Insight into diversity of bacteria belonging to the order Rickettsiales in 9 arthropods species collected in Serbia.

Rickettsiales bacteria in arthropods play a significant role in both public health and arthropod ecology. However, the extensive genetic diversity of Rickettsiales endosymbionts of arthropods is still to be discovered. In 2016, 515 arthropods belonging to 9 species of four classes (Insecta, Chilopoda, Diplopoda and Arachnida) were collected in Serbia. The presence and genetic diversity of Rickettsiales bacteria were evaluated by characterizing the 16S rRNA (rrs), citrate synthase (gltA) and heat shock protein (groEL) genes. The presence of various Rickettsiales bacteria was identified in the majority of tested arthropod species. The results revealed co-circulation of five recognized Rickettsiales species including Rickettsia, Ehrlichia and Wolbachia, as well as four tentative novel species, including one tentative novel genus named Neowolbachia. These results suggest the remarkable genetic diversity of Rickettsiales bacteria in certain arthropod species in this region. Furthermore, the high prevalence of spotted fever group Rickettsia in Ixodes ricinus ticks highlights the potential public health risk of human Rickettsia infection.

Introduction

The order Rickettsiales, belonging to the class Alphaproteobacteria, represents a rather diverse group of endosymbiotic gram-negative bacteria. The order Rickettsiales comprises of two established families, Anaplasmataceae, Rickettsiaceae, and 2 tentative families, Candidatus Holosporaceae and Candidatus Midichloriaceae[1,2]. Within the order, bacteria from the genera Rickettsia, Ehrlichia, Anaplasma and Candidatus Neoehrlichia are the most studied due to their known pathogenicity to animals and humans. They are strikingly widespread in various hosts of different kingdoms, including Animalia (arthropods and vertebrates), Protista and even Plantae[2-4]. Nevertheless, along with vertebrates, arthropods are considered to be among the primary hosts for most members of the order Rickettsiales. For the genera Rickettsia, Anaplasma, Ehrlichia and Candidatus Neoehrlichia, Ixodid ticks are important natural reservoirs and vectors. Furthermore, Wolbachia is one of the most common parasitic microbes and its hosts cover a great many of arthropod species, including a large proportion of insects and some nematodes[5]. Notably, some of these endosymbiotic bacteria are mutualistic with their arthropod hosts. In some cases, the infection by these bacteria is beneficial or even essential for the development and/or reproduction of their hosts (e.g. manipulating sex ratio, effecting parthenogenesis, influencing the fitness, etc)[6].

Arthropods harbor a substantial diversity of bacterial endosymbionts. In recent years, the improving techniques of pathogen screening have contributed to a remarkable increase in our knowledge of the number and diversity of endosymbiont bacteria from arthropods. Especially, in arthropod species highly relevant to human health, such as ticks and mosquitoes, bacterial endosymbionts have been extensively investigated[7]. However, they have been much less studied in most other arthropod species so far. Hence, the considerable genetic diversity of Rickettsiales endosymbionts coupled to the enormous wealth of arthropod species is still to be discovered.

In Serbia, a number of arthropod borne pathogens are known to be present, both endemic and epidemic, with existing reports of both human and reservoir/vector infection, e.g. arboviruses such as Crimean-Congo haemorrhagic fever virus, west-Nile virus, etc[8,9]. Notably, data about bacterial agents associated to arthropods in Serbia, endosymbiotic or other, are still rather scarce[10,11].

The aim of this study was to screen for the presence of Rickettsiales bacteria in several arthropod species (including mosquitoes, ticks, bedbugs, millipedes, centipedes) collected in Serbia.

