Department of Veterinary Pathology, Faculty of Veterinary Sciences, University of Liverpool, Neston, Cheshire CH64 7TE,1 Respiratory and Systemic Infection Laboratory, Public Health Laboratory Service, Central Public Health Laboratory, London NW9 5HT, United Kingdom,3 Unité des Rickettsies, Faculté de Médecine, 13385 Marseille, France,2 Instituto de Medicina Tropical Alexander Von Humboldt, Universidad Peruana Cayetano Heredia,4 Instituto de Medecina Tropical Daniel A. Carrion, Universidad Nacional Mayor de San Marcos,5 Instituto Nacional de Salud, Lima, Peru6
Received 7 February 2002/ Returned for modification 10 April 2002/ Accepted 13 July 2002
| ABSTRACT |
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| INTRODUCTION |
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Although most text books state that, classically, verruga peruana occurs in patients who have suffered and recovered from Oroya fever, this progression is, in fact, just one of several possible disease courses. Severe Oroya fever is rarely seen among the population in regions of endemicity, but verruga peruana is common (17). In areas of nonendemicity, Oroya fever appears to be more common (13, 24), although this is not always the case (15). The basis for these observations has been proposed as either variation in host immunity (24) (although the immunological parameters of patients have never been assessed) or variation in pathogenicity between B. bacilliformis strains (15). In addition to these overt clinical manifestations, asymptomatic infections have also been frequently encountered, supporting the idea that humans are maintenance hosts for the bacterium (13, 15, 25). A recent serological survey of healthy volunteers living in an area of bartonellosis endemicity found that 45% of 387 people tested were seropositive for Bartonella antibodies (5), further corroborating the view that infection by B. bacilliformis is common.
Outbreaks of bartonellosis not only continue in recognized regions of endemicity but are also now being reported with increasing frequency in areas where the disease has not previously been encountered (8, 15). The public health impact of bartonellosis in these areas is at least as significant as it is in regions of endemicity. For example, a survey of 554 individuals (55% of the population) living in a new focus of bartonellosis in the north of Peru found that 77% had serological evidence of B. bacilliformis infection (15). Furthermore, the proportion of this community who suffered overt symptoms was remarkably high, with 14% developing Oroya fever and 18% developing verruga peruana.
Despite being recognized for almost 100 years, B. bacilliformis remains little studied, and fundamental issues regarding the epidemiology of bartonellosis remain unanswered. It is therefore extremely timely to exploit some of the new microbiological methods described for the characterization and epidemiological surveillance of B. henselae and B. quintana for the study of B. bacilliformis. For the first time, this report compares the genotypes of clinical isolates of B. bacilliformis obtained from patients in different regions of Peru and on different dates. Bacterial typing was achieved using a combination of established sequence comparison-based methods (3, 19, 20) and a sensitive PCR-based pan-genomic sampling method, amplified fragment length polymorphism (AFLP) analysis (23).
| MATERIALS AND METHODS |
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Bacterial isolates. A total of 26 isolates of B. bacilliformis were included in the study. The sources of these isolates, together with their date of isolation, are presented in Table 1. The isolates CON600-1 and Cond044 were kindly provided by Larry Laughlin and Judith Chamberlin of the Uniformed Services University of the Health Sciences, Bethesda, Md.
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DNA extraction, PCR amplifications, and nucleotide sequence determinations. Crude DNA extracts, suitable for use as templates in PCR-based amplification reactions, were prepared from sweeps of bacterial colonies using the QIAamp DNA extraction kit (Qiagen, Crawley, West Sussex, United Kingdom) by following the manufacturer's instructions. Each extract was then incorporated into two previously described PCRs. A citrate synthase gene (gltA) fragment was amplified using a Bartonella-specific PCR incorporating the primer pair 443f-1137r (3, 19) as previously described (3). The complete intergenic spacer region (ISR) between the 16S and 23S rRNA genes was amplified using a broad-spectrum PCR incorporating the primer pair 16S1386f-23S115r (7, 16). Each 50-µl reaction mixture contained 2 µl of each primer at 10 pmol/µl, 2 µl of DNA extract, 25 µl of 2x extensor PCR mastermix (ABgene, Epsom, United Kingdom), and 19 µl of sterile distilled water. The thermal cycle consisted of an initial denaturation at 96°C for 3 min, followed by 40 cycles of denaturation at 96°C for 10 s, primer annealing at 48°C for 20 s, and primer extension at 72°C for 40 s. The program was completed with a stage at 72°C for 6 min. The success of each PCR was gauged by UV visualization of ethidium bromide-stained 1% agarose gels on which 10 µl of each amplification product had been electrophoretically resolved.
