Comparative genome and phenotypic analysis of three Clostridioides difficile strains isolated from a single patient provide insight into multiple infection of C. difficile

Isolation of strains

A stool sample from a patient with diarrhea was cultivated anaerobically on Clostridium difficile (CLO) agar plates (bioMérieux, Nürtingen, Germany), which is a selective medium for C. difficile. After 48 h of cultivation at 37 °C, colonies characteristic for C. difficile were visible and were confirmed by MALDI-TOF mass spectrometry (Biotyper, Bruker Daltonics, Bremen, Germany) with score values of ≥2000. Isolated strains were deposited at the DSMZ under the accession numbers DSM 27638, DSM 27639 and DSM 27640.

Phenotypic characterization

Sporulation assay

Sporulation rates were determined according to Burns et al., [22]. Briefly, an overnight culture of the respective strain was diluted 1:100 with fresh BHIS and was grown until an optical density (OD₆₀₀) of 0.2 to 0.4. This culture was again diluted 1:100 with fresh BHIS and cultivated for five days. An aliquot of the culture was heated for 25 min at 60 °C to kill the vegetative cells. Dilution series of an untreated and the heated sample with sterile saline was performed and spotted on CDIFF plates. Colony forming units (CFU) were analyzed after 24 h of incubation.

Co-cultivation of C. difficile strains

An overnight culture was adjusted to an OD₆₀₀ of 0.1 in fresh BHIS. 400 μl of the cells were incubated in one well of a 24-well plate (Greiner Bio-One, Frickenhausen, Germany). A ThinCert™ insert (pore size 0.4 μm) was placed in this well and 400 μl of the respective C. difficile strain was added. The insert allows the diffusion of metabolites between the two cultures but not of cells or spores. A dilution series of the cells at the time point zero was spotted on CDIFF plates to ensure that equal amounts of the respective strains were used for co-cultivation. After 24 h of incubation, the cells in the wells and inserts were resuspended thoroughly and adjusted to equal volumes. A dilution series of the cells was performed on CDIFF agar plates and incubated for 24 h. To assess whether the insert membrane is tight for C. difficile, controls were performed with (i) bacteria in the insert and sterile medium in the well and (ii) sterile medium in the insert and bacteria in the well. After plating aliquots on CDIFF plates, no colonies were formed after a 24 h incubation time for the medium controls, indicating that bacteria do not pass the insert membrane in relevant numbers within the 24 h incubation time.

Mobility assay

The motility of C. difficile strains was tested by stab-inoculation of a fresh single colony grown on BHI-agar in 0.175–0.3% semi-solid BHI-agar. Anaerobic incubation at 37 °C, and monitoring of the developed diffusion radius around the inoculation stab for the following days, were performed. 0.3% BHI-agar plates were prepared and anaerobically incubated for 3 h before inoculation. Plates were inoculated in the center of the plate with a single fresh C. difficile colony and incubated under anoxic condition (5% H₂, 5% CO₂, 90% N₂) at 37 °C. 1 and 2 d post inoculation, plates were removed from the anaerobic atmosphere for scanning of the plates. Motility assay on agar plates was performed incubating plates upside down and with the lid upturned to avoid problems with condensing water. Hungate tubes containing semi-solid 0.175% BHI-agar were incubated anaerobically overnight before inoculation. Agar was inoculated in the center of the hungate tube with a single fresh C. difficile colony using an inoculation needle in four replicates and incubated anaerobically (5% H₂, 95% N₂) at 37 °C. Diffusion radius around the inoculation stab was monitored taking pictures 1, 2 and 3 d post inoculation.

Transmission electron microscopy

For visualization of C. difficile cells via Transmission Electron Microscopy (TEM) cells were negatively stained using 1% (w/v) uranyl acetate. C. difficile cultures were inoculated and grown to exponential or stationary phase. Cultures were either used directly for sample preparation, or were previously washed to get rid of media ingredients. Therefore 2 ml liquid culture were centrifuged at 4000 rpm for 5 min, washed with 1 ml 50 mM Tris and centrifuged again. Subsequently, the pellet was resolved in 200 μl Tris. For sample preparation, an EM S160–3 cupper grid was incubated on a droplet of liquid C. difficile culture, or washed cells, for 1 min to allow absorption of cells to the grid’s carbon film. The grid was carefully semi-dried with a filter, preventing crystallization of media ingredients on the carbon film. The grid was washed in a droplet of deionized H₂O, filter-dried and negatively stained on a droplet of 1% (w/v) uranyl acetate solution for 15 s. Afterwards the grid was completely dried with a filter and analyzed using a Jeol JEM-1011 TEM.

