Crystal structure and DNA cleavage mechanism of the restriction DNA glycosylase R.CcoLI from Campylobacter coli.

While most restriction enzymes catalyze the hydrolysis of phosphodiester bonds at specific nucleotide sequences in DNA, restriction enzymes of the HALFPIPE superfamily cleave N-glycosidic bonds, similar to DNA glycosylases. Apurinic/apyrimidinic (AP) sites generated by HALFPIPE superfamily proteins are cleaved by their inherent AP lyase activities, other AP endonuclease activities or heat-promoted ß-elimination. Although the HALFPIPE superfamily protein R.PabI, obtained from a hyperthermophilic archaea, Pyrococcus abyssi, shows weak AP lyase activity, HALFPIPE superfamily proteins in mesophiles, such as R.CcoLI from Campylobacter coli and R. HpyAXII from Helicobacter pylori, show significant AP lyase activities. To identify the structural basis for the AP lyase activity of R.CcoLI, we determined the structure of R.CcoLI by X-ray crystallography. The structure of R.CcoLI, obtained at 2.35-Å resolution, shows that a conserved lysine residue (Lys71), which is stabilized by a characteristic ß-sheet structure of R.CcoLI, protrudes into the active site. The results of mutational assays indicate that Lys71 is important for the AP lyase activity of R.CcoLI. Our results help to elucidate the mechanism by which HALFPIPE superfamily proteins from mesophiles efficiently introduce double-strand breaks to specific sites on double-stranded DNA.

A Study on Campylobacter jejuni and Campylobacter coli through Commercial Broiler Production Chains in Thailand: Antimicrobial Resistance, the Characterization of DNA Gyrase Subunit A Mutation, and Genetic Diversity by Flagellin A Gene Restriction Fragment Length Polymorphism.

Contaminated poultry meat is regarded as the main source of human campylobacteriosis. During September 2014 and February 2015, breeder flocks, hatcheries, and broiler farms from two chicken production chains were investigated chronologically. Five commercial breeder flocks (Breeder Flocks 1-5), two hatcheries (Hatcheries A and B), and five broiler flocks (Broiler Flocks 1-5) were sampled in this study. Campylobacter colonization of both breeder and broiler flocks was determined from cloacal swabs and environmental samples (pan feeders, footwear, darkling beetles, flies, feed, and water). The eggs from the breeder flocks were followed to hatcheries. At the hatcheries, early embryonic deaths, egg trays, eggshells, hatchers, and water were investigated. Cloacal swabs were taken from broilers at Days 1, 14, and 28 (all broiler flocks), and either 35 (Broiler Flocks 1 and 2) or 43 (Broiler Flocks 3-5). Thirty-six Campylobacter jejuni and 94 Campylobacter coli isolates collected through two broiler production chains were tested by twofold agar dilution for their susceptibility to antimicrobial agents. Most Campylobacter isolates were multidrug resistant (MDR), defined as being resistant to three or more antimicrobial classes ( C. jejuni : 100%; C. coli : 98.9%), and exhibited high resistance to enrofloxacin ( C. jejuni : 100%; C. coli : 98.9%). The vast majority of C. coli were resistant to tetracycline (97.9%), trimethoprim-sulfamethoxazole (81.9%), and doxycycline (79.8%), but only 55.6%, 36.1%, and 50% of C. jejuni isolates revealed resistance to these antimicrobial agents, respectively. A selected subset of 24 C. jejuni and 24 C. coli were characterized for their mutations in the quinolone resistance determining region of the DNA gyrase subunit A gene by nucleotide sequence analysis. The Thr-86-Ile substitution (ACA-ATA in C. jejuni or ACT-ATT in C. coli ) was found in all isolates. Moreover, a total of 130 Campylobacter isolates were typed with the use of polymerase chain reaction-restriction fragment length polymorphism of the flagellin A gene (flaA-RFLP) to determine their genetic relationships. Ten distinct clusters were recognized by flaA-RFLP typing. The results showed that horizontal transmission was the major route of Campylobacter transmission in this study. In conclusion, the emergence of MDR and high resistance rates to several antimicrobials are major concerns identified in this study. The prudent use of these agents and active surveillance of resistance at the farm level are essential steps to reduce the public health risks identified in this work.

