Differentiation of rickettsiae by groEL gene analysis

Comparative Evaluation of Different Tissues and Molecular Techniques for the Zoonotic Surveillance of Scrub Typhus

Background and Objectives: Scrub typhus (ST) is detected in one-fourth of patients with acute febrile illnesses, confirming its nationwide re-emergence. The disease, if not diagnosed, can lead to multiple organ dysfunction and mortality. Being a vector-borne zoonotic disease, the molecular survey for pathogens in animal hosts is essential to predict the risk of its transmission to humans. Hence, this study aimed at identifying the effective animal tissue and molecular technique for zoonotic surveillance of ST infection in small animal hosts. Methods: Rodents/shrews were trapped from seventeen randomly selected villages in Puducherry between July and September, 2022. The presence of Orientia tsutsugamushi in ectoparasites and tissues including blood, lung, liver, spleen, kidney, heart, brain, and intestine retrieved from the animals was screened by nested PCR targeting 56 kDa, real-time PCR (qPCR) targeting 47 kDa and traD, and conventional PCR targeting groEL. The Weil-Felix test was carried out to detect antibodies against O. tsutsugamushi in rodent/shrew serum samples. Diagnostic accuracy measures of the molecular tests were calculated for each of the tissues by latent class modeling. Results: O. tsutsugamushi detected in the rodents/shrews were identified to be Karp-like and Kawasaki-like strains. Upon statistical analysis, qPCR targeting 47 kDa exhibited the highest accuracy measures in most of the tissues analyzed, with perfect sensitivity and specificity of 100% and 97% for intestine and lung samples for the epidemiological surveillance, respectively. Interpretation and Conclusion: The study recommends qPCR targeting 47 kDa gene and analysis of intestine and lung along with blood for the zoonotic surveillance of ST infection.

First detection of Candidatus Rickettsia tarasevichiae in Hyalomma marginatum ticks

Ticks are important vectors of zoonotic diseases and play a major role in the circulation and transmission of many rickettsial species. The aim of this study was to investigate the carriage of Candidatus Rickettsia tarasevichiae (CRT) in a total of 1168 ticks collected in Inner Mongolia to elucidate the potential public health risk of this pathogen, provide a basis for infectious disease prevention, control and prediction and contribute diagnostic ideas for clinical diseases that present with fever in populations exposed to ticks. A total of four tick species, Haemaphysalis concinna (n = 21), Dermacentor nuttalli (n = 122), Hyalomma marginatum (n = 148), and Ixodes persulcatus (n = 877), were collected at nine sampling sites in Inner Mongolia, China, and identified by morphological and molecular biological methods. Reverse transcription PCR targeting the 16S ribosomal RNA (rrs), gltA, groEL, ompB and Sca4 genes was used to detect CRT DNA. Sequencing was used for pathogen species confirmation. The molecular epidemiological analysis showed that three species of ticks were infected with CRT, and the overall positive rate was as high as 42%. The positive rate of I. persulcatus collected in Hinggan League city was up to 96%, and that of I. persulcatus collected in Hulun Buir city was 50%. The pool positive rates of D. nuttalli and H. marginatum collected in Bayan Nur city and H. concinna collected in Hulun Buir city were 0%, 28% and 40%, respectively. This study revealed the high prevalence of CRT infection in ticks from Inner Mongolia and the first confirmation of CRT detected in H. marginatum in China. The wide host range and high infection rate in Inner Mongolia may dramatically increase the exposure of CRT to humans and other vertebrates. The role of H. marginatum in the transmission of rickettsiosis and its potential risk to public health should be further considered.

Molecular detection of Orientia tsutsugamushi in ectoparasites & their small mammal hosts captured from scrub typhus endemic areas in Madurai district, India

BACKGROUND OBJECTIVES

Scrub typhus, caused by Orientia tsutsugamushi present in small mammals harbouring the ectoparasites. A study was undertaken to detect the pathogen present in small mammals and its ectoparasites in the scrub typhus-reported areas.

METHODS

The small mammals (rodents/shrews) and its ectoparasites were screened for O. tsutsugamushi using nested PCR amplification of the groEL gene. Small mammals were collected by trapping and screened for ectoparasites (mites, ticks and fleas) by combing method.

