Molecular serotyping of Klebsiella species isolates by restriction of the amplified capsular antigen gene cluster

The objective of the present work was to develop a molecular method that would enable determination of the capsular serotypes of Klebsiella isolates without the use of antiserum. PCR amplification of the capsular antigen gene cluster (cps) was followed by digestion with the restriction enzyme HincII (cps PCR-restriction fragment length polymorphism [RFLP] analysis). The profiles (C patterns) obtained for 224 strains representing the 77 known K serotypes showed 3 to 13 fragments ranging in size from 0.2 to 4.4 kb. A total of 97 distinct C patterns were obtained; 100% of 61 pairs of samples tested twice showed reproducible C patterns. The C patterns were K-type specific; i.e., the C pattern(s) of any K serotype was distinct from the C patterns of all other K serotypes, with the only exceptions being serotypes K22 and K37, which are known to cross-react. For 12 of 17 K types for which at least two strains were included, C-pattern variations were found among strains with the same K serotype. Therefore, cps PCR-RFLP analysis has a higher discriminatory power than classical K serotyping. C-pattern identity was observed among strains with a given K type that were collected many years apart and from distinct sources, indicating C-pattern stability. Only 4.5% of the strains were nontypeable, because of unsuccessful PCR amplification (whereas 8 to 23% are nontypeable by classical K serotyping). Three of four noncapsulated strains analyzed showed recognizable C patterns. The K serotypes of 18 (82%) of 22 recent Klebsiella pneumoniae clinical isolates could be deduced from their C patterns. In conclusion, cps PCR-RFLP analysis allows determination of the K serotype, while it is easier to perform and more discriminatory than classical serotyping.     

Development and application of a new scheme for typing Campylobacter jejuni and Campylobacter coli by PCR-based restriction fragment length polymorphism analysis

A molecular typing approach for Campylobacter jejuni and Campylobacter coli was developed with restriction fragment length polymorphism analysis of a 9.6-kb PCR-amplified portion of the lipopolysaccharide gene cluster. Sixty-one Penner serotype reference strains were analyzed with this new genotyping scheme, and 32 genogroups were found. Eleven additional genogroups were obtained from 87 clinical C. jejuni strains tested. This molecular typing method shows a correlation with the Penner heat-stable serotyping method, a phenotypic typing method based on lipopolysaccharide structures that is often used as a "gold standard" for subtyping Campylobacter spp. This strong correlation suggests that the data obtained can be directly compared with epidemiological data collected in the past by classical serotyping of C. jejuni and C. coli. In contrast to the high percentage of nontypeability by phenotyping, this molecular typing method results in 100% typeability and provides a superior alternative to serotyping.     

Flagellin gene typing of Campylobacter jejuni by restriction fragment length polymorphism analysis.

We developed and studied a molecular typing approach for Campylobacter spp. with restriction fragment length polymorphism (RFLP) analysis of the flagellin gene flaA in C. jejuni. Using polymerase chain reaction, we amplified the flaA gene from strains comprising different HL:O serotypes by using a primer set directed at the conserved 5' and 3' flaA gene sequence to generate a 1.7-kb amplicon. The amplicon was further digested with the restriction enzyme DdeI, and the fragments generated were analyzed by agarose gel electrophoresis. In 43 non-outbreak strains of six common HL serotypes (HL 1, 2, 4, 5, 9, and 36) in the United States, 18 RFLP patterns were observed. In U.S. outbreak strains previously studied by 10 other typing methods, flaA typing correlated with the HL serotype within each outbreak, and six additional flaA types were identified. Our results suggest that RFLP analysis of the flaA gene from Campylobacter spp. has sufficient discrimination to be useful as a practical typing method for clinical and epidemiologic investigations.     

Discrimination of major capsular types of Campylobacter jejuni by multiplex PCR

The polysaccharide capsule (CPS) of Campylobacter jejuni is the major serodeterminant of the Penner serotyping scheme. There are 47 Penner serotypes of C. jejuni, 22 of which fall into complexes of related serotypes. A multiplex PCR method for determination of capsule types of Campylobacter jejuni which is simpler and more affordable than classical Penner typing was developed. Primers specific for each capsule type were designed on the basis of a database of gene sequences from the variable capsule loci of 8 strains of major serotypes sequenced in this study and 10 published sequences of other serotypes. DNA sequence analysis revealed a mosaic nature of the capsule loci, suggesting reassortment of genes by horizontal transfer, and demonstrated a high degree of conservation of genes within Penner complexes. The multiplex PCR can distinguish 17 individual serotypes in two PCRs with sensitivities and specificities ranging from 90 to 100% using 244 strains of known Penner type.     

Genotypic and serotypic stability of Campylobacter jejuni strains during in vitro and in vivo passage.