Identification of a Campylobacter coli methyltransferase targeting adenines at GATC sites.

Campylobacter coli can infect humans and colonize multiple other animals, but its host-associated genes or adaptations are poorly understood. Adenine methylation at GATC sites, resulting in MboI resistance of genomic DNA, was earlier frequently detected among C. coli from swine but not among turkey-derived isolates. The underlying genetic basis has remained unknown. Comparative genome sequence analyses of C. coli 6461, a swine-derived strain with MboI-resistant DNA, revealed two chromosomal ORFs, 0059 and 0060, encoding a putative DNA methyltransferase and a conserved hypothetical protein, respectively, which were lacking from the genome of the turkey-derived C. coli strain 11601, which had MboI-susceptible DNA. To determine whether ORF0059 mediated MboI resistance and hence encoded a putative N6-adenine DNA methyltransferase, the gene was cloned immediately upstream of a chloramphenicol resistance cassette (cat) and a PCR fragment harboring ORF0059-cat was transformed into C. coli 11601. The transformants had MboI-resistant DNA, suggesting a direct role of this gene in methylation of adenines at GATC sites. In silico analyses suggested that the ORF0059-ORF0060 cassette was more frequent among C. coli from swine than certain other sources (e.g. cattle, humans). Potential impacts of ORF0059-mediated methylation on C. coli host preference and other adaptations remain to be elucidated.

Variation in the limit-of-detection of the ProSpecT Campylobacter microplate enzyme immunoassay in stools spiked with emerging Campylobacter species.

Campylobacter enteritis in humans is primarily associated with C. jejuni/coli infection. The impact of other Campylobacter spp. is likely to be underestimated due to the bias of culture methods towards Campylobacter jejuni/coli diagnosis. Stool antigen tests are becoming increasingly popular and appear generally less species-specific. A review of independent studies of the ProSpecT® Campylobacter Microplate enzyme immunoassay (EIA) developed for C. jejuni/coli showed comparable diagnostic results to culture methods but the examination of non-jejuni/coli Campylobacter spp. was limited and the limit-of-detection (LOD), where reported, varied between studies. This study investigated LOD of EIA for Campylobacter upsaliensis, Campylobacter hyointestinalis and Campylobacter helveticus spiked in human stools. Multiple stools and Campylobacter isolates were used in three different concentrations (10(4)-10(9)CFU/ml) to reflect sample heterogeneity. All Campylobacter species evaluated were detectable by EIA. Multivariate analysis showed LOD varied between Campylobacter spp. and faecal consistency as fixed effects and individual faecal samples as random effects. EIA showed excellent performance in replicate testing for both within and between batches of reagents, in agreement between visual and spectrophotometric reading of results, and returned no discordance between the bacterial concentrations within independent dilution test runs (positive results with lower but not higher concentrations). This study shows how limitations in experimental procedures lead to an overestimation of consistency and uniformity of LOD for EIA that may not hold under routine use in diagnostic laboratories. Benefits and limitations for clinical practice and the influence on estimates of performance characteristics from detection of multiple Campylobacter spp. by EIA are discussed.

Antibiotic resistance and polymorphism in the quinolone resistance-determining region of Campylobacter spp. isolated from 1-day-old ducklings.

Thirty-three isolates of Campylobacter coli and three isolates of Campylobacter jejuni were recovered from 150 1-day-old ducklings. All isolates were sensitive to chloramphenicol and amikacin, but resistant to sulfamethoxazole-trimethoprim (SXT) by the disc diffusion method. Most isolates were susceptible to tetracycline and erythromycin, but resistant to ofloxacin and ciprofloxacin. Of the 33 C. coli isolates, nine were positive for the tetracycline resistance gene tet(O), although only two of these were resistant to tetracycline in the disc diffusion test. None of the isolates possessed mutations in the quinolone resistance-determining region (QRDR) of the gyrA gene infrequently linked to FQ-resistance. The finding indicated that ducklings may be a source of antibiotic resistant Campylobacter spp. with potential poultry and public health hazard.

Investigating the host specificity of Campylobacter jejuni and Campylobacter coli by sequencing gyrase subunit A.