Material and Methods

Collection and processing of arthropods

During June to September of 2016, arthropod samples were collected from 27 sites in Serbia. Majority of collection sites (23/27) was within the city of Belgrade and its nearest surroundings (20.40°E, 44.59°N) (Fig. 1). Two sites were in the Pannonian Plain, around 150 km to the north-west and 70 km to the northeast of Belgrade (N44.935 E21.136 and N45.455 E19.220, respectively), whereas two sites were in the southern part of the country (N42.924 E22.169 and N42.710 E22.342, respectively) (Table S1). For mosquitoes, arthropod collection was performed by using BG sentinel trap (A kind of widely used mosquito monitoring trap) with dry ice container. Ticks were collected by flagging over vegetation and grassland. Other arthropod species included in the study were directly picked from the ground. Notably, flea specimens were the only ones collected from infested animals – bats of the species Nyctalus noctula that were subsequently released to freedom (in accordance with the protocol approved by the Ethical Committee). Upon collection, the arthropods were immediately stored at −80 °C, while transport to China CDC was performed in nucleic acid preservative (DNA/RNA Shield, Zymo Research, Irvine, CA, USA) at room temperature until RNA/DNA extraction. Upon collection the arthropods were morphologically identified, and then further confirmed by sequencing the 18S ribosomal RNA (18S rRNA) gene.

Figure 1

A map of Belgrade city, Serbia, showing the location of sites from which arthropods were collected.

Sample processing, DNA extraction, PCR and DNA sequencing

For nucleic acid extraction the arthropods were removed from the DNA/RNA shield and washed three times with phosphate-buffered saline (PBS). Larger specimens, of a size in the range of centimeters and more were cut into pieces. All samples were homogenized in 0.8 ml PBS solution using Retsch MM400 homogenator. The suspension was subjected to 2500 g centrifugation for 5 min, and the supernatant was collected for DNA extraction. QIAamp DNA Mini Kit (Qiagen GmbH, Hilden, Germany) was used for DNA extraction according to the manufacturer’s instructions.

Screening for Rickettsia, Wolbachia, Ehrlichia and Anaplasma was performed by nested or semi-nested PCR targeting a conserved sequence of the 16S rRNA (rrs) gene (1509 bp), as described previously[12,13]. For amplification of partial heat shock protein (groEL) (614 bp) and citrate synthase (gltA) (760 bp) genes a nested PCR protocol was applied, with the use of primers that were either previously described[13] or designed for the current study (Table S2). In positive samples, for the purpose of further exploration of phylogenetic positioning of bacterial strains representing prospective novel genera, partial RNA polymerase β-subunit-encoding (rpoB) gene sequence (2673 bp) was also amplified, by DNA walking (Primers shown in Table S2).

PCR amplicons were analyzed by electrophoresis in 1.0% agarose gels. The bands were compared to standard molecular size DNA ladders. Positive PCR products shorter than 800 bp were subjected to direct Sanger sequencing (Sangon Biotechnology Company, Shanghai, China). Purified DNA fragments of a size longer than 800 bp were cloned into cloning vector pMD19-T (TaKaRa, Dalian, China), transformed into E. coli and plated onto culture dish. The obtained clones were picked and sent for Sanger DNA sequencing (Sangon Biotechnology Company, Shanghai, China).

Sequence data and phylogenetic analyses

Nucleotide sequence similarities between the recovered bacterial sequences and those existing in the GenBank were calculated using DNAStar (DNASTAR, Inc., Madison, WI). For phylogenetic analysis, the recovered sequences were aligned with reference sequences using ClustalW (default parameters) within the MEGA program, version 5.2[14]. The best-fit evolutionary model for all sequence alignments was determined using jModel Test[15]. The General Time Reversible (GTR) nucleotide substitution model, with a gamma (Γ)-distribution model of among-site rate variation and a proportion of invariable sites (i.e. GTR + Γ + I), was found to be the best-fit model for these sequences. Phylogenetic trees were then estimated using the Maximum Likelihood (ML) method implemented in PhyML, version 3[16]. To estimate the support for individual nodes, 1000 bootstrap replicates were obtained under the same procedure. All trees were mid-point rooted for clarity only.

Results

Arthropod collection and Rickettsiales bacteria detection

During the four months study period, a total of 515 arthropods (including ticks, mosquitoes, bedbugs, centipedes, millipedes, fleas) were collected from 27 sites in Serbia (Fig. 1). In total, nine arthropod species were identified among collected specimens, namely Culex pipiens, Ixodes ricinus, Cimex lectularius, Polydesmus complanatus, Clinopodes flavidus, Cryptops anomalans, Pachyiulus hungaricus, Strigamia sp., Ischnopsyllus sp. (Table 1). Species identification based on morphological examination and sequence analysis of the 18S rRNA gene was obtained for all collected arthropods. The collected arthropods were divided into 39 pools of different size (ranging from 1–31 specimens per pool) according to species, trapping site location and collection date. The pool size, species, collection date and geographic distribution are described in Table S1.