RESULTS

All the chigger mites collected were tested negative for O. tsutsugamushi . Interestingly, adult non-trombiculid mites ( Oribatida sp., Dermanyssus gallinae ), fleas ( Xenopsylla astia, X. cheopis, Ctenophalides felis and Ctenophalides sp.) and ticks ( Rhipicephalus sanguineus , R. haemaphysaloides ) screened were found to be positive for O. tsutsugamushi , which the authors believe is the first report on these species globally. Bandicota bengalensis with O. tsutsugamushi infection is reported for the first time in India. The O. tsutsugamushi groEL sequences from the positive samples were similar to the reference strains, Karp and Ikeda and phylogenetically clustered in clade IV with less evolutionary divergence. The blood samples of Rattus rattus , Suncus murinus and B. bengalensis collected from this area were tested positive for O. tsutsugamushi ; interestingly, the sequence similarity was much pronounced with their ectoparasites indicating the transmission of the pathogen to host or vice versa .

INTERPRETATION CONCLUSIONS

The outcome of the present investigations widened our scope on the pathogens present in ectoparasites and rodents/shrews from this area. This will help to formulate the required vector control methods to combat zoonotic diseases.

Seasonal abundance of Leptotrombidium deliense, the vector of scrub typhus, in areas reporting acute encephalitis syndrome in Gorakhpur district, Uttar Pradesh, India

The rickettsial pathogen Orientia tsutsugamushi, causing scrub typhus, has been implicated as a major cause of acute encephalitis syndrome (AES) in many places in India including Gorakhpur district of Uttar Pradesh. Seasonal abundance of the principal vector mite of the pathogen, Leptotrombidium deliense, its animal hosts, and prevalence of infection on them are important attributes in the assessment of outbreaks of the disease. Hence, these aspects were investigated, seasonally, in rural villages of Gorakhpur district, where peak incidence of AES cases were reported. A total of 903 animals (rodents/shrews) was collected using 6484 Sherman traps in eight study villages (14% overall trap rate). A sum of 5526 trombiculid mites comprising 12 species was collected from 676 live rodents/shrews screened. Suncus murinus, the Asian house shrew was the predominant species (67%). Among trombiculids, the principal vector mite, L. deliense, was predominant (64.7%) and its infestation index (i.e., average number of chiggers per host animal) was 5.3. The L. deliense infestation index was higher during July to November with a peak in October. Out of 401 animal sera samples screened, 68% were positive for antibodies against O. tsutsugamushi. Of 465 blood samples tested by nested PCR, seven were positive for the 56 kDa gene of O. tsutsugamushi. In conventional PCR, 41 out of 265 samples were positive for the 60 kDa groEL gene of O. tsutsugamushi. Among the 5526 mite samples, tested as 352 pools through nested PCR, four pools were positive for 56 kDa gene. Phylogenetic analysis of 56 and 60 kDa genes confirmed circulation of Karp and TA678 (rodents) and TA678 (mite) serotypes of O. tsutsugamushi in Gorakhpur. Peak incidence of AES in Gorakhpur district occurs during the rainy season (July-October), coinciding with the peak abundance of L. deliense. These results indicate involvement of L. deliense as the vector mite transmitting the scrub typhus pathogen O. tsutsugamushi to humans in the rural areas of Gorakhpur district, India.

Molecular Detection of Spotted Fever Group Rickettsia (Rickettsiales: Rickettsiaceae) in Ticks of Iran

Ticks are reservoir hosts of pathogenic Rickettsia in humans and domestic animals. Most pathogenic Rickettsia species belong to the spotted fever group (SFG). The present study aimed to determine the tick species infected with Rickettsia based on the genus-specific 23S ribosomal ribonucleic acid (rRNA), 16S rRNA, and citrate synthase (gltA) gene fragments. A total of 61 tick specimens were selected for molecular assay and 12 samples for sequencing. Phylogenetic analysis was conducted using neighbor-joining and Bayesian inference methods. Argas persicus, Haemaphysalis sulcata, Ha. inermis, and Hyalomma asiaticum were infected by spotted fever Rickettsia. The SFG is the main group of Rickettsia that can be detected in the three genera of ticks from Iran.