BACKGROUND: Surveillance and field investigations of Campylobacter infections require molecular tools with genetic markers appropriate for tracing purposes, i.e. based on the principle that some Campylobacter lineages acquire a host signature under adaptive selection pressure. We developed a sequence-based method targeting the quinolone resistance determining region within the subunit A of DNA gyrase (gyrA). Host specificity was evaluated by characterizing two collections of Campylobacter jejuni (N = 430) and Campylobacter coli (N = 302) originating from surface waters, domestic mammals and poultry. RESULTS: Based on nucleotide identity, a total of 80 gyrA alleles were observed. Thirty nine alleles assigned to C. coli encoding two peptides fell into three clades: two associated with surface waters and one associated with domestic mammals and poultry. The variability in GC content generated by synonymous mutations suggested that surface waters isolates originated from two distinct ecological niches. A total of 42 alleles were recorded from C. jejuni strains and encoded 8 peptides including one lying in a distinct lineage associated with wildlife. Seven of the 23 alleles encoding peptide #1 displayed the synonymous mutation G408A not identified in poultry isolates. By contrast, the substitution Ser22Gly observed in 4 different peptide groups was significantly associated with domestic birds (P = 0.001). The change in amino acid sequences Thr86Ile conferring resistance to quinolones was significantly associated with poultry (P < 0.001) in both C. jejuni and C. coli with 38.7% and 67.9% of quinolone-resistant strains, respectively. CONCLUSIONS: The gyrA typing method presented here is an informative tool as sequences appear to be predictive of particular ecological niches. Combined with multi-locus sequence typing, it could increase the resolution of source attribution, and combined with porA/flaA typing it could be suitable for detecting temporal clusters of human cases. All gyrA alleles identified were deposited in the freely accessible online database http://pubmlst.org/campylobacter.

Report of ribosomal RNA methylase gene erm(B) in multidrug-resistant Campylobacter coli.

OBJECTIVES: Campylobacter is a major foodborne enteric pathogen and macrolides are the drug of choice for the clinical therapy of campylobacteriosis. Macrolide resistance among Campylobacter compromises clinical treatment, is associated with adverse health events and is a significant public health concern. Here, we report the first identification of a horizontally transferrable macrolide resistance mechanism in porcine Campylobacter coli ZC113 that is mediated by a ribosomal RNA methylase, Erm(B). METHODS: Horizontal transfer of a macrolide resistance determinant between C. coli and Campylobacter jejuni was performed by natural transformation. Whole-genome sequencing was initially used to identify the ribosomal methylase-encoding gene erm(B) in Campylobacter. Cloning of erm(B) into C. jejuni NCTC 11168 was performed to evaluate whether the erm(B) gene is responsible for high-level macrolide resistance in Campylobacter. RESULTS: The erm(B) gene was identified in ZC113, conferred high-level resistance to macrolides and was associated with a chromosomal multidrug-resistant genomic island (MDRGI). The MDRGI probably originated from Gram-positive bacteria and was horizontally transferred between C. coli and C. jejuni via natural transformation. Furthermore, the erm(B)-positive isolate ZC113 was resistant to all clinically important antibiotics used for treating campylobacteriosis and is essentially multidrug-resistant Campylobacter. CONCLUSIONS: To the best of our knowledge, this is the first report of a horizontally transferable macrolide resistance mechanism in thermophilic Campylobacter. Surveillance of erm(B) and its associated MDRGI in both C. coli and C. jejuni is urgently warranted.

Role of efflux pumps and topoisomerase mutations in fluoroquinolone resistance in Campylobacter jejuni and Campylobacter coli.

Point mutations in the topoisomerase (DNA gyrase A) gene are known to be associated with fluoroquinolone resistance in Campylobacter. Recent studies have shown that an efflux pump encoded by cmeABC is also involved in decreased susceptibilities to fluoroquinolones, as well as other antimicrobials. Genome analysis suggests that Campylobacter jejuni contains at least nine other putative efflux pumps. Using insertional inactivation and site-directed mutagenesis, we investigated the potential contributions of these pumps to susceptibilities to chloramphenicol, ciprofloxacin, erythromycin, and tetracycline in C. jejuni and Campylobacter coli. Insertional inactivation of cmeB resulted in 4- to 256-fold decreases in the MICs of chloramphenicol, ciprofloxacin, erythromycin, and tetracycline, with erythromycin being the most significantly affected. In contrast, inactivation of all other putative efflux pumps had no effect on susceptibility to any of the four antimicrobials tested. Mutation of gyrA at codon 86 (Thr-Ile) caused 128- and 64-fold increases in the MICs of ciprofloxacin and nalidixic acid, respectively. The replacement of the mutated gyrA with a wild-type gyrA allele resulted in a 32-fold decrease in the ciprofloxacin MIC and no change in the nalidixic acid MIC. Our findings indicate that CmeABC is the only efflux pump among those tested that influences antimicrobial resistance in Campylobacter and that a point mutation (Thr-86-Ile) in gyrA directly causes fluoroquinolone resistance in Campylobacter. These two mechanisms work synergistically in acquiring and maintaining fluoroquinolone resistance in Campylobacter species.

