Development of a Multiple-Locus Variable number of tandem repeat Analysis (MLVA) for Leptospira interrogans and its application to Leptospira interrogans serovar Australis isolates from Far North Queensland, Australia

Leptospirosis, is the zoonotic disease caused by the spirochete Leptospira. Leptospirosis is characterised either as a febrile illness with sudden onset, or a 'flu like' illness. Patients present with chills, headaches, myalgia, and abdominal pain. In addition, patients may present with renal and pulmonary complications. It is considered an emerging infectious disease with large documented outbreaks occurring world-wide [2]. The majority of isolates detected in Queensland, Australia belong to the genomospecies, L. interrogans, with the dominant serovars being Zanoni or Australis. Typically Leptospirosis infections in Queensland are a result of occupational exposure with the majority of cases occurring in farming or animal based industries [3].

The genus Leptospira contains 17 genomospecies as shown by DNA-DNA hybridisation [4]. Under the current genotypic classification system, pathogenic and non pathogenic serovars may reside within the same genomospecies [2]. Many animals both domesticated and native serve as the reservoir for this bacterium. Leptospires are shed into the environment via the urine of these animals, where they survive in the soil or freshwater. Human infections result from contact with the contaminated soil/water or from direct contact with animals or their infectious body fluids [5].

Epidemiological investigation of this organism is important for the ability to distinguish individual cases from related cases such as in an outbreak situation. Also of importance is determining which animal is the likely common source of the infection, as containing or preventing the spread of the vector is paramount to controlling the disease.

Molecular typing methods have been described for L. interrogans including Randomly Amplified Polymorphic DNA (RAPD) [6–9], Pulsed Field Gel Electrophoresis (PFGE) [10], Arbitrarily Primed PCR (AP-PCR) [11, 12] and most recently Fluorescent Amplified Fragment Length Polymorphism (FAFLP) [13]. Each of these methods have their disadvantages such as insufficient discriminatory power, poor inter-lab and intra-lab reproducibility, difficulties with database and dissemination of data [14]. They may also require specialised equipment such as DNA sequencers or contour-clamped homogeneous electric field electrophoresis systems. In addition leptospires have their own particular problems when using the above methods, the fastidious nature of the organism does not easily allow for the large volume of culture material required for PFGE and cultures can be quite prone to contamination with other bacteria, which may influence the accuracy of low stringency PCR methods or AFLP. As an alternative to the above methods, investigation of Variable Number of Tandem Repeats (VNTR) has been described for various organisms. These include Salmonella enterica [14, 15], Staphylococcus aureus [16], Yersinia pestis [17], Mycobacterium tuberculosis [18], Francisella tularensis [19], Legionella pneumophila [20], Brucella spp. [6, 21], Escherichia coli O157:H7 [22]and Borrelia spp[23]. VNTR are repeated DNA sequences of varying copy number. They are caused by slipped strand mispairing during DNA replication [24, 25]. VNTRs can provide information relating to both the evolutionary and functional areas of bacterial diversity[25]. The ability to detect VNTRs in micro-organisms has been greatly enhanced by the availability of whole genomic sequences and software that can search for VNTR loci from these sequences. 1, [26, 27] Once these polymorphisms are located, flanking primers can then be designed to amplify these variable length regions thus allowing differentiation of copy numbers using the size of the resultant amplicon. This can be done using standard agarose gel electrophoresis and if a higher resolution is required, fluorescent labelling and fragment sizing via a DNA sequencer can be used. VNTR is therefore applicable to a wide range of laboratories, including those which may have simple equipment such as thermal cyclers and agarose gel electrophoresis but do not have access to sophisticated equipment such as DNA sequencers. Furthermore when VNTR is applied to multiple loci as a typing scheme such as in Multiple Locus VNTR Analysis (MLVA) greater discriminatory power and more accurate determination of genetic relatedness is achieved [17, 19, 28, 29]. Recently Majed et al [30]described a MLVA typing scheme for L. interrogans Sensu Stricto, this research highlighted the value of using VNTR as a typing scheme but was limited to the identification of serovar by comparing the size of the repeat to that of known reference strains. It should be noted that in that study several reference strains had identical VNTR patterns including serovars Australis and Bratislava, serovars Copenhageni and Icterohaemorragiae and serovars Romanica and Wolffi. It was subsequently validated against a small number of clinical isolates. In this paper, we report on the development of a MLVA scheme using novel VNTR loci selected from the sequence of a published L. interrogans genome [1] and evaluate its usefulness as a phylogenetic typing method using reference strains and clinical isolates from Far North Queensland, Australia.