The stability of four typing methods and the sero- and genotypic stability of three Campylobacter jejuni strains were evaluated after subculturing 50 times in triplicate and after colonising mice for up to 26 days. The employed methods were Penner heat-stable serotyping; automated ribotyping (RiboPrinting) using HaeIII restriction enzyme; pulsed-field gel electrophoresis (PFGE) using SmaI, SalI and KpnI; and random amplified polymorphic DNA analysis (RAPD) using primers 1254, 1281 and HLWL85. No changes in any of the DNA profiles or in the reactions to heat-stable antigens were identified among these strains after the in vitro and in vivo passages. However, one isolate became untypeable with RAPD after passage in one of the mice. In addition, eleven other C. jejuni strains of four different serotypes were subcultured ten times to screen for instability. Neither of these showed instability using PFGE and serotyping. Furthermore, three of four strains previously identified as unstable, showed to consist of mixed cultures, which explains the reported profile changes. The results indicate that the applied typing methods are reliable and applicable for typing of Campylobacter isolates from different sources over time, and that many C. jejuni strains are genetically stable as tested by these methods.     

Detection of heat-stable antigens of Campylobacter jejuni and C. coli by direct agglutination and passive hemagglutination

The two serotyping schemes for the detection of heat-stable antigens of Campylobacter jejuni and Campylobacter coli use the same strains for antiserum production but differ in the detection systems used for identifying agglutination. The Penner method uses passive hemagglutination (PHA) while the Laboratory of Enteric Pathogens method uses the same antisera but in a whole-bacterial-cell direct agglutination (DA) protocol. C. jejuni produces a polysaccharide capsule, which is antigenic, and is the main component detected by the PHA method. The DA method will detect both capsule antigens and lipopolysaccharide (LPS) or lipooligosaccharide (LOS) surface antigens. Comparison of both methods by using a selection of isolates from human infection has shown a range of variation in agglutination specificity, reflecting the differences in antigens detected by the two methods. While 27.4% of the 416 C. jejuni isolates reacted with the antisera raised against the same type strains by either method, the majority showed a range of more complex relationships. None of the 37 C. coli isolates reacted with the same antiserum by both methods. Together the two schemes gave a total of 102 distinct combined serogroups for C. jejuni and 16 for C. coli. Thus, while some clonally related isolates share the same capsule and LOS or LPS antigens, other strains appear to have a common capsule antigen but differ in their LPS or LOS structures or vice versa.     

Molecular characterization of Campylobacter jejuni from patients with Guillain-Barré and Miller Fisher syndromes

Campylobacter jejuni has been identified as the predominant cause of antecedent infection in Guillain-Barré syndrome (GBS) and Miller Fisher syndrome (MFS). The risk of developing GBS or MFS may be higher after infection with specific C. jejuni types. To investigate the putative clonality, 18 GBS- or MFS-related C. jejuni strains from The Netherlands and Belgium and 17 control strains were analyzed by serotyping (Penner and Lior), restriction fragment length polymorphism analysis of PCR products of the flaA gene, amplified fragment length polymorphism analysis, pulsed-field gel electrophoresis, and randomly amplified polymorphic DNA analysis. Serotyping revealed 10 different O serotypes and 7 different Lior serotypes, thereby indicating a lack of serotype clustering. Two new O serotypes, O:35 and O:13/65, not previously associated with GBS or MFS were found. Serotype O:19 was encountered in 2 of 18 strains, and none was of serotype O:41. The results of all genotypic methods also demonstrated substantial heterogeneity. No clustering of GBS- or MFS-related strains occurred and no molecular marker capable of separating pathogenic GBS or MFS from non-GBS- or non-MFS-related enteritis strains could be identified in this study. Sialic-acid-containing lipopolysaccharides (LPS) are thought to be involved in the triggering of GBS or MFS through molecular mimicry with gangliosides in human peripheral nerves. Therefore, further characterization of GBS- or MFS-related C. jejuni should target the genes involved in the synthesis of LPS and the incorporation of sialic acid.     

Temporal and geographical distribution and overlap of Penner heat-stable serotypes and pulsed-field gel electrophoresis genotypes of Campylobacter jejuni isolates collected from humans and chickens in Finland during a seasonal peak

The association of Penner heat-stable serotypes and pulsed-field gel electrophoresis genotypes of 208 human and 30 chicken Campylobacter jejuni isolates was studied. Overall, 46% of the human strains had overlapping sero- and genotype combinations with chicken strains. The percentage was reduced to 31% for strains that were considered temporally related. This suggests common environmental sources.     

Comprehensive ribotyping scheme for heat-stable serotypes of Campylobacter jejuni.

Strains from diverse sources belonging to all 47 heat-stable Penner serotypes of Campylobacter jejuni were examined for polymorphism around the 16S rRNA genes. Penner serotype reference strains and a group of nonserotypeable isolates were included in the study. Complete typeability was obtained; 30 distinct PstI and 42 HaeIII polymorphisms were found. Three bands were detected in almost all strains with these enzymes, confirming that three copies of the 16S rRNA gene are typical for C.jejuni. By combination of the two enzyme polymorphisms, 77 16S ribotypes were defined among the 261 strains analyzed. With two exceptions, no specific association was observed between these ribotypes and heat-stable serotypes. Nine serotypes were homogeneous with respect to the 16S ribotype. Most nonserotypeable strains belonged to ribotypes defined elsewhere in the study. The 16S ribotypes of C.jejuni described here were not found in strains of Campylobacter coli, and vice versa.     