Table 1

Prevalence of Rickettsiales bacteria in arthropods collected in Belgrade, Serbia, during 2016.

Species	Rickettsia monacensis	Rickettsia helvetica	Rickettsia spp.	Rickettsia endosymbiont of Polydesmus complanatus	Ehrlichia HF	Wolbachia pipientis	Wolbachia endosymbiont of Cimex lectularius	Wolbachia endosymbiont of Ischnopsyllus sp.	Candidatus Neowolbachia serbia	Total
Culex pipiens	0	0	0	0	0	5	0	0	0	5/18
Ixodes ricinus	3	1	1	0	1	0	0	0	0	6/8
Cimex lectularius	0	0	0	0	0	0	5	0	0	5/5
Polydesmus complanatus	0	0	0	1	0	0	0	0	0	1/1
Clinopodes flavidus	0	0	0	0	0	0	0	0	0	0/1
Cryptops anomalans	0	0	0	0	0	0	0	0	0	0/3
Strigamia sp.	0	0	0	0	0	0	0	0	1	1/1
Pachyiulus hungaricus	0	0	0	0	0	0	0	0	0	0/1
Ischnopsyllus sp.	0	0	0	0	0	0	0	1	0	1/1

Amplicons of the Rickettsial rrs gene were successfully generated and DNA sequences obtained from 19/39 arthropod pools, comprising six different arthropod species. Bacterial DNA was detected in 5/18 C. pipiens (27.78%), in 6/8 I. ricinus (75.00%), in 5/5 C. lectularius (100.00%), in 1/1 Strigamia sp., in 1/1 P. complanatus and in 1/1 Ischnopsyllus sp. pools, whereas tested samples of three species (Clinopodes flavidus, Cryptops anomalans, Pachyiulus hungaricus) were found negative. A total of 30 new bacterial sequences were recovered and have been deposited in the GenBank, with the accession numbers MH618374 to MH618404. The obtained sequences exhibited similarity in the rrs gene with those of the genera Ehrlichia, Rickettsia, and Wolbachia, with percentage identities from 91.2–100%. Among the samples found positive for gltA and groEL gene sequences, within each species, the similarities between the sequences recovered here and known reference sequences from GenBank varied from 71.6% to 100% for the gltA gene sequences, and from 71.3% to 100% for the groEL gene sequences.

Diverse Ehrlichia and Rickettsia bacteria circulating in arthropods

Based on molecular detection and phylogenetic analysis of the target rrs, gltA and groEL genes, the presence of one Ehrlichia and four Rickettsia bacterial species was revealed in the analyzed arthropods from Serbia (Table 1, Fig. 2). On the basis of gene similarity and positioning in the phylogenetic trees, the newly detected Ehrlichia sequence in I. ricinus ticks was identified as Ehrlichia sp. HF, whereas the newly detected Rickettsia included three species: Rickettsia monacensis, Rickettsia helvetica and one Rickettsia sp. that remained unassigned to any defined species cluster. In phylogenetic trees for all three studied genes, rrs, groEL and gltA, it was found within a larger monophyletic group that, among others, included strains of spotted fever group Rickettsia species: Rickettsia raoultii, Rickettsia japonica, Rickettsia heilongjiangensis, Rickettsia slovaca, Rickettsia parkeri. However, it clustered separately, indicating a separate, new species. R. monacensis was found in 3 pools, while R. helvetica, Ehrlichia sp. HF and a Rickettsia sp. were identified in one pool each of I. ricinus ticks. These findings implied the co-circulation of various bacteria of spotted fever group (SFG) Rickettsia in Serbia.

Figure 2

Phylogenetic analysis of Rickettsia strains based on nucleotide sequences of rrs, gltA and groEL genes, as well as those retrieved from GenBank.

