Presence of methylated adenine in GATC sequences in chromosomal DNAs from Campylobacter species

SMRT sequencing of the Campylobacter coli BfR-CA-9557 genome sequence reveals unique methylation motifs

BACKGROUND

Campylobacter species are the most prevalent bacterial pathogen causing acute enteritis worldwide. In contrast to Campylobacter jejuni, about 5 % of Campylobacter coli strains exhibit susceptibility to restriction endonuclease digestion by DpnI cutting specifically 5'-G(m)ATC-3' motifs. This indicates significant differences in DNA methylation between both microbial species. The goal of the study was to analyze the methylome of a C. coli strain susceptible to DpnI digestion, to identify its methylation motifs and restriction modification systems (RM-systems), and compare them to related organisms like C. jejuni and Helicobacter pylori.

RESULTS

Using one SMRT cell and the PacBio RS sequencing technology followed by PacBio Modification and Motif Analysis the complete genome of the DpnI susceptible strain C. coli BfR-CA-9557 was sequenced to 500-fold coverage and assembled into a single contig of 1.7 Mbp. The genome contains a CJIE1-like element prophage and is phylogenetically closer to C. coli clade 1 isolates than clade 3. 45,881 6-methylated adenines (ca. 2.7 % of genome positions) that are predominantly arranged in eight different methylation motifs and 1,788 4-methylated cytosines (ca. 0.1 %) have been detected. Only two of these motifs correspond to known restriction modification motifs. Characteristic for this methylome was the very high fraction of methylation of motifs with mostly above 99 %.

CONCLUSIONS

Only five dominant methylation motifs have been identified in C. jejuni, which have been associated with known RM-systems. C. coli BFR-CA-9557 shares one (RAATTY) of these, but four ORFs could be assigned to putative Type I RM-systems, seven ORFs to Type II RM-systems and three ORFs to Type IV RM-systems. In accordance with DpnI prescreening RM-system IIP, methylation of GATC motifs was detected in C. coli BfR-CA-9557. A homologous IIP RM-system has been described for H. pylori. The remaining methylation motifs are specific for C. coli BfR-CA-9557 and have been neither detected in C. jejuni nor in H. pylori. The results of this study give us new insights into epigenetics of Campylobacteraceae and provide the groundwork to resolve the function of RM-systems in C. coli.

Differences in methylation at GATC sites in genomic DNA of Campylobacter coli from turkeys and swine

A significant fraction (46/108, 43%) of swine isolates of Campylobacter coli but none of 81 isolates of C. coli from turkeys had genomic DNA that was resistant to digestion by MboI, suggesting methylation of adenines at GATC sites. No consistent association was noted between antimicrobial resistance and MboI resistance. Seven swine-associated multilocus sequence typing-based sequence types (STs) were detected among multiple isolates with MboI-resistant DNA. The data suggest host-associated DNA modification system(s) specific for adenine at GATC sites in C. coli from swine.

Antibiotic resistance of Campylobacter jejuni and Campylobacter coli clinical isolates from Poland

We tested 102 Campylobacter jejuni and 6 Campylobacter coli clinical isolates from Poland. All were susceptible to erythromycin. Among the tested C. jejuni isolates 55.9% and 13.7% were resistant to ciprofloxacin and tetracycline, respectively. Replacement of Thr86 with Ile in GyrA and a plasmid-borne tet(O) gene were the main resistance mechanisms for fluoroquinolones and tetracycline, respectively.

Tetracycline resistance of Australian Campylobacter jejuni and Campylobacter coli isolates

OBJECTIVES

Tetracycline resistance in Campylobacter is encoded by the tet(O) gene and is usually associated with conjugative plasmids. Little was known about tetracycline resistance in Australian Campylobacter species, therefore we investigated this resistance in 41 Campylobacter jejuni and five Campylobacter coli strains from humans and healthy chickens.

METHODS

Tetracycline MICs were determined for each isolate using an agar dilution method. The distribution and localization of tet(O) on plasmid and chromosomal DNA was determined by Southern-blot experiments. The ability to transfer resistance to recipient strains was examined through conjugation studies. Identity of transconjugants was confirmed by PCR and flaA-restriction fragment length polymorphism analysis.