GroEL gene typing and genetic diversity of Anaplasma bovis in ticks in Shaanxi, China

Anaplasma bovis, causative agent of bovine anaplasmosis, is usually identified by nested-PCR amplifying the rrs gene. However, it is difficult to determine the genetic relationship among different variants within A. bovis using this gene because of high conservation. In this study, two tick species, identified as Rhipicephalus microplus and Haemaphysalis longicornis based on morphological and molecular methods by analyzing COI gene, were collected from cattle, goat or sheep. Subsequently, A. bovis was initially detected by PCR amplifying the rrs gene in ticks in Shaanxi Province, China. The sequencing and Blast results showed that some false positive samples were found when only based on the amplification of partial rrs gene, presenting these sequences resembled those of other Alphaproteobacteria rather than A. bovis. Although major surface proteins genes were proposed and used successfully to identify members within Anaplasmataceae, these genes were unavailable for A. bovis. Hence, primers targeting the groEL gene were designed and a PCR assay was developed. The PCR products were sequenced and similarity and phylogenetic analysis suggested all these sequences are the groEL gene of A. bovis. In addition, phylogenetic analysis based on the groEL gene also revealed the genetic diversity of A. bovis worldwide, as well as in Shaanxi Province of China, which wasn't reflected by analyzing the rrs gene. In sum, groEL gene is important for molecular detection and phylogenetic analysis of A. bovis.

Strain diversity of Rickettsia amblyommatis in ticks infesting birds in the North Huetar conservation area of Costa Rica

Although the presence of rickettsial agents in ticks infesting wild birds in Costa Rica has been recently reported, information on strain diversity is limited to selected rickettsial species. In order to mine deeper into rickettsial agents of ticks infesting Costa Rica wild birds a total of 399 birds from the North Huetar Conservation Area of Costa Rica were captured, and 134 immature ticks (76 larvae and 58 nymphs) were recovered from 61 birds. Ticks were tested for the presence of Rickettsia spp. by conventional PCR and sequencing of the gltA, ompA, ompB, 17 kDa, and groEL genes. Six (11.3%) Amblyomma longirostre and Amblyomma geayi ticks collected from passeriform birds, yielded amplicons of the expected size. Amplicons were sequenced, and BLAST results collectively showed that all sequences had 99-100% nucleotide identity with Rickettsia amblyommatis (formerly, 'Candidatus Rickettsia amblyommii'). Three different R. amblyommatis strains were identified. Four new tick species-host associations and the first detection of R. amblyommatis in A. geayi in Costa Rica are also reported.

Occurrence of Orientia tsutsugamushi, the Etiological Agent of Scrub Typhus in Animal Hosts and Mite Vectors in Areas Reporting Human Cases of Acute Encephalitis Syndrome in the Gorakhpur Region of Uttar Pradesh, India

Outbreaks of acute encephalitis syndrome (AES) with high fatality and disability, are reported every year in the Gorakhpur region of Uttar Pradesh, India, with the etiology of >60% of the cases being attributed to scrub typhus. In the present study, the prevalence of Orientia tsutsugamushi, the etiological agent of scrub typhus, was investigated among animal hosts and their ectoparasitic trombiculid mites prevalent in AES-reported areas of Gorakhpur. A total of 154 rodents/shrews were collected using 777 Sherman traps set in 12 study villages, and the overall trap rate was 19.8%. In total, 2726 trombiculid mites belonging to 12 species were collected from 154 rodents/shrews trapped. The shrew mouse Suncus murinus was the predominant animal species (78.6%) collected. The principal vector mite Leptotrombidium deliense was the predominant species (82.7%), and its index was 14.6 per animal. Of 114 rodent/shrew sera samples screened through the Weil-Felix test, 57% were positive for antibodies against O. tsutsugamushi. Of 128 blood samples tested by polymerase chain reaction (PCR), one rodent sample was positive for the gene encoding 56 kDa protein and 25 for 60 kDa. Among 2726 mite samples tested as 315 pools through nested PCR, seven pools were positive for 56 kDa gene. Phylogenetic analysis confirmed circulation of Gilliam, Karp, and TA678 serotypes of O. tsutsugamushi in Gorakhpur. The study clearly demonstrated natural infection of O. tsutsugamushi in both small-animal hosts and vector mites in the AES-reporting villages of Gorakhpur, which confirms transmission of the scrub typhus pathogen in this region. The high infestation rate of L. deliense with O. tsutsugamushi infection indicates that the people living in the rural villages of Gorakhpur are at risk of infection with scrub typhus, which might lead to AES.