Furthermore, a divergent Rickettsia strain was identified from P. complanatus. As indicated in the phylogenetic trees, the rrs and gltA genes of Rickettsia endosymbiont sampled from P. complanatus clustered with those of Rickettsia symbiont of Nephotettix cincticeps with the identity of 99.62% and 98.11% respectively. However, the groEL of Rickettsia endosymbiont of P. complanatus formed an independent branch in the phylogenetic tree with highest 80.52% identity to Rickettsia bellii and Rickettsia endosymbiont of Bemisia tabaci, suggesting that it may represent a novel species (Rickettsia endosymbiont of P. complanatus) belonging to Rickettsia Torix group.

Diverse Wolbachia and Neowolbachia bacteria circulating in arthropods

Wolbachia bacterial DNA was found in arthropod pools of C. pipiens L and C. lectularius, but also in a pool comprised of specimens of Ischnopsyllus sp. (Table 1). In the rrs, gltA and groEL gene trees (Fig. 3), the Wolbachia sequences from Serbian arthropods fell into three lineages, W. pipientis, Wolbachia endosymbiont of C. lectularius (wCl), and Wolbachia endosymbiont of Ischnopsyllus sp. (wIs) (Fig. 3). Notably, Ischnopsyllus hosts have never been described previously to be infected by Wolbachia. In this study, we identified the wIs Bel-A04 strain, which was phylogenetically related to the Wolbachia endosymbiont of Bryobia spec (wBs) (Fig. 3). The rrs, gltA and groEL genes of wIs Bel-A04 showed moderate similarity to the known Wolbachia sequences, with highest nucleotide similarity of 98.3%, 93.8% and 87.6% in the rrs, gltA and groEL genes, respectively, to the Wolbachia endosymbiont of Bryobia spec (wBs) and Wolbachia endosymbiont of Nasutitermes sp. (wNs) (Fig. 3). Although the Wolbachia surface protein (wsp) gene or other key genes were not obtained, we propose that it may represent a novel Wolbachia species (Wolbachia endosymbiont of Ischnopsyllus sp).

Figure 3

Phylogenetic analysis of Wolbachia and Candidatus Neowolbachia strains based on nucleotide sequences of rrs, gltA, groEL and rpoB genes, as well as those retrieved from GenBank.

Remarkably, a divergent bacterial strain from Strigamia sp. was identified, of which the rrs gene showed highest similarity of 91.2% and 91.0% to Candidatus Ehrlichia shimanensis and Wolbachia endosymbiont of Mesaphorura yosii, respectively. As to the gltA and groEL genes, 71.6% and 71.3% similarity to the known Wolbachia strains was observed, respectively. Notably, the rpoB gene of this strain shares 74.1% homology to Wolbachia and 73.9% homology to Ehrlichia (Table S3). In the phylogenetic trees based on the rrs, gltA and rpoB genes, the Bel-57 strain formed a distinct lineage and is most closely related to Wolbachia (Fig. 3). Based on the nucleotide identity and phylogenetic analysis, we propose that this Wolbachia-like strain might belong to a novel genus mostly related to Wolbachia. Therefore, we tentatively nominate it Candidatus Neowolbachieae and the strain name Candidatus Neowolbachia serbia Bel-57.

Discussion

The phenomenon of endosymbiosis, or one organism living within another, is considered to have substantially influenced the evolution of numerous species, with continuing impact[4,17]. Arthropods are believed to be one of the main reservoirs of bacterial endosymbionts which have co-speciated and co-evolved with their arthropod hosts for a long time[4,17], leading to enormous bacterial species diversity.