Phenotypic characterisation of flagellin and flagella of urease-positive thermophilic campylobacters.

In this study, flagellin is purified biochemically from eight urease-positive thermophilic camplylobacters (UPTC) isolated from river water, sea water and mussels, and purified also from two isolates of Campylobacter jejuni and C. coli and fractionated by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). Results showed that no flagellin components were detected in the two Japanese UPTC isolates (CF89-12 and CF89-14) and the two UPTC NCTC strains (NCTC12893 and NCTC12894). Flagellin components, each consisting of a single peptide, with a heterogeneous molecular mass of approximately 52-63 kDa were demonstrated in the other four UPTC isolates (NCTC12892, NCTC12895, NCTC12896 and NI15F [from Northern Ireland]) and the two Japanese isolates of C. jejuni (JCM2013 and C. coli 27). The approximate molecular mass of flagellin from the flagellin-positive UPTC isolates was smaller than those of C. jejuni and C. coli. Flagella were not detected by electron microscopy in the four flagellin-negative UPTC isolates but they were detected in the four flagellin-positive UPTC isolates and the two isolates of C. jejuni and C. coli. Thus, significant phenotypic diversity for flagellin, which must be due to genotypic variations, was demonstrated among the UPTC isolates.

Use of a LightCycler gyrA mutation assay for identification of ciprofloxacin-resistant Campylobacter coli.

A fluorescence resonance energy transfer-based assay has been employed to detect mutations at the 86 codon in the DNA gyrase A (gyrA) gene in Campylobacter coli strains. These mutations were associated with ciprofloxacin resistance in strains isolated in Italy in 2000. The mutations in the gyrA gene were detected by real-time PCR amplification followed by hybridization with two fluorescent probes designed with sequences complementary to the wild-type C. coli gyrA gene. Mutation detection was performed by melting peak analysis of the probe-PCR product hybrid performed on a LightCycler (Roche Diagnostic). This gyrA mutation assay allows a rapid and reproducible screening method of ciprofloxacin-resistant C. coli strains.

Subspecies characterization of porcine Campylobacter coli and Campylobacter jejuni by multilocus enzyme electrophoresis typing.

Enteropathogenic Campylobacterjejuni, C. coli and C. lari are currently the most common causes of acute infectious diarrhoeal illness in the UK. Many domestic animals, including pigs, act as natural reservoirs of these organisms and infection may occur through the ingestion of contaminated foodstuffs. C jejuni and C. coli, isolated from the livers of bacon pigs, were examined at subspecies level by multilocus enzyme electrophoresis (MEE) typing with seven enzymic loci. Polymorphological variation was highest with indophenol oxidase, isocitrate dehydrogenase and L-phenylalanyl-L-leucine peptidase giving 5. 5 and 4 alleles at these loci, respectively. The 35 Campylobacter isolates examined in this study (12 C. jejuni and 23 C coli) represented 30 unique electrophoretic types (ETs). Of these ETs, 8 unique types were detected for the 12 C jejuni isolates and 19 unique ETs were detected for the 23 C coli isolates. In addition, 3 types (ETs 2, 5, 10) were shared in common among C. jejuni and C coli. The average number of alleles per enzyme locus was 3.28. The mean genetic diversity, i.e. arithmetic average over all loci assayed, including monomorphic values, was 0.5573 and 0.5350 for C jejuni and C coli. respectively. Alleles were shared by C jejuni and C coli, suggesting an exchange of genetic material between the species. MEE analyses of isolates showed that there was a wide range of subspecies types within both C. jejuni and C coli in porcine livers. In certain cases, up to four phenotypically different strains of C coli were isolated from one liver, indicating multiple infections.