Microbial taxonomy in the era of OMICS: application of DNA sequences, computational tools and techniques

The current prokaryotic taxonomy classifies phenotypically and genotypically diverse microorganisms using a polyphasic approach. With advances in the next-generation sequencing technologies and computational tools for analysis of genomes, the traditional polyphasic method is complemented with genomic data to delineate and classify bacterial genera and species as an alternative to cumbersome and error-prone laboratory tests. This review discusses the applications of sequence-based tools and techniques for bacterial classification and provides a scheme for more robust and reproducible bacterial classification based on genomic data. The present review highlights promising tools and techniques such as ortho-Average Nucleotide Identity, Genome to Genome Distance Calculator and Multi Locus Sequence Analysis, which can be validly employed for characterizing novel microorganisms and assessing phylogenetic relationships. In addition, the review discusses the possibility of employing metagenomic data to assess the phylogenetic associations of uncultured microorganisms. Through this article, we present a review of genomic approaches that can be included in the scheme of taxonomy of bacteria and archaea based on computational and in silico advances to boost the credibility of taxonomic classification in this genomic era.

Improving the Diagnosis of Scrub Typhus by Combining groEL Based Polymerase Chain Reaction and IgM ELISA

INTRODUCTION

Scrub typhus, an acute febrile illness, caused by Orientia tsutsugamushi, is an important cause of pyrexia of unknown origin in regions of endemicity. This disease is mostly underdiagnosed or misdiagnosed, the reasons for this being a combination of factors which include clinical manifestations that can mimic other infections, lack of easy and reliable diagnostic methods and variation among strains in endemic areas. Hence, easy and reliable methods of diagnosis will contribute to rapid identification and treatment of the infection.

AIM

The aim of the study was to compare four different methods of detection of scrub typhus and to identify one single test or a combination of tests detecting maximum number of cases.

MATERIALS AND METHODS

One hundred and forty-five suspected scrub typhus cases were included in this study. Duration of fever and presence of eschar in each patient was noted down. Enzyme-Linked Immunosorbent Assay (ELISA) to detect Immunoglobulin M (IgM) antibodies and Polymerase Chain Reaction (PCR) to detect three genes of Orientia, namely, 56 kDa, 16S rRNA, and groEL were done on these samples. The results of each test were analyzed to identify the test picking up maximum number of positive samples. Statistical analysis was performed using Chi-square test. The level of significance was set at p<0.05.

RESULTS

These tests showed that IgM ELISA (93%) and PCR (68%) picked up maximum number of positives. Statistical analysis performed using Chi-square test between the diagnostic assays showed that the p - value <0.001 was significant for IgM ELISA. Among the molecular markers, p-value was significant (<0.001) for groEL PCR. Further analysis of eschar positivity and duration of fever also showed that groEL PCR could detect DNA of the bacterium even in cases with 10 days of fever and this PCR was the best among the molecular markers used to detect the infection.

CONCLUSION

This study suggests that IgM detection by ELISA and conventional groEL PCR, either in combination or alone, depending on the duration of fever, would enhance the diagnosis of scrub typhus.

Molecular detection and groEL typing of Rickettsia aeschlimannii in Sardinian ticks

Rickettsia aeschlimannii is an emerging tick-borne pathogen of the spotted fever group Rickettsiae with considerable impact on both human and animal health. This study reports the molecular detection and groEL characterization of R. aeschlimannii in ticks collected from birds and ruminants in a typical Mediterranean environment. Phylogeny of R. aeschlimannii and species representative of the spotted fever and typhus groups based on the groEL gene is reconstructed for the first time. Results expand the knowledge on distribution and typing of emerging human tick-borne diseases in Sardinia and pave the way for future molecular epidemiology studies of zoonotic Rickettsiae.

Cultivation of Rickettsia amblyommii in tick cells, prevalence in Florida lone star ticks (Amblyomma americanum)

Background

Rickettsia amblyommii is a bacterium in the spotted fever group of organisms associated with the lone star tick (LST), Amblyomma americanum. The LST is the most commonly reported tick to parasitize humans in the southeastern US. Within this geographic region, there have been suspected cases of Rocky Mountain spotted fever (RMSF) where the causative agent, R. rickettsii, was not identified in the local tick population. In these areas, patients with clinical signs of RMSF had low or no detectable antibodies to R. rickettsii, resulting in an inability to confirm a diagnosis.