Antibiotic resistance susceptibility tests

DNA extraction, genome sequencing, de novo genome assembly and genome annotation

For genome sequencing the strains were cultivated anaerobically in Wilkins-Chalgren Anaerobe Broth (Oxoid, Basingstore, United Kingdom) at 37 °C. Genomic DNA was extracted as described previously [23, 24].

Genome sequencing of the C. difficile strains was carried out on the PacBio RSII (Pacific Biosciences, Menlo Park, CA) using P5 chemistry. Genome assembly was performed with the RS_HGAP_Assembly.3 protocol included in SMRT Portal version 2.3.0. The chromosomal contigs generated were trimmed, circularized, and adjusted to dnaA as the first gene.

In parallel, genome sequencing of the C. difficile strains was carried out on a Genome Analyzer GAIIx (Illumina, San Francisco, CA) in a 112 bp paired-end single-indexed run Quality improvement of the final consensus sequence was performed with the Burrows-Wheeler Aligner (BWA) using bwa aln and bwa sampe [25] mapping the Illumina reads onto the obtained chromosomal contigs from the PacBio sequencing. A final quality score of QV60 was attained. Automated genome annotation was carried out using Prokka [26]. Subsequentially, selenocysteine proteins were annotated manually. Complete genome sequences have been submitted to GenBank under the accession numbers CP011846.1 (DSM 27638), CP011847.1 (DSM 27639) and CP011848.1 (DSM 27640). No extrachromosomal genetic elements were observed within this sequencing study.

Comparative genomics

Phenotypic characterization

Three C. difficile strains (DSM 27638, DSM 27639 and DSM 27640) exhibiting different phenotypes on solid medium have been isolated from one stool sample of a single patient suffering from CDI. The isolate DSM 27639 formed colony types that were white and smooth with clearly defined edges (Fig. 1). The other two isolates DSM 27638 and DSM 27640 had a rougher surface and seemed to spread on the agar plate (Fig. 1). Both isolates mainly differed in color; isolate DSM 27638 was grayish compared to isolate DSM 27640 which appeared rather gray beige. This initial observation indicated that the patient was infected with more than only one C. difficile strain. Since it has been reported that multiple infection with pathogens like C. difficile occur [20, 21], we aimed to more precisely characterize the respective phenotypic and genotypic differences that occurred during this multiple infection.

Toxinotyping has been used for distinguishing C. difficile strains. In this regard, toxin A and B genes located on the PaLoc are considered to be the major virulence factors of C. difficile. Sequencing of the complete genomes showed that the PaLocs from all three isolates were intact. As expected, the toxin loci of DSM 27638 and DSM 27640 grouped to toxinotype III, which is observed for strains belonging to RT 027 [35]. The toxin locus of isolate DSM 27639 belonged to toxinotype 0, which correlated with strains grouping into RT 012 [35].

Both RT 027 isolates DSM 27638 and DSM 27640 exhibited the typical antimicrobial susceptibility pattern of this RT, including high resistance against erythromycin and moxifloxacin (Table 1). In contrast, the RT 012 isolate DSM 27639 was susceptible to moxifloxacin. All isolates were susceptible to vancomycin and metronidazole that are antibiotics commonly used in CDI therapy [36].

It has been reported that multiple C. difficile strains can co-exist in an in-vitro human gut model although exhibiting different growth rates [37], we investigated the growth behavior of the three isolates under pure culture conditions as well as under co-cultivation conditions. However, the strains showed an identical growth behavior in BHIS under standard conditions (Additional file 1: Figure S1) In addition, all strains had the same maximal sporulation ability shown by comparable amounts of germinated spores on plates after incubation under harsh nutrient starvation (Additional file 2: Figure S2). Co-cultivation of the isolates showed that none of them had either a negative or a positive effect on the growth of any of the other isolates or the growth of reference strain 630 (data not shown). The absence of intra-species competition most likely has supported their co-existence in the patient. However, those in vitro results obviously cannot reflect the complex situation in the human host where nutrients are limiting and the different isolates are challenged by the host immune system and complex gut microbial community.