RESULTS

High-level tetracycline resistance was observed, ranging from 32 to >256 mg/L. Plasmids were detected in 74% of isolates with plasmids between 30 and 40 kb in size most frequently isolated. tet(O) was present in all tetracycline-resistant isolates. In the majority of strains under study the tet(O) gene was chromosomally encoded. Tetracycline resistance of six C. jejuni strains in which tet(O) was plasmid mediated was transferred by conjugation to a C. jejuni recipient strain. Transfer did not occur between tetracycline-resistant C. jejuni strains and a C. coli recipient. No difference in MICs, plasmid carriage and tet(O) localization was detected between human and chicken isolates.

CONCLUSIONS

These data indicate that the tet(O) gene, previously reported in Campylobacter strains throughout the world, is present in Australian Campylobacter. This study will lead to a greater understanding of antibiotic resistance distribution in Campylobacter spp. in Australia.

Variation of the natural transformation frequency of Campylobacter jejuni in liquid shake culture

Natural transformation, a mechanism that generates genetic diversity in Campylobacter jejuni, was studied in a novel liquid shake culturing system that allowed an approximately 10 000-fold increase in cell density. C. jejuni transformation frequency was analysed in this system under 10 %, 5·0 % and 0·7 % CO2 atmospheres. At 5·0 % and 10 % CO2 concentrations, when purified isogenic chromosomal DNA was used to assess competence, transformation frequency ranged from 10−3 to 10−4 at low cell concentrations and declined as cell density increased. Transformation frequency under a 0·7 % CO2 atmosphere was more stable, maintaining 10−3 levels at high cell densities, and was 10- to 100-fold higher than that under a 10 % CO2 atmosphere. Three of four C. jejuni strains tested under a 5·0 % CO2 atmosphere were naturally competent for isogenic DNA; competent strains demonstrated a lack of barriers to intraspecies genetic exchange by taking up and incorporating chromosomal DNA from multiple C. jejuni donors. C. jejuni showed a preference for its own DNA at the species level, and co-cultivation demonstrated that DNA transfer via natural transformation occurred between isogenic populations during short periods of exposure in liquid medium when cell density and presumably DNA concentrations were low. Transformation frequency during co-cultivation of isogenic populations was also influenced by CO2 concentration. Under a 0·7 % CO2 atmosphere, co-cultivation transformation frequency increased approximately 500-fold in a linear fashion with regard to cell density, and was 1000- to 10 000-fold higher during late-exponential-phase growth when compared to cultures grown under a 10 % CO2 atmosphere.

Campylobacter upsaliensis: waiting in the wings

Despite strong epidemiological evidence supporting an important role for Campylobacter upsaliensis as a human enteropathogen, it remains relatively unknown in the realm of clinical microbiology. Clinical studies indicate that infection with this organism usually is associated with benign self-limiting diarrhea. However, more serious illnesses, including spontaneous abortion and hemolytic-uremic syndrome, recently have been associated with human infections. Understanding of the virulence properties and molecular biology of C. upsaliensis is beginning to evolve. There is now a pressing need for controlled, prospective epidemiologic studies in addition to further in-depth investigation of the pathogenesis of this enteric campylobacter to more precisely define its role in human disease. Furthermore, since C. upsaliensis is sensitive to the antibiotics routinely used in Campylobacter selective media, widespread appreciation of the importance of this organism will rely on the development of widely applicable, effective techniques for its isolation.

Host-mediated modification of Sau3AI restriction in Listeria monocytogenes: prevalence in epidemic-associated strains

Most major food-related outbreaks of listeriosis have been traced to a cluster of genetically related strains of serovar 4b (epidemic clone). In spite of numerous searches, distinct bacteriologic or virulence-related features unique to these strains have eluded identification, although a restriction fragment length polymorphism (RFLP) characteristic of the epidemic clone has previously been described (W. Zheng and S. Kathariou, Appl. Environ. Microbiol. 61:4310-4314, 1995). We found that DNAs from 75 strains which were derived from three separate outbreaks and which had the epidemic clone-specific RFLP were also invariably resistant to digestion by Sau3AI and other restriction endonucleases sensitive to cytosine methylation at 5' GATC 3' sites. This modification of Sau3AI restriction was host mediated, as it did not persist when DNA was cloned and propagated in Escherichia coli, and was uncommon among other Listeria strains. Epidemic-associated strains with this modification were resistant to infection by phage propagated in a serotype 4b strain which was not known to be involved in an epidemic and which lacked the epidemic clone-specific RFLP. Screening for susceptibility to MboI digestion revealed that these epidemic strains lacked methylation of adenines at GATC sites. This type of modification was rare among Listeria strains and was found in only three (of eight screened) strains of serovar 1/2b, possibly representing one clonal lineage.