Methods

R. amblyommii was cultivated from host-seeking LSTs trapped in Central Florida and propagated in ISE6 (Ixodes scapularis) and AAE2 (A. americanum) cells. Quantitative PCR targeting the 17-kD gene of Rickettsia spp. identified the genus of the organism in culture. Variable regions of groEL, gtlA and rompA genes were amplified and sequenced to confirm the species. The prevalence of R. amblyommii in LSTs within the geographic region was determined by qPCR followed by conventional PCR and direct sequencing.

Results

Analyses of amplified sequences from the cultured organism were 100% homologous to R. amblyommii. The overall prevalence of Rickettsia spp. in the local population of LSTs was 57.1% and rompA sequence analysis identified only R. amblyommii in LSTs.

Conclusions

A Florida strain of R. amblyommii was successfully cultivated in two tick cell lines. Further evaluation of the new strain and comparisons to the other geographic strains is needed. The prevalence of this SFG organism in the tick population warrants further investigation into the organism’s ability to cause clinical disease in mammalian species.

Laboratory diagnosis and genotype identification of scrub typhus from Pinggu district, Beijing, 2008 and 2010

This study was conducted to determine the diagnosis and genotype of Orientia tsutsugamushi in Pinggu district, Beijing. Indirect immunofluorescence assay (IFA) was performed to detect O. tsutsugamushi-specific immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies. Nested polymerase chain reaction (PCR) and DNA sequencing analysis targeting the O. tsutsugamushi-specific groEL gene and 56 kDa protein gene were performed on whole-blood samples from scrub typhus patients. We confirmed that 47 patients were infected with scrub typhus in Pinggu district, Beijing. Representative sequences amplified by primers according to the groEL gene (BJ-PG-2008; GenBank accession No. JQ894502) and the 56 kDa protein gene (PG-56kDa; GenBank accession No. JX843795) both clustered with Kawasaki. PG-56kDa had sequence homology of 100% with TADY12-0308, shandong-XDM2, Neimeng-90, and sdu-1 and sequence homology of 96% with Kawasaki, Taguchi, Oishi, and Kanda. We confirmed the genotype of O. tsutsugamushi in Pinggu district, Beijing, as Kawasaki, and the patient in 2008 confirmed in this study was the first patient with confirmed scrub typhus in Beijing.

Diversity of the 47-kD HtrA nucleic acid and translated amino acid sequences from 17 recent human isolates of Orientia

Orientia tsutsugamushi, the etiologic agent of potentially fatal scrub typhus, is characterized by a high antigenic diversity, which complicates the development of a broadly protective vaccine. Efficacy studies in murine and nonhuman primate models demonstrated the DNA vaccine candidate pKarp47, based upon the O. tsutsugamushi Karp 47-kD HtrA protein gene, to be a successful immunoprophylactic against scrub typhus. To characterize 47-kD HtrA protein diversity among human isolates of Orientia, we sequenced the full open reading frame (ORF) of the 47-kD HtrA gene and analyzed the translated amino acid sequences of 17 patient isolates from Thailand (n=13), Laos (n=2), Australia (n=1), and the United Arab Emirates (UAE) (n=1) and 9 reference strains: Karp (New Guinea), Kato (Japan), Ikeda (Japan), Gilliam (Burma), Boryong (Korea), TA763, TH1811 and TH1817 (Thailand), and MAK243 (China). The percentage identity (similarity) of translated amino acid sequences between 16 new isolates and 9 reference strains of O. tsutsugamushi ranged from 96.4% to 100% (97.4% to 100%). However, inclusion of the recently identified Orientia chuto sp. nov. reduced identity (similarity) values to 82.2% to 83.3% (90.4% to 91.4%). These results demonstrate the diversity of Orientia 47-kD HtrA among isolates encountered by humans and therefore provide support for the necessity of developing a broadly protective scrub typhus vaccine that takes this diversity into account.

Use of DNA sequences for Rickettsia identification in Ixodes ricinus ticks: the first detection of Rickettsia monacensis in Poland

The cosmopolitan tick Ixodes ricinus inhabiting Europe, including Poland, is a vector for many pathogens, such as various Rickettsia species, which spread to new territories. They are present mainly in the Mediterranean countries, but have also been found in Central Europe at increasing frequency. In the present study, the gltA gene, encoding citrate synthase, and an internal transcribed spacer (ITS) were employed to detect the DNA and identify the species of tick-borne pathogens of the Rickettsia genus. The presence of bacterial DNA was detected in 9.5% of the examined I. ricinus individuals. Based on the nucleotide sequences of the analysed genomic fragments, most pathogens were identified as Rickettsia helvetica, while Rickettsia monacensis was revealed in one case. We have described for the first time, to our knowledge, the occurrence of this species in Poland. Both markers employed in the experiments were successful in species identification of R. helvetica. The newly described species R. monacensis may be identified by the protein-coding gene, but the ITS nucleotide sequences proved insufficient.