Roles of Fe superoxide dismutase and catalase in resistance of Campylobacter coli to freeze-thaw stress.

We demonstrated that oxidative stress plays a role in freeze-thaw-induced killing of Campylobacter coli following analysis of mutants deficient in key antioxidant functions. Superoxide anions, but not H(2)O(2), were formed during the freeze-thaw process. However, a failure to detoxify superoxide anions may lead to spontaneous disproportionation of the radicals to H(2)O(2).

Generation of a superoxide dismutase (SOD)-deficient mutant of Campylobacter coli: evidence for the significance of SOD in Campylobacter survival and colonization.

The microaerophilic nature of Campylobacter species implies an inherent sensitivity towards oxygen and its reduction products, particularly the superoxide anion. The deleterious effects of exposure to superoxide radicals are counteracted by the activity of superoxide dismutase (SOD). We have shown previously that Campylobacter coli possesses an iron cofactored SOD. The sodB gene of C. coli UA585 was insertionally inactivated by the site-specific insertion of a tetO cassette. Organisms harboring the inactivated gene failed to produce a biologically functional form of the enzyme. While the ability of this mutant to grow in aerobic conditions was unchanged relative to the parental strain, its survival was severely compromised when nongrowing cells were exposed to air. Accordingly, the SOD-deficient mutant was unable to survive for prolonged periods in model foods. Furthermore, inactivation of the sodB gene decreased the colonization potential in an experimental infection of 1-day-old chicks. In contrast, strain CK100, which is deficient in catalase activity, showed the same survival and colonization characteristics as the parental strain. These results indicate that SOD, but not catalase, is an important determinant in the ability of C. coli to survive aerobically and for optimal colonization within the chicken gut.

The use of hipO, encoding benzoylglycine amidohydrolase (hippuricase), as a reporter of gene expression in Campylobacter coli.

A novel integrative promoter probe vector which utilizes the Campylobacter jejuni hipO gene as a reporter of gene expression was developed as a genetic tool in Campylobacter coli. The utility of the system was demonstrated by coupling expression of the hipO reporter to the promoters of flaA, flaB and katA. Subsequently, expression of these genes could be monitored accurately from chromosomally-borne transcriptional fusions using a simple non-destructive colorimetric assay. The system should serve as a useful tool for studying the response of Camp. coli to environmental stresses.

Cloning, sequencing, and characterization of the lipopolysaccharide biosynthetic enzyme heptosyltransferase I gene (waaC) from Campylobacter jejuni and Campylobacter coli.

Campylobacter jejuni and Campylobacter coli are common causes of gastrointestinal disease and a proportion of C. jejuni infections have been shown to be associated with the Guillain-Barré syndrome. The waaC gene from Campylobacter coli, involved in lipopolysaccharide core biosynthesis, was cloned by complementation of a heptose-deficient strain of Salmonella typhimurium, as judged by novobiocin sensitivity, lipopolysaccharide (LPS)-specific phage sensitivity, and polyacrylamide-resolved lipopolysaccharide profiles. The C. jejuni waaC gene was subsequently cloned using the waaC gene isolated from C. coli as a probe. The C. jejuni and C. coli waaC genes are capable of encoding proteins of 342 amino acids with calculated molecular masses of 39381Da and 39317Da, respectively. Sequence and in-vitro analyses suggested that the C. coli waaC gene may be transcribed from its own promoter. Translation of the C. coli waaC gene in a cell-free system yielded a protein with a Mr of 39000. The waaC gene was detected in every C. jejuni and C. coli isolate tested as judged by dot-blot hybridization analysis. Southern hybridization analysis indicated that both Campylobacter species contain a single copy of the waaC gene. Unlike Escherichia coli and S. typhimurium isolates, the waaC gene in C. jejuni and C. coli isolates does not appear to be linked to the waaF (rfaF) gene.

Antimicrobial susceptibilities of Campylobacter jejuni and Campylobacter coli to 12 beta-lactam agents and combinations with beta-lactamase inhibitors.

