Campylobacter within 3 h, with a hands on time of only 15 min. Using the DNA-microarrays, two closely related Campylobacter species, Campylobacter jejuni and Campylobacter coli could be detected and differentiated directly from chicken faeces. The DNA-microarray method has a high potential for automation and incorporation into a dedicated mass screening microsystem.

Bacterial 16S rRNA gene analysis revealed that bacteria related to Arcobacter spp. constitute an abundant and common component of the oyster microbiota (Tiostrea chilensis).

To explore the bacterial microbiota in Chilean oyster (Tiostrea chilensis), a molecular approach that permits detection of different bacteria, independently of their capacity to grow in culture media, was used. Bacterial diversity was assessed by analysis of both the 16S rDNA and the 16S-23S intergenic region, obtained by PCR amplifications of DNA extracted from depurated oysters. RFLP of the PCR amplified 16S rDNA showed a prevailing pattern in most of the individuals analyzed, indicating that a few bacterial species were relatively abundant and common in oysters. Cloning and sequencing of the 16S rDNA with the prevailing RFLP pattern indicated that this rRNA was most closely related to Arcobacter spp. However, analysis by the size of the amplified 16S-23S rRNA intergenic regions revealed not Arcobacter spp. but Staphylococcus spp. related bacteria as a major and common component in oyster. These different results may be caused by the absence of target for one of the primers employed for amplification of the intergenic region. Neither of the two bacteria species found in large abundance was recovered after culturing under aerobic, anaerobic, or microaerophilic conditions. This result, however, is expected because the number of bacteria recovered after cultivation was less than 0.01% of the total. All together, these observations suggest that Arcobacter-related strains are probably abundant and common in the Chilean oyster bacterial microbiota.

Rapid detection and identification of Streptococcus macedonicus by species-specific PCR and DNA hybridisation

The aim of this study was to develop a simple and specific method for the rapid detection and identification of Streptococcus macedonicus. The method was based on polymerase chain reaction (PCR) using species-specific primers derived from the 16S rRNA gene. Specific identification was proven on seven S. macedonicus strains, while 16 strains belonging to different lactic acid bacteria species were tested negative. The PCR assay was capable of detecting 100 pg of S. macedonicus DNA, and it was also efficient on single colonies of the bacterium. Furthermore, the same bacterial strains were used for the specificity evaluation of a S. macedonicus species-specific probe. Neither species-specific PCR nor DNA hybridisation experiments could differentiate Streptococcus waius from S. macedonicus, due to the identity of the 16S rRNA gene of the two species, indicating high phylogenetical relatedness. This was further confirmed by the comparative sequence analysis of the 16S–23S rRNA intergenic regions. It was thus clearly demonstrated that S. waius, recently described as a novel Streptococcus species, is phylogenetically identical to S. macedonicus.

Restriction fragment length polymorphism of rRNA operons for discrimination and intergenic spacer sequences for cataloging of Bacillus subtilis sub-groups

Restriction fragment length polymorphism of rRNA operons (RFLP) and 16S–23S rRNA intergenic region (ISR) sequences of Bacillus subtilis subsp. subtilis, B. subtilis subsp. spizizenii, and B. atrophaeus were compared. ISR sequences of the B. subtilis subspecies were extremely similar (W23 versus 168 rrn H, J, G,W; 96.8%; rrn D, E; 98.4%; rrnB; 97.9%) and, therefore, not useful for their differentiation. However, RFLP of rRNA operons of the B. subtilis subspecies were distinct in terms of numbers and organization within the genome (e.g. the 168 sub-group generally contained 8.3- and 8.0-kb fragments absent in the W23 sub-group). The more distantly related B. atrophaeus was distinct from both B. subtilis subspecies in terms of ISR sequence and rRNA operon number and organization. RFLP of rRNA operons discriminates the two sub-groups of Bacillus subtilis that are indistinguishable by ISR sequence. However, ISR sequence defines the relatedness of B. subtilis to other species (e.g. B. atrophaeus) within the genus Bacillus.

Rapid identification and differentiation of Bartonella species using a single-step PCR assay.

Five species of Bartonella have been reported to infect humans and cause a variety of diseases that can be difficult to diagnose. Four species of Bartonella have been reported to infect cats and dogs, and two of these species are considered to be zoonotic pathogens. Diagnosis of Bartonella infections is hampered by the slow, fastidious growth characteristics of Bartonella species. We report on the development of a single-step PCR-based assay for the detection and differentiation of medically relevant Bartonella species. PCR-mediated amplification of the 16S-23S rRNA intergenic region resulted in a product of a unique size for each Bartonella species, thereby allowing differentiation without the necessity of restriction fragment length polymorphism analysis or sequencing of the amplified product. The ability of the single-step PCR assay to differentiate between Bartonella species was determined with characterized isolates and blood samples from animals known to be infected with either Bartonella henselae, B. clarridgeiae, or B. vinsonii subsp. berkhoffii. The sensitivity of the single-step PCR assay relative to that of in vitro culture was determined with blood samples from B. henselae-infected cats. B. henselae target DNA was amplified from 100% of samples with greater than 50 CFU/ml and 80% of samples with 10 to 30 CFU/ml. The single-step assay described in the report expedites PCR-based detection and differentiation of medically relevant Bartonella species.