Simultaneous analysis of foodborne pathogenic bacteria by an oligonucleotide microarray assay

A rapid and accurate method for simultaneous identification of foodborne infectious pathogens was developed based on oligonucleotide microarray technology. The proposed identification method is based on PCR amplification of the target region of the groEL genes with degenerate primers, followed by the PCR products hybridization with oligonucleotide probes specific for species. The groEL gene amplification products of seventeen species of pathogenic bacteria were hybridized to the oligonucleotide array. Hybridization results were analyzed with digoxigenin-linked enzyme reaction. Results indicated that fifteen species of pathogenic bacteria showed high sensitivity and specificity for the oligonucleotide array, while two other species gave cross-reaction with the E. coli. Our results suggested that microarray analysis of foodborne infectious pathogens might be very useful for simultaneous identification of bacterial pathogens. The oligonucleotide array can also be applied to samples collected in clinical settings of foodborne infections. The superiority of oligonucleotide array over other tests lies on its rapidity, accuracy and efficiency in the diagnosis, treatment and control of foodborne infections.

Antigenic protein modifications in Ehrlichia

To develop effective vaccination strategies againstEhrlichia, we have previously reported developing an animal model of cross-protection in which C57BL/6 mice primed withE. muris were resistant to lethal infection withIxodes ovatus ehrlichia (IOE). Polyclonal antibody produced in mice after priming withE. muris and later injected with IOE-detected antigenic proteins inE. muris and IOE cell lysates. Cross-reaction of antigenic proteins was observed when we probed both theE. muris and IOE cell lysates with IOE andE. muris-specific polyclonal antibody. Analysis of the total proteins ofE. muris and IOE by two dimensional electrophoresis showed that bothE. muris and IOE have the same antigenic proteins. Finally, studies on post-translational protein modifications using a novel technique, Eastern blotting, showed thatE. muris proteins are more lipoylated and glycosylated than those of IOE.

A highly sensitive quantitative real-time PCR assay based on the groEL gene of contemporary Thai strains of Orientia tsutsugamushi

Partial nucleotide sequences (459 bp) of the groEL gene (encoding the 60-kDa heat shock protein, HSP60) from 23 contemporary isolates of Orientia tsutsugamushi isolated from patients with acute scrub typhus in Thailand were compared with 16 reference strain sequences to evaluate the potential of groEL as a conserved and representative target for molecular diagnostics.. Overall nucleotide identity within all available O. tsutsugamushi isolates (n = 39) was 98.8% (range: 95.0-100), reflecting a high degree of conservation; nucleotide identities were 67.5% and 65.6%, respectively, when typhus and spotted fever group rickettsiae were included.. A highly sensitive and quantitative real-time PCR assay was designed and evaluated using 61 samples, including buffy coats from patients in Thailand and Laos. Reliable and accurate quantitation of bacterial loads allows further investigation of other diagnostic methods and may lead to an improved understanding of the pathophysiology of acute scrub typhus, an important but under-recognized disease.

Simple, rapid and sensitive detection of Orientia tsutsugamushi by loop-isothermal DNA amplification

We present a loop-mediated isothermal PCR assay (LAMP) targeting the groEL gene, which encodes the 60kDa heat shock protein of Orientia tsutsugamushi. Evaluation included testing of 63 samples of contemporary in vitro isolates, buffy coats and whole blood samples from patients with fever. Detection limits for LAMP were assessed by serial dilutions and quantitation by real-time PCR assay based on the same target gene: three copies/microl for linearized plasmids, 26 copies/microl for VERO cell culture isolates, 14 copies/microl for full blood samples and 41 copies/microl for clinical buffy coats. Based on a limited sample number, the LAMP assay is comparable in sensitivity with conventional nested PCR (56kDa gene), with limits of detection well below the range of known admission bacterial loads of patients with scrub typhus. This inexpensive method requires no sophisticated equipment or sample preparation, and may prove useful as a diagnostic assay in financially poor settings; however, it requires further prospective validation in the field setting.