Amplification products were purified for use as templates in nucleotide base sequencing reactions using the QIAquick purification kit (Qiagen) according to the manufacturer's instructions. Cycle sequencing reactions were prepared using the dRhodamine terminator cycle sequencing ready reaction kit (Perkin-Elmer, Warrington, United Kingdom) according to the manufacturer's instructions. Reactions for gltA analysis incorporated the primers used in the initial amplification reactions. Reactions for ISR analysis incorporated the primers used in initial PCRs together with the previously described QHVE1 and QHVE3 (20). The thermal program employed for all sequencing reactions was 30 cycles of 95°C for 20 s, 50°C for 10 s, and 60°C for 4 s. Reaction products (10 µl) were mixed with 74 µl of 70% ethanol-0.5 M MgCl2, and, after being held for 1 h at 4°C, precipitating DNA was collected by centrifugation at 14,000 x g for 12 min. DNA pellets were dried and resuspended in 3 µl of a 5:1 mixture of formamide-1% dextran blue and 0.025 M EDTA. Purified products were resolved on a 5% denaturing acrylamide gel (Long Ranger Singel 377-36; FMC Bioproducts, Rockland, Maine), and sequence data were captured and prepared using an ABI 377 automated sequencer and related software (Perkin-Elmer).
AFLP analysis. Genomic DNA suitable for use as a template in the PCR was extracted with the Nucleon genomic DNA extraction kit (GeneSys Biotech Ltd., Coatbridge, Strathclyde, United Kingdom). DNA concentration was determined spectrophotometrically by measuring the absorbance at 260 nm. The AFLP method used here is based on the Standard European Working Group on Legionella Infections protocol (9) but uses the selective primer PstI-C. Restriction-ligation reactions were performed at 37°C for 3 h in a total volume of 20 µl. Each mix comprised approximately 1.5 µg of genomic DNA, 200 ng of each adapter-oligonucleotide (AFLP-LG1, 5'-CTCGTAGACTGCGTACATGCA-3'; AFLP-LG2, 5'-TGTACGCAGTCTAC-3'), 20 U of PstI (Boehringer Mannheim GmbH, Mannheim, Germany), 1 U of T4 DNA ligase (Boehringer), and 1x ligation buffer (10x ligation buffer is 660 mM Tris [pH 7.5], 50 mM MgCl2, 10 mM dithiothreitol, 10 mM ATP; Boehringer). Prior to the PCR, tagged DNA fragments were precipitated using a final concentration of 2.5 M ammonium acetate in 100 µl and an equal volume of absolute ethanol. After incubation for 5 min at room temperature, centrifugation was carried out at 12,000 x g for 10 min, and the pellet washed once with 70% ethanol. The precipitate was air dried and resuspended in 100 µl of TE buffer (10 mM Tris, 1 mM EDTA [pH 8.0]). Before the PCR a 1-in-100 dilution of the resuspended DNA was prepared, and 5 µl of this dilution was used as a template DNA in the PCR. PCR was performed in a reaction mixture of 25 µl using the Ready-To-Go PCR beads (0.5-ml format; Amersham Pharmacia Biotech). Each reaction mixture comprised template DNA and 75 ng of selective primer (AFLP-PstI-C, 5'-GACTGCGTACATGCAGC-3'), and the magnesium concentration was adjusted to 2.5 mM MgCl2. Amplification was performed using the following parameters: initial denaturation at 94°C for 4 min followed by 33 cycles of denaturation at 94°C for 1 min, annealing at 60°C for 1 min, and elongation at 72°C for 2.5 min. Amplified products (20 to 40% of the reaction mix; i.e., 5 to 10 µl) were separated by electrophoresis on 1.5% agarose (UltraPure agarose; Life Technologies) gels in 1x TBE (0.089 M Tris-borate, 1 mM EDTA) for 4 h at 3.5 V/cm. The MBI Fermentas (Sunderland, United Kingdom) Ladder mix (catalog no. SM0331) was used as molecular size markers (at 0.75 to 1.0 µg/lane). To aid normalization of the gels each sample lane was adjacent to a marker lane. Gels were stained with ethidium bromide (0.5 to 1.0 µg/ml) for 30 min and photographed under UV transillumination using Polaroid film 667 (Sigma).