The clinical isolates DSM 27638, DSM 27639 and DSM 27640 exhibit representative phenotypic features of the toxinotype they belong to which is confirmed by the phylogenetic clustering based on whole genome sequence comparison (Fig. 2). However, phenotypic analysis could not explain the presence of two RTs in one patient.

General genome comparison

To determine the genomic features correlating with the observed colony phenotypes we performed complete genome sequencing of all three isolates. Their genomes were compared with seven publicly available closed C. difficile genomes including reference genomes of four different PCR ribotypes. A whole genome alignment using Phylomark [33] was used to assign strains DSM 27638 and DSM 27640 to RT 027 and the isolate DSM 27639 to RT 012 (Fig. 2). The genome alignment of these isolates and reference strains using MAUVE showed that all C. difficile strains share a complete syntenic chromosome interrupted by mobile elements, as it has been observed in other virulent clostridia [38] (Additional file 3: Figure S3).

To determine the core genome orthologous coding sequences (CDS) between all C. difficile strains were identified. Thus, we identified a core genome of 2669 CDS shared by all strains (Fig. 3). Consistent with the antibiotic dependent pathogenicity of CDI the core genomes comprises a number of genes assigned to antimicrobial resistances (Additional file 4: Table S1), including the beta-lactamase-inducing penicillin-binding protein BlaR; the quaternary ammonium compound-resistance protein SugE, and the vancomycin/teicoplanin-resistance proteins VanG, VanV and VanW. Resistance of C. difficile against the fluoroquinolone moxifloxacin is characteristic for most RT 027 strains and provides them with a selective advantage in comparison to other ribotypes when this antibiotic is used. The historical RT 027 strain CD196 in contrast to recently isolated RT 027 strains is moxifloxacin susceptible [39]. It was already shown that a single point mutation in the DNA gyrase subunit A-encoding gene gyrA of C. difficile leads to fluoroquinolone resistance [40]. In contrast to C. difficile reference strain 630 and isolate DSM 27639, the RT 027 strain 2,007,855 and the isolates DSM 27638 and DSM 27640 are resistant to fluoroquinolones. Sequence analysis of the GyrA protein confirmed that all moxifloxacin-resistant C. difficile strains contain a single transition mutation resulting in the amino acid substitution Thr-82-Ile (Additional file 5: Figure S4) [41].

In addition, strain-specific and ribotype-specific CDS were identified. The locations of regions of genetic difference between the strains are highlighted in the concentric circular chromosome representations of the analyzed ten genomes (Fig. 4). Strain specific genes are often found to be encoded in regions that have been identified as prophages or conjugative transposons (Table 3).

Start	Stop	Length [bp]	ORFs	Mobile element and gene content
DSM 27638
284,586	301,831	17,244	16	PHAGE (P1) (not found in 012 and 017 ribotypes)
398,255	402,824	4569	7	ABC transporter, two-component system, transposase
501,871	511,046	9229	10	transposase, hydrolases, transcriptional regulator, oligo-1,6-glucosidase, PTS system transporter subunit IIABC
518,083	528,817	10,734	10	lantibiotic resistance, two two-component systems, ABC transporter
662,517	674,897	12,380	11	ABC transporter, two-component system, transcriptional regulator
934,705	938,946	4241	5	lantibiotic resistance two-component system, two-component system
1,438,093	1,465,397	27,304	30	PHAGE (P2)
1,680,933	1,736,907	55,974	69	PHAGE (P3) (ribotype 027 specific)
2,046,513	2,066,289	19,776	6	PHAGE (P4) (ribotype 027 specific)
3,441,029	3,447,002	5973	6	conjugative transposon
3,478,606	3,491,098	12,492	8	integrase, chromosome segregation ATPase
3,489,961	3,527,152	37,191	26	PHAGE (P5) (ribotype 027 specific)
3,769,213	3,775,340	6127	7	conjugative transposon
3,775,480	3,844,734	69,254	54	PHAGE (P6) (DSM 27638 specific)
3,846,878	3,869,593	22,715	22	conjugative transposon
4,100,257	4,105,353	5096	5	ABC transporter, two-component system
4,134,037	4,164,119	30,082	34	conjugative transposon, multidrug resistance protein (ribotype 027 specific)
DSM 27639
1,170,734	1,205,103	34,369	33	conjugative transposon, lantibiotic ABC transporter (DSM 27639 specific)
1,461,445	1,488,797	27,352	30	PHAGE (P1)
1,578,539	1,595,263	16,724	17	conjugative transposon (DSM 27639 specific)
1,580,053	1,595,960	15,907	9	PHAGE (P2) (DSM 27639 specific)
2,047,626	2,068,044	20,418	7	PHAGE (P3) (ribotype 012 specific)
2,083,042	2,091,718	8676	9	PHAGE (P4)
2,263,687	2,285,988	22,301	26	conjugative transposon (DSM 27639 specific)
2,267,275	2,285,716	18,441	11	PHAGE (P5) (DSM 27639 specific)
2,536,302	2,550,493	14,191	23	PHAGE (P6) (ribotype 012 specific)
3,282,029	3,362,995	80,966	84	PHAGE (P7) (DSM 27639 specific)