PCR-RFLP assay for species and subspecies differentiation of the Streptococcus bovis group based on groESL sequences

The sequence diversity of groESL genes among Streptococcus bovis group isolates was analysed, including five reference strains and 36 clinical isolates. Phylogenetic analysis of the groES and groEL sequences showed that the isolates that belonged to the same species or subspecies usually clustered together. The intergenic spacer region between groES and groEL was variable in size (67–342 bp) and sequence and appeared to be a unique marker for species or subspecies determination. Sequence similarities of the groESL genes among species and subspecies ranged from 84.2 to 99.0 % in groES, and from 88.0 to 99.0 % in groEL. Based on the sequences determined, a Streptococcus bovis group-specific PCR assay was developed, which may provide an alternative means of distinguishing the bovis group from other viridans streptococci. Restriction digestion of the amplicon with AclI further differentiated the species and subspecies.

Extensive genetic recombination occurs in the field between different genotypes of Ehrlichia ruminantium

The intracellular bacterium Ehrlichia ruminantium is the causative agent of heartwater throughout sub-Saharan Africa, Madagascar, and some islands of the Caribbean. The disease is tick-borne and causes substantial livestock losses, threatening food security and productivity in both the commercial and small-scale farming sectors in endemic areas. Immunization by infection and treatment is currently practised in South Africa, and it is known that a variety of immunotypes of the organism occur in the field, and that cross-protection between them varies widely from total to minimal. Future vaccines may therefore need to incorporate components from different genotypes so it is essential to have information on the extent of genetic variation among isolates. To obtain this information we amplified and sequenced a panel of eight core function genes from 12 different cultured stocks originally isolated in different areas of Africa and the Caribbean. Phylogenetic trees inferred from the sequences yielded different branching orders for different genes, and the reason for this inconsistency appears to be that extensive recombination takes place between different genotypes in the field. It is possible that recombination occurs during the period when the organisms are extracellular within the tick, immediately after feeding and before intracellular infection is established, although detection of more than one genotype in DNA from single ticks is encountered infrequently. The results of the analysis show that the phylogenetic variation is greatest among the isolates of southern African origin, suggesting that this is the region where the parasite first evolved. It also appears likely that the Gardel genotype, isolated in the Caribbean, originally came from west central Africa, not from west Africa as had long been assumed.

Species-level identification of clinical staphylococcal isolates based on polymerase chain reaction--restriction fragment length polymorphism analysis of a partial groEL gene sequence

A pair of degenerate primers that amplified, by polymerase chain reaction (PCR), a partial groEL gene sequence (550 bp) was used for the identification of the 12 most common human staphylococcal pathogens. The amplified products were digested by AluI endonuclease, and distinctive PCR restriction fragment length polymorphism (RFLP) patterns for reference strains were obtained. This protocol was validated by the identification of 89 clinical staphylococcal isolates, and the results were compared with those obtained by the reference biochemical identification, showing 100% concordant results. Two species, Staphylococcus aureus and Staphylococcus lugdunensis, showed intraspecies polymorphisms on their PCR-RFLP patterns. All strains were also identified using the API Staph ID test (bioMérieux, Durham, NC) and the MicroScan WalkAway automated system (Dade Behring, West Sacramento, CA). When 17 Staphylococcus isolates were tested in a blind experiment by the PCR-RFLP of the groEL gene method, all strains were also correctly identified. We propose the PCR-RFLP of the groEL gene with AluI as a reliable and reproducible method for identification of Staphylococcus spp.

Contribution of polymorphisms in ankA, gltA, and groESL in defining genetic variants of Anaplasma phagocytophilum

Analysis of several nucleotide polymorphisms in polymorphic genes (ankA, gltA, and groESL) from 16S rRNA gene-based genetic variants of Anaplasma phagocytophilum from dogs in the western United States defined at least two sets of multigene polymorphisms to further characterize these variants. The multigene polymorphism approach holds promise for development of a genotyping scheme for this important pathogen.

Differentiation of Anaplasmataceae through partial groEL gene analysis

The nucleotide sequences (287 bp) of the partial groEL gene from 14 reference strains of Anaplasmataceae were determined and compared. A partial groEL gene is useful for the identification and characterization of Anaplasmataceae, in spite of its short nucleotide sequences.