Here, we present a study exploring the presence of bacteria belonging to the order Rickettsiales in 9 species of arthropod samples from Serbia, collected over several months period in different sites, mainly in the capital city of Belgrade. Belgrade is located at the confluence of Sava river to Danube river, where the Balkan Peninsula meets the Pannonian Plain. With a moderate continental climate of four seasons, sufficient rainfall and enough warm weather condition to support diverse flora and abundant animals, such as diverse arthropods and mammals, environment in Belgrade could provide wide host reservoir for various bacterial endosymbionts. So far, Serbia and Belgrade comprise a known endemic region for arthropod borne pathogens such as arboviruses - autochthonous cases of arboviral diseases have continuously been reported[8,9]. Nevertheless, the real epidemiological situation regarding arthropod borne infections might be underestimated, since details about arthropod related bacterial agents in Serbia are largely unknown[18]. Majority of previous studies have explored the presence of bacteria in ticks[19-21]. In the presented study, species of arthropods derived from four different classes (Insecta, Chilopoda, Diplopoda and Arachnida) were collected from several sites in Serbia and found to contain considerable diversity of Rickettsiales bacteria. Arthropod species included mosquitoes, ticks, bedbugs, millipedes, centipedes, fleas, whereas among the found bacteria, various Rickettsia, Ehrlichia, Wolbachia and a prospective novel genus designated Neowolbachia gen. nov. were identified. Of note, arthropod samples preparation included washing in PBS, but not using 70% ethanol, hence a possibility of environmental contamination might exist. However, in view of the detection rate and scope of the found species, we believe that these endosymbiontic bacterial sequences are from the tested arthropods themselves. Considering that the current survey for endosymbiotic bacteria included only 9 species of arthropods, in view of the obtained findings, it is conceivable that much more additional arthropod-associated Rickettsiales and other bacteria are still to be discovered in the studied geographic region.

Spotted fever group Rickettsia including R. monacensis, R. helvetica, R. massiliae and R. aeschlimannii, are known to cause spotted fever in Europe[22]. In the present study, majority of the tested pools of I. ricinus 62.5% (5/8) were found positive for SFG Rickettsia bacteria, including R. monacensis, R. helvetica and newly found Rickettsia sp. Up to now, there is only one previous study describing the presence of R. monacensis and R. helvetica in ixodid ticks in Serbia[23]. However, serological evidence of human rickettsial exposure in Serbia had been reported, with the prevalence of seropositivity of up to 23% in some regions[24], in spite of no cases of clinically manifested human infection reported in Serbia so far. Together with our results, these findings imply potential for significant public health risk associated with human tick-borne rickettsial diseases, with further studies needed to estimate the conceivable risk and burden of rickettsial disease in Serbia.

Additionally, we also identified a Rickettsia strain from P. complanatus. Regardless of the known considerable prevalence of endosymbionts including Rickettsiales in terrestrial arthropods[4], this is the first report on infection of arthropods of the subphylum Myriapoda by the Rickettsiales bacteria. Remarkably, this strain was distinct from those of any known Rickettsia in the rrs, gltA and groEL gene trees, with 99.62%, 98.11% and 80.52% nucleotide identity, suggesting that it may represent a novel species. Hence, these data may extend our knowledge on bacterial endosymbionts in the previously ignored Myriapoda hosts.

Further on, one of the I. ricinus ticks pools tested positive for Ehrlichia sp. HF. This bacterium has so far been known to be present mostly in Japan[25]. This is the first report of this bacterium in Serbia and among the first ones in Europe, besides France and Romania, where it was only recently described[26,27].

More importantly, the obtained results indicate that we may have identified, through genetic detection, a Candidatus novel Anaplasmataceae genus in centipede Strigamia sp. Phylogenetic analyses of the recovered rrs, groEL, gltA and rpoB genes provided evidence for the uniqueness of the Bel-57 strain, and suggest its placement into a novel genus within the order Rickettsiales and the family Anaplasmataceae. According to the nucleotide identity and phylogenetic analysis, the Candidatus Neowolbachia is mostly related to the genus Wolbachia, which interact with host cells and induce reproductive manipulations, such as feminization, parthenogenesis, male killing, etc. However, all efforts to obtain the sequences of other key genes (wsp, ftsZ, fbpA, etc) in the Candidatus Neowolbachia serbia Bel-57 sample have failed. Notably, 16S rRNA gene sequences alone do not describe a species, but may provide the first indication that a novel species has been detected (less than 97% gene sequence similarity)[28]. A multigenic approach, as in our study, is used to improve phylogenetic and species resolution. However, the proposed assignment to a new genus is still to be considered as provisional. Noteworthy question remains whether the newly identified Candidatus Neowolbachia does possess homologous key genes (wsp, ftsZ, fbpA, etc) in the genome and whether those have similar manipulation effect on host cells as in other Wolbachia.