^aDSM 27,640 is not included because it is identical to DSM 27638 in all elements. All mobile elements have been predicted by IslandViewer 3, PHASTER and have been manually curated

The overall similarity strongly underlines that RT 027 strains are closely related. Sequence data show that six genetic regions (two transposons and four prophages P1, P3, P4, and P5) are unique to the RT 027. The biggest difference observed in the genome of DSM 27638 is the presence of a predicted prophage integrated at 3.78 to 3.84 Mbp flanked by conjugative transposons (Fig. 4, Table 3). Interestingly, there is a conjugative transposon present at position 3.84 to 3.87 Mbp shared by the strains DSM 27638 and DSM 27640 as well as strain R20291 but not by the RT 027 reference strain CD196. This indicates that the four strains might share a common history starting at a RT 027 ancestor that did not contain the conjugative transposon. The ancestor of strains DSM 27638, DSM 27640 and R20291 might have acquired the transposon locus, which in the ancestor of strains DSM 27638 and DSM 27640 was the integration locus of a prophage.

Sequence comparison of two RT 012 genomes (630 (DSM 27543) and DSM 27639) revealed a high degree of synteny except for those regions that encode mobile elements (Additional file 3: Figure S3). A circular BLAST based comparison of the DSM 27639 genome focused on the RT 012 genomes revealed that the difference between both genomes correlates directly to predicted prophages and conjugative transposons (Fig. 4 b). Two prophages (P3 and P5) and five transposons are shared exclusively by the genomes of the strains DSM 27639 and 630 and might therefore be acquired by an RT 012 ancestor. The remaining two prophages (P1 and P4) are specific for strain DSM 27639. One prophage region is shared by all nine analyzed strains.

Comparative genomics revealed that the biggest difference of the strains isolated from the same patient to the reference genomes is the acquisition or loss of prophages and conjugative transposons, which fits to the observations of Hargreaves et al. and Mullany et al. [18, 42]. Thus we conclude that the strain-specific genes are a result of acquisition of mobile elements, which indicates the importance of these elements for the emergence of virulence. In contrast to the prophage regions, all conjugative transposons correlate with GC-content variations compared to the average GC-content (see Fig. 4). This indicates that the acquisition of the transposons are a more recent event and thus the forces of amelioration of newly acquired genome regions (described in [43] and references therein) to the host genome have had less time to operate.