Differentiation of Mycobacterium species by analysis of the heat-shock protein 65 gene (hsp65)

The nucleotide sequences (604 bp) of partial heat-shock protein genes (hsp65) from 161 Mycobacterium strains containing 56 reference Mycobacterium species and 105 clinical isolates were determined and compared. hsp65 sequence analysis showed a higher degree of divergence between Mycobacterium species than did 16S rRNA gene analysis. Generally, the topology of the phylogenetic tree based on the hsp65 DNA sequences was similar to that of the 16S rRNA gene, thus revealing natural relationships among Mycobacterium species. When a direct sequencing protocol targeting 422 bp sequences was applied to 70 non-tuberculous mycobacterium (NTM) clinical isolates, all NTMs were clearly identified. In addition, an XhoI PCR restriction fragment length polymorphism analysis method for the differentiation of Mycobacterium tuberculosis complex from NTM strains was developed during this study. The results obtained suggest that 604 bp hsp65 sequences are useful for the phylogenetic analysis and species identification of mycobacteria.

Identification of clinically relevant enterococcus species by direct sequencing of groES and spacer region

We determined the groESL sequences (groES, groEL, and the intergenic spacer) of 10 clinically relevant Enterococcus species and evaluated the feasibility of identifying Enterococcus species on the basis of these sequences. Seven common clinical Enterococcus species, E. faecalis, E. faecium, E. casseliflavus, E. gallinarum, E. avium, E. raffinosus, and E. hirae, and three less common Enterococcus species, E. cecorum, E. durans, and E. mundtii, were examined in this study. We found that the groES genes of these enterococcal species are identical in length (285 nucleotides) and contain an unusual putative start codon, GTG. The lengths and sequences of the intergenic regions (spacers between the groES and groEL genes) are quite variable (17 to 57 bp in length) among Enterococcus species but are conserved in strains within each species, with only a few exceptions. Considerable variation of groES or groEL sequences was also observed. The evolutionary trees of groES or groEL sequences revealed similarities among Enterococcus species. However, the overall intraspecies variation of groES was less than that of groEL. The high interspecies variation and low intraspecies variation indicate that the groES and spacer sequences are more useful than groEL for identification of clinically relevant Enterococcus species. The sequences of these two genetic traits, groES and spacer, can be determined by a single PCR and direct sequencing and may provide important information for the differentiation of closely related species of Enterococcus.

Phylogenetic analysis and PCR-restriction fragment length polymorphism identification of Campylobacter species based on partial groEL gene sequences

The phylogeny of 12 Campylobacter species and reference strains of Arcobacter butzleri and Helicobacter pylori was studied based on partial 593-bp groEL gene sequences. The topology of the phylogenetic neighbor-joining tree based on the groEL gene was similar to that of the tree based on the 16S rRNA gene. However, groEL was found to provide a better resolution for Campylobacter species, with lower interspecies sequence similarities (range, 65 to 94%) compared with those for the 16S rRNA gene (range, 90 to 99%) and high intraspecies sequence similarities (range, 95 to 100%; average, 99%). A new universal reverse primer that amplifies a 517-bp fragment of the groEL gene was developed and used for PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of 68 strains representing 11 Campylobacter species as well as reference strains of A. butzlerii and H. pylori. Digestion with the AluI enzyme discriminated all Campylobacter species included in the study but showed more intraspecies diversity than digestion with the ApoI enzyme. A hippurate-negative variant of Campylobacter jejuni with a high level of groEL sequence similarity to both C. jejuni (96%) and C. coli (94%) gave a unique AluI profile and an ApoI profile identical to those of other C. jejuni strains. In conclusion, groEL gene sequencing and PCR-RFLP analysis are recommended as valuable tools for the identification of Campylobacter species.

Fatal Nocardia farcinica bacteremia in a patient with lung cancer

Nocardia farcinica is an emerging pathogen in immunocompromised patients, accounting for approximately 20% of Nocardia clinical isolates in various countries. A case of fatal N. farcinica bacteremia in a 52-year-old man with lung cancer is described. He was admitted with severe respiratory distress, and despite the early onset of empirical antibiotic treatment, he failed to respond and died of septic shock 24 hours later. N. farcinica was isolated from blood cultures obtained at hospital admission and was identified by conventional methods. Strain identification was confirmed by nucleotide sequencing of the 16S rRNA gene. N. farcinica bacteremia is a life-threatening infection. Because of the actinomycete's highly-resistant antibiotic profile, early identification and antibiotic susceptibility testing are necessary to improve the chances of survival.