The MLVA assay presented was easy to perform and analyse, as it consisted of six individual PCR reactions and agarose gel electrophoresis. Selected reference strain isolates were run in tandem during the initial evaluation by different individuals to assess reproducibility, each time they displayed identical fragment sizes as determined by sequencing and agarose gel electrophoresis (data not shown). Dilutions of the template DNA were used to evaluate whether the fragment sizes were template concentration dependant. Dilutions of 1:10 and 1:100 did not effect fragment size but did result in reduced PCR product yield (data not shown). The MLVA assay was proven to be reproducible under varying laboratory conditions. The two limitations of this assay are firstly the use of agarose gel electrophoresis to separate fragments for allelic sizing, due to inherent inaccuracies of this method to size bands of close molecular weights given that the resolution is dependant on agarose composition and concentration and secondly in rounding partial repeat copy numbers to the nearest whole number to make the data analysis easier, isolates that had partial repeats were treated as if they contained whole repeats. As illustrated in Additional file 1, by simplifying the repeat copy numbers we have artificially reduced the resolution of the method and its ability to distinguish between closely related strains that may only vary by a partial repeat at one or more of the loci.

The diversity index calculated for each locus suggests that the loci selected are of highly polymorphic nature and therefore have greater discriminatory power between similar strains than loci with a lower diversity indexes would have. Whilst it has been previously reported in organisms such as Francisella tularensis [19] and Yersinia pestis [29] that higher copy repeat numbers may confer higher allelic variability, it was not demonstrated with this study. This may be due to the loci having similar repeat copy sizes (36–47 bp) with the exception of locus V27 with a repeat size of 138 bp. The lack of amplification from loci V8, V27, V29, V36 and V50 from certain reference strains may be due to sequence diversity in the flanking regions up or downstream from the repeat regions or the lack of the VNTR loci all together. Further investigations using isolates of these serovars is needed to determine whether there is sufficient diversity in the remaining loci for it to be valid as a typing method. In the study by Majed et al. [30], they noted from the dendrogram that the isolates had clustered into distinct global geographical regions. Interestingly in this study, we found that the dendrogram showed no bias towards this global geographical clustering of reference strains.

The different genomospecies of Leptospira were not used in the selection and development of the VNTR loci for this typing scheme. The basis for this decision was that the other genomospecies are considered to be significantly different from L. interrogans based upon DNA-DNA Hybridisation [32, 33] and may not possess the same primer binding sites or indeed the same VNTR loci. In addition due to the use of a serologically based Leptospiral taxonomy system, several serovars belong to more than one genomospecies [32, 33], thus it would be doubtful that the MLVA typing scheme described in this article would be useful in determining the genomospecies of these related serovars due to the significant genetic differences[34]

When the MLVA assay was applied to L. interrogans serovar Australis isolates collected from 1995 to 2004, the six selected loci appeared to show less diversity. This could be due to the fact that the isolates were taken from within a limited geographical area of Far North Queensland. Despite this apparent limited diversity, the phylogenetic analysis revealed several large albeit weakly linked clusters. All of these clusters contained a mixture of hosts, and it would be possible to speculate that the transmission of serovar Australis to humans in that area is via the native rodent population indigenous to that area. Another possible risk whilst not proven in Australia, is that transmission of the organism may occur via canines to humans [2]. Indeed in this study the two strains isolated from canines are genetically similar to two strains isolated from humans. Also of interest, the reference culture for serovar Australis; strain Ballico which was isolated from a patient in North Queensland in 1934, shows homology with LT958 and QHR371A a human and Rattus sordidus isolate respectively, both from the Tully region. Further investigations using MLVA of isolates, could add further detail to the depth of knowledge into the population of serovar Australis and to determine other possible transmission sources to humans.

Further improvements to this method are possible to increase both practicality and discriminatory power for typing of L. interrogans isolates. These improvements could include the use of fluorescently labelled primers and fragment analysis using a DNA sequencer to accurately assign repeat sizes. Multiplexing of the six targets would rationalise the number of PCR reactions needed to complete the MLVA and would also decrease costs in terms of reagents and labour. Improvements that could be introduced to the analysis of the data may include using an allele designation system as described by Lindstedt et al [34]. In addition to improving the method, comparisons between other molecular typing methods such as FAFLP or a sequence based typing scheme, would ultimately determine the validity of the MLVA assay as molecular epidemiology tool for L. interrogans.

The method has potential application in furthering the understanding of Leptospiral molecular epidemiology. As this method can be performed without specialised equipment, a broader range of laboratories including those in developing countries could potentially use this scheme as part of their isolate typing. This method was also easily standardised within our laboratory, with multiple users and different thermal cyclers employed to achieve the same results. This level of standisation at an inter laboratory level would allow the transfer of the method into another laboratory more effectively than that of a method that was operator or equipment specific. The simplification of MLVA data into a concise and portable numerical format as suggested in this article makes it easier to be comprehended by non-technical staff such as public health authorities. In addition, the format of allele data is similar to the allele string that is used for Multiple Locus Sequence Typing (MLST). As an alternative to using Bionumerics, software freely available on the internet such as Sequence Type Analysis and Recombinational Tests (START) http://pubmlst.org/software/analysis/[35] could be used for the phylogenetic analysis. Bionumerics was ultimately selected over START due to the advanced features of Bionumerics including evolutionary and population modelling.

Further assessment of L. interrogans isolates globally is required to confirm that the selected VNTR loci possess sufficient diversity to be used a typing scheme on an international level.