Data analysis. Black-and-white photographs of the gels were scanned with a ScanMaker (Microtek Lab) into Adobe Photoshop with 256 levels of grey and 400 dpi. The resultant TIFF files were then analyzed using BioNumerics software (version 2.5; Applied Maths BVBA, Sint-Martens-Latem, Belgium). AFLP patterns were analyzed using the clustering (curve based) option (Pearson correlation) with the unweighted pair group method with averages method. Percentage similarity thresholds were used to divide the output from the dendrograms into types.
ISR sequences were assembled using Align Plus 4 (Scientific and Educational Software, Durham, N.C.). An alignment of complete sequence data was made, and a matrix of uncorrected distances was calculated (BioNumerics). A relatedness dendrogram was derived using neighbor-joining analysis, and bootstrapping of this data was performed using 1,000 replications (BioNumerics).
Statistical methods. Determination of the limitation of the sample size in estimating the diversity of B. bacilliformis genotypes present in the areas surveyed was based on a binomial probability distribution (26). From this analysis, the probability that the new foci of bartonellosis were caused by strains extant at an undetected, low prevalence in the zone of endemicity could also be estimated.
Nucleotide sequence accession numbers. The five new ISR sequences have been deposited in GenBank under the indicated accession numbers: LA6.3, AJ422181; Monz-269, AJ422182; CON600-01, AJ422179; Cusco407, AJ422180; ER-Yal, AJ422178.
| RESULTS |
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ISR analysis. Complete ISR sequences were obtained for all 26 isolates of B. bacilliformis. All ISR sequences possessed a general structure very similar to that previously described for the ISR of the type strain. All contained genes encoding isoleucine tRNA and alanine tRNA that were separated by a centrally located variable region of approximately 120 bp and that were flanked by regions of approximately 300 bp. All sequences also contained previously described direct and inverted repeats (18). The sequences of both tRNA genes were identical in all isolates tested. Alignment and comparison of the 26 sequences revealed six variants. These different sequences varied in length as well as base sequence, ranging from 887 to 933 bp. The distribution of the six ISR genotypes among the 26 isolates is presented in Table 1, and the details of the differences between them are presented in Table 2. The shortest sequence was that obtained for the three isolates that possessed gltA heterogeneity. This sequence did not contain a 19-bp fragment present in the inter-tRNA gene region of the other five ISR genotypes. The longest sequences were those obtained from isolates from Urubamba and Monzon. These strains contained a 25-bp fragment lying between the two inverted repeat sequences towards the 3' end of the ISR which was not present in other isolates tested. Compared to the ISR of the KC583 type strain, the isolates that bore the 25-bp insert and the isolates from Pisuquia also possessed two point insertions at 110 and 114 bp from the 5' end of the ISR. On the same comparison, the ISR of the isolate CON600-01 and the three isolates obtained from the collection of the Institut Pasteur had a single base deletion at 267 bp from the 5' end of the sequence. In addition to these insertion-deletion events, the six ISR genotypes differed by numerous base substitutions, as detailed in Table 2. Analysis of the single-nucleotide polymorphisms (SNPs) among the six ISRs indicated that isolates from Monzon, Urubamba, and Pisuquia differed from one another by fewer than 6 SNPs but differed from all other genotypes by more than 12 SNPs. Two of the genotypes associated with isolates from the zone of endemicity for bartonellosis differed by 6 SNPs but differed by more than 12 SNPs from other genotypes. The ISR of the gltA variant isolates differed by 20 or more SNPs compared with all other ISRs.
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A total of 17 B. bacilliformis isolates used in this survey were recovered from individuals living in the zone of endemicity for bartonellosis. Based on a binomial probability distribution analysis, only genotypes occurring at a prevalence of 16.2% or more among the B. bacilliformis population in the zone of endemicity would be 95% likely to be present in a sample of this size. However, the maximum probability that three genotypes with a cumulative prevalence of less than 16.2%, rather than more prevalent genotypes, were independently introduced from the zone of endemicity into the three sites where new foci of bartonellosis occurred was only 1.6 x 10-4 (maximum probability occurs when the three genotypes are at an equal [5.4%] prevalence).