The in vitro activities of 12 beta-lactam agents against 100 thermophilic Campylobacter strains were tested. Beta-Lactamase production was detected in 88% of all strains tested. Clavulanic acid was the best inhibitor by susceptibility testing. The beta-lactams which displayed high levels of in vitro activity against Campylobacter isolates were imipenem, amoxicillin-clavulanic acid, and cefepime and, to a lesser degree, amoxicillin, ampicillin, and cefotaxime.

The changing patterns of Campylobacter jejuni/coli in Lagos, Nigeria after ten years.

One hundred and forty-five stool samples from children with diarrhoea at various health centres in Lagos were investigated for Campylobacter jejuni/coli. These organisms were isolated from 24 samples (16.5%). They were later biotyped as 23 C. jejuni and one C. coli. Previous studies (3,6) recorded isolation rates of 5.2% and 11% respectively. No Campylobacter species was isolated from 100 control patients who did not have diarrhoea. Diarrhoea due to Campylobacter jejuni/coli is still common in males, and the ration of males to females is still 2:1 but the isolation rate is now 11.7%:4.8%. All the isolates of Campylobacter jejuni are still from children under two years of age. Campylobacter jejuni biotype 1 accounted for 52.5% in an earlier study (18), but accounted for 87.5% in this study. Serogroup 29(70.8%) was the commonest in this study, whereas serogroup 36(20.7%) was very common in an earlier study(18). Erythromycin, which is the drug of choice for the treatment of campylobacter enteritis, had 82% sensitivity to the organism(6) but in the present study only 20.8% of the isolates were sensitive to the antibiotic. Betalactamase production was detected in 12.5% of the isolates as against 6.4% earlier reported(17).

Characterization of the sat4 gene encoding a streptothricin acetyltransferase in Campylobacter coli BE/G4.

The sat4 streptothricin resistance gene from Campylobacter coli BE/G4 was cloned into pUC18, and its nucleotide sequence was determined. Streptothricin acetyltransferase activity was detected in Escherichia coli cells containing recombinant plasmid pAT132 which carries the sat4 gene as an insert. The deduced amino acid sequence displayed 21-27% amino acid identity with streptothricin acetyltransferases from E. coli and streptothricin producers Streptomyces lavendulae and Streptomyces noursei. The sat4 gene was detected by hybridization in clinical and environmental isolates of Campylobacter spp.

Cloning, nucleotide sequence and characterization of a gene encoding superoxide dismutase from Campylobacter jejuni and Campylobacter coli.

Genes encoding superoxide dismutase (SOD: EC 1.15.1.1) were cloned from Campylobacter jejuni NCTC 11351 and Campylobacter coli UA585 by heterologous complementation of a SOD-deficient Escherichia coli mutant. Deletion analysis of the cloned C. jejuni DNA assigned the sod gene to a 1.2 kb insert and this contained an open reading frame of 660 bp. The deduced gene product of 220 amino acids was 71% identical to the E. coli iron-containing SOD and 60% identical to the E. coli manganese-containing SOD. The recombinant SOD was expressed at high levels in E. coli and protected a sodA sodB double mutant from the toxic effects of methyl viologen. Nucleotide sequence analysis of the corresponding gene from C. coli showed it to be 92% identical to that from C. jejuni.

Construction of new Campylobacter cloning vectors and a new mutational cat cassette.

We have developed new Campylobacter shuttle vectors which are 6.5-6.8-kb plasmids carrying Campylobacter and Escherichia coli replicons, a multiple cloning site (MCS), the lacZ alpha gene, oriT and either a kanamycin or chloramphenicol resistance-encoding gene (KmR or CmR) from Campylobacter which functions in both hosts. These vectors can be mobilized efficiently from E. coli into C. jejuni or C. coli, and stably maintained in these hosts. Plasmids pRY107 and pRY108 carry a KmR marker and 17 unique cloning sites in two different orientations in lacZ alpha, allowing easy blue/white color selection. Plasmids pRY111 and pRY112 contain a CmR gene and 17 unique sites in both orientations. In addition, MCS are flanked by T7 and T3 late promoters and M13 forward and reverse primer sites, facilitating expression in T7 or T3 expression systems and sequence analysis. A Campylobacter CmR gene cartridge, bracketed by six restriction sites, has been developed for use in site-specific mutagenesis of Campylobacter genes.