In infectio genome dynamics of DSM 27638 and DSM 27640

The genome sequences of the two RT 027 isolates DSM 27638 and DSM 27640 are almost identical (Additional file 6: Figure S5), which suggest a clonal history of them within the patient [14, 44]. The isolates encode the same number of predicted proteins and differ by only 69 bp in size (Table 2, Fig. 5). A whole genome BLAST comparison of the genomes revealed the differences within six genome regions five of them being found within intergenic regions (Table 4). Two loci represent imperfect inverted repeats upstream of operons, a motif which has been found in Salmonella enterica as regulatory element where the inverted repeat regulates the downstream operon upon inversion [45]. Johnson described the regulation as a reversible flip/flop mechanism. Three inverted loci flanked by inverted repeats have been described as well as a difference between the originally published of the C. difficile genome 630Δerm and a high quality re-sequenced version in Dannheim at el. [27] indicating a reversible nature of these genomic elements. However, a comparison of the reverse complement sequence from isolate DSM 27638 with the sequence of DSM 27640 revealed that the regions differ in six base positions between the two strains. In contrast to the 630Δerm strains the locus differs between strains DSM 27638 and DSM 27640 not only in a reversible inversion. The locus is located upstream of the first CDS of the late flagellum genes and has been investigated in detail by Anjuwon Foster et al. [46] who named the regulatory element as flagellum switch. The sequence of strain DSM 27638 is identical to the 154 bp sequence described for RT 027 in contrast to the DSM 27640 version that contains additionally 4 bp. In contrast, the second inverted repeat, which is located upstream of a diguanylate cyclase, exhibits no difference compared to the reverse complement sequence of the corresponding locus of strain DSM 27640. This observation and the possibility that this kind of inverted repeat may be reversibly inverted [45, 47] challenges the hypothesis that the two genome regions really can be considered as different. Furthermore, the operons located adjacent to the inverted repeat encode transporters where a possible contribution to a macroscopic visible strain difference is at least not obvious. The most prominent sequence difference between the two isolates is generated by the insertion of eight instances of an octamer repeat-unit in isolate DSM 27638 at position 594,943 to 595,006. This 64 bp insertion is responsible for almost the complete size difference of 69 bp of the two genomes (Table 2). As a result DSM 27638 contains 21 repeat-units and DSM 27640 13 repeat-units at the corresponding locus. The repetitive region is located within the intergenic region of a locus that encodes several genes assigned to spore surface components. However, although it is possible that a modification of the regulation of spore surface components might result in the observed phenotypic differences a comparative investigation of the sporulation behavior and the viability of the spores revealed no significant differences between the three isolates (Additional file 2: Figure S2). Since the two isolates are - in contrast to the well investigated reference strain 630 - not yet genetically accessibility, a systematic investigation of the multiple repeat region and its putative contribution to the observed differences of growth phenotypes is not possible to date. The remaining genome sequence differences are three single base insertion, two of them located in intergenic regions and only one impacts an encoding signal peptidase.

DSM 27638	DSM 27640	Description
321,766 to 321,922	321,766 to 321,918	six base variations within the flagellum switch, an invertible element downstream of a c-di-GMP riboswitch within the 5’UTR of the flgB-gene
594,884 to 595,051	594,880 to 594,983	octamer repeat upstream of glutaminase GlsA, DSM 27638 contains eight additional instances
. Gap at 1,411,589	T at 1,411,522	single base deletion within a poly T stretch generates a disfunctional signal peptidase Sip3 gene in DSM 27638
1,793,982 to 1,794,196	1,793,915 to 1,794,129	invertible element upstream of signaling protein (CDIF27640_01720 resp. CDIF27638_01720). The reverse complement of the DSM 27638 sequence is identical to the DSM 27640 sequence
T at 2,096,993	. Gap 2,096,925	single T insertion within an poly T stretch, upstream of stage V sporulation protein S SpoVS
A at 2,964,477	. Gap 2,964,408	single A insertion within a poly A stretch, upstream of a purine riboswitch regulated permease (CDIF27638_02797 resp. CDIF27640_02796)

The fli locus

The fli locus encodes the flagellum of C. difficile, which results in motile peritrichous C. difficile cells [48]. A genome analysis of the fli loci of the three isolates and comparisons with RT 027 and RT 012 reference strains as well as with a non-motile RT 078 control strain confirmed that all structural genes necessary to encode a functional flagellum are present in all three isolates, which could be confirmed via TEM (Fig. 6). Note that that all amino acid sequences of the fli-gene products of strains DSM 27638 and DSM 27640 are identical. Since the intergenic regulatory region upstream of the early stage fli genes is one of only three regional sequence differences identified in the complete genome sequences of DSM 27638 and 27,640 we performed additional phenotypic investigations to verify the expression of a functional flagellum (Fig. 7). In contrast to the non-motile RT 078 control strain, both RT 027 isolates as well as the RT 012 isolate DSM 27639 and the respective control isolates R20291 (RT 027) and 630 (DSM 27543, RT 012) exhibited a spreading diffuse growth indicative for active motility (Additional file 7: Figure S6). Thus the impact of the described genome difference on the initially observed growth phenotype (Fig. 1) remains unsolved. However, it has been reported that the flagellum can have an impact on the adherence to intestinal mucosa and might eventually also influence growth on solid surfaces such as agar plates [46, 49, 50]. Thus it is tempting to speculate that the sequence difference within the fli locus contributes to the observed growth phenotype of the three patient isolates.