| DISCUSSION |
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As has been observed for other Bartonella species, ISR sequence comparison proved to be a markedly more sensitive approach to strain differentiation than gltA analysis (2, 20). The nature of the variation between the six different ISR sequences encountered was interesting. The presence of direct repeats in the ISR of other Bartonella species has been noted, and different isolates of the same species have been found to possess various numbers of these features (2). The application of an approach similar to the AFLP analysis described herein for the differentiation of Bartonella species has been previously reported (12). These studies highlighted the practicality of this approach, in relation to arbitrary PCR methods or macrorestriction analysis using pulsed-field gel electrophoresis (21), for the study of fastidious organisms such as bartonellae, and our use of the approach on B. bacilliformis supports these findings. The general consensus of pan-genomic sampling, as determined by AFLP analysis, and DNA sequence comparison is very satisfying considering the current concern regarding the relative value of these two approaches in phylogenetic, population genetic, or epidemiological studies (10). For such studies, the use of multilocus sequence comparison circumvents the potential pitfalls associated with relying solely on analysis of a single genetic locus in determining an accurate genetic identity for bacterial strains. However, reliance solely on comparison of sequences, even at several loci, ignores the importance of genomic rearrangement in shaping the genetic character of a bacterium. A combination of gene sequence analysis and an assessment of the overall genomic architecture of a bacterium should, therefore, serve as a practical means of sampling genotype, providing accurate and sensitive differentiation between strains.
The relatively small scale of this study dictates that any conclusions drawn from the comparison of B. bacilliformis genotypes and the epidemiological data available for the isolates should be considered with care. For example, the number of isolates surveyed from the zone of endemicity was such that we could only be confident of encountering genotypes that occurred at a prevalence of >16%. Nonetheless, our study yielded several observations from which noteworthy conclusions can be drawn. The three recent outbreaks of bartonellosis that occurred in Urubamba, Pisuquia, and Monzon, where the disease had not previously been known, were each caused by a unique genotype of B. bacilliformis and not by the genotype most often encountered in the region of Peru where bartonellosis is considered to be endemic. For each outbreak, all isolates obtained possessed the same genotype, indicating the epidemicity of the disease in each area. Even in the bartonellosis-endemic region, genotypic differences were observed. However, the most frequently encountered genotype was identified among isolates from patients from seven different locations in this region ranging from Churcampa in the south to Sihuas, which is over 600 km further north. Furthermore, as isolates collected more than 40 years ago also possessed this genotype, there appears to be a good degree of genetic stability among this bacterial population.
The basis for the apparent recent spread of bartonellosis into new areas of Peru remains unknown. Indeed, it may be foolhardy to assume that all new foci have appeared for the same reason. Our demonstration of genetic diversity among B. bacilliformis isolates associated with the new foci suggests that, rather than strains being introduced into the areas where these occurred, discrete populations of the species already existed. Such a hypothesis is supported by the demonstration that, even if the genotypes associated with new foci of infection were present at a low prevalence in the zone of endemicity, the likelihood that the new foci resulted from the chance introduction of these genotypes, and not those encountered at a higher prevalence, from the zone of endemicity was negligible. The possibility that B. bacilliformis populations can exist in areas where clinical bartonellosis is absent is intriguing and revives suspicion of nonhuman maintenance hosts. Equal intrigue surrounds the factors that underlie the appearance of bartonellosis in these areas. As recent vagaries in the epidemiologies of several infectious diseases in Peru and the South Pacific region have been associated with the El Niño phenomenon (6, 11), this climatic event may also have modulated changes in the epidemiology of bartonellosis.
The apparent variations in bartonellosis-related morbidity and mortality associated with different outbreaks of the disease have been previously highlighted. Specifically, Kosek and colleagues (15) hypothesized that the B. bacilliformis strain implicated in the disease focus they investigated may have possessed diminished virulence. Interestingly, the clinical observations supporting this hypothesis were also noted among patients in the Pisuquia outbreak, namely, that blood smears revealed an uncharacteristically low level of bacteremia and no patients developed a fulminant hemolytic disease (E. Sanchez, unpublished observations). Kosek and colleagues (15) suggested that strain differences may, in part, account for this disparity and called for further studies to address strain heterogeneity. Our study is the first to answer this request and to demonstrate that isolates derived from asymptomatic patients (CON600-01 and Cusco407) were indistinguishable from those causing overt disease.
Although this study has provided fundamental information regarding the epidemiology of bartonellosis in Peru, its findings have provoked questions rather than provided answers. Considerable work in this field is clearly necessary to improve our understanding of a disease of significant and increasing public health importance in the Andean region of South America.
| ACKNOWLEDGMENTS |
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R. J. Birtles is supported by a Wellcome Trust Medical Microbiology Research Fellowship.
| FOOTNOTES |
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