Wolbachia is a highly diverse genus that has been divided into 16 supergroups (A to F, H to Q) on the basis of nucleotide sequences[29]. As intracellular parasites, they maneuver the reproduction of their arthropod hosts in numerous ways, induce evolutionary alterations and are being considered as potential biological pest control. It is estimated that 66% of all insect species are infected with Wolbachia[5]. W. pipientis is a well-known endosymbiont harbored by C. pipiens, itself being the most ubiquitous mosquito in temperate zones. However, the presence and prevalence of mosquito infestation by Wolbachia has not been studied so far in the region of Serbia and this is the first study reporting about it. It has been widely accepted that the Wolbachia prevalence in Culex pipiens is 100%[30], however, in this study the positive rate is quite low (5/18). It is supposed that this abnormal positive rate might be due to the inadequate primers for W. pipientis. In addition to the W. pipientis identified from mosquitoes and wCl from bedbugs, a tentative novel Wolbachia strain was identified in the flea (Siphonaptera) Ischnopsyllus sp., collected from N. noctula bat. Bats are increasingly recognized as reservoirs of emerging pathogens[31,32]. This feature is underlined by their ubiquitous occurrence, long life-span, social behaviour (close contacts in colonies) and tendency for persistent infections[33]. Bats also serve as the final or intermediate host to a great diversity of ecto- and endoparasites. Because this animal group is isolated from other vertebrate species ecologically and behaviorally, their parasite species and communities are specific and quite distinct from those of other vertebrates and tend to be uniquely adapted to bats. Importantly, bats are frequently found flying and roosting in close proximity to human abodes, in a way that direct contact with bats is not a prerequisite for humans to contract bat-associated pathogens or to become infested with bat ectoparasites. Fleas are important vectors and reservoirs of several pathogens that cause emerging or re-emerging infectious diseases such as Yersinia pestis, Rickettsia typhi, Rickettsia felis, and Bartonella henselae and other dangerous pathogens[34]. Wolbachia spp. have also been previously detected within members of the Siphonaptera, including some bat fleas[35]. However, in spite of the estimated high prevalence of Wolbachia in arthropods species, to our knowledge, this is the first report of Wolbachia from Ischnopsyllus host. In the phylogenetic tree, the wIs Bel-A04 strain is closely related to the wBs which represents the K supergroup. Bryobia is a genus of mites in the spider mite family, Tetranychidae, Bryobia praetiosa being perhaps the best known species. It is herbivorous, with occasional reports of it occurring as an ectoparasite on humans, causing an itchy skin irritation[36]. Isolated cases of infestation in animals have also been reported[37]. To be noticed, Ischnopsyllus sp. is a member of class Insecta while Bryobia spec belongs to class Arachnida. It is interesting that these two phylogenetically distant arthropods carry genetically related Wolbachia bacteria. Horizontal transfer of Wolbachia has been well described, both within the same species or among different species[38], nevertheless, the occurrence of the interactions between these two vectors/hosts would not be easy to foresee.

A potential limitation of the presented study regards the choice and number of the tested arthropod species. One might argue that the included spectrum of species is insufficient and not random (only 9 species with 5 millipede species) to describe the overall variability of bacterial endosymbionts in arthropod hosts, however, the obtained results do undoubtedly provide an insight into novel host-parasite associations and give new information about geographical spread and occurrence of diverse Rickettsiale species.

In conclusion, 9 species of arthropods were sampled on the territory of Serbia, mostly in the capital city of Belgrade. From these samples, five recognized species and four prospective newly detected species, were recovered, including Rickettsiaceae, Anaplasmataceae and a novel Candidatus Neowolbachieae. The obtained results highlight considerable diversity of Rickettsiales bacteria in arthropods in this region. Furthermore, due to the high prevalence of SFG Rickettsia in ticks, regular surveillance on Rickettsiales infection should be strongly considered. This is also the first study to report the detection of Rickettsial infection in an arthropod of the subphylum Myriapoda (P. complanatus) and the Ischnopsyllus bat flea. In summary, the finding may shed a light into further understanding on the diversity of endosymbiotic bacteria in arthropods, and the co-evolution between bacterial endosymbionts and their hosts.

Supplementary Tables