Comparison of Campylobacter jejuni lipooligosaccharide biosynthesis loci from a variety of sources

Campylobacter jejuni strains exhibit significant variation in the genetic content of the lipooligosaccharide (LOS) biosynthesis loci with concomitant differences in LOS structure. The C. jejuni LOS loci have been grouped into six classes based on gene content and organization. Utilizing PCR amplifications of genes from these loci, we were able to classify a majority (80%) of the LOS biosynthesis loci from 123 strains of C. jejuni that included 39 of the Penner serotype reference strains. We found that a particular LOS class was not always associated with a specific Penner serotype, and 14 of 16 Guillain-Barré syndrome-associated isolates tested in this study shared the same LOS class. The remaining isolates that could not be classified were often distinguishable from each other based on the results of gene-specific PCR and the lengths of their LOS biosynthesis loci as determined by long (XL) PCR. Sequence analysis of two of these unique XL PCR products demonstrated two new LOS classes. These results support the hypothesis that the LOS locus is a hot spot for genetic exchange and rearrangements. Analysis of the LOS biosynthesis genes by PCR assays can be used for typing C. jejuni and offers the advantage of inferring potential LOS structures.     

Common somatic O and heat-labile serotypes among Campylobacter strains from sporadic infections in the United States.

Somatic O (formerly heat-stable) and heat-labile (HL) serotyping methods are commonly used to type Campylobacter jejuni and Campylobacter coli isolates. Although both systems are effective, the labor and time required for each have limited their application. These systems can be simplified by reducing the number of antisera used. To find an appropriate panel of antisera, we determined the distribution of common serotypes in the United States among a representative sample of 298 Campylobacter isolates. The strains, obtained between July 1989 and June 1990 from persons with sporadic cases of diarrhea, were collected from 19 randomly chosen counties in all geographic (census) regions of the United States. All strains were serotyped by the O and HL systems. By phenotypic methods, 288 C. jejuni, 9 hippurate-negative C. jejuni/C. coli, and 1 Campylobacter lari were identified. Of 57 O antisera, 24 typed 252 (84.6%) strains. Of the 55 HL antisera, 23 serotyped 253 (84.9%) strains. All strains were typeable in the unabsorbed O antisera. In the absorbed HL antisera, four strains were nontypeable and 14 were rough and untypeable. In each geographic region, 9 or more O and HL serotypes were found. Serotypes O:1, O:4, and O:13,16,43,50 and HL 1 were identified in all regions. The combination of both schemes gave greater discrimination than either system alone, but the maintenance of both requires a large resource investment. A serotyping scheme incorporating the 24 most prevalent O and 23 most prevalent HL serotypes could be useful for outbreak support and for surveillance. In the near future, we anticipate using a molecular subtyping method in combination with limited serotyping to distinguish Campylobacter strains.     

In vitro antimicrobial susceptibility, plasmid analysis, and serotyping of epidemic-associated Campylobacter jejuni.

Campylobacter jejuni strains from 11 outbreaks were characterized by antimicrobial susceptibility, plasmid profile, and serotyping by the methods of Lior et al. and Penner and Hennessy. All 31 strains were susceptible to erythromycin, clindamycin, chloramphenicol, kanamycin, tobramycin, streptomycin, and gentamicin. A total of 21 strains from nine outbreaks were resistant to one or more of the following antimicrobial agents: tetracycline, metronidazole, ampicillin, or carbenicillin. Of the 31 strains, 19 possessed plasmid DNA; 4 of the strains containing plasmids were sensitive to all antimicrobial agents tested. All of the strains that were resistant to tetracycline contained a 38-megadalton plasmid, and these plasmids shared common nucleic acid sequences. No other antimicrobial resistance was associated with the presence of plasmid DNA. Eight outbreaks appeared to have been caused by a single serotype, whereas in three outbreaks multiple serotypes were found. In two of the three outbreaks with multiple serotypes, plasmid profiles were also indicative of multiple strains of C. jejuni. Antimicrobial susceptibility and plasmid profile are potentially useful epidemiological markers for C. jejuni and may be used to supplement serotyping.     

Can the fliC PCR-restriction fragment length polymorphism technique replace classic serotyping methods for characterizing the H antigen of enterotoxigenic Escherichia coli strains?

In this study, we performed fliC PCR-restriction fragment length polymorphism (RFLP) to investigate whether this technique would be better than classic serotyping for the characterization of the H antigen in enterotoxigenic Escherichia coli (ETEC) strains. We showed that the fliC genes from ETEC strains can be characterized by restriction analysis of their polymorphism. Only one allele of the fliC gene from ETEC strains was found for each flagellar antigen, with the exception of H21. Nonmotile strains could also be characterized using this molecular technique. Moreover, determination of the somatic antigen was guided by the identification of the flagellar antigen from previously unknown serotypes of ETEC strains by PCR-RFLP, thus reducing the number of anti-antigen O sera used. The PCR-RFLP technique proved to be faster than classic serotyping for the characterization of the E. coli H antigen, taking 2 days to complete instead of the 7 or more days using classic serotyping. In conclusion, the H molecular typing for Enterobacteriaceae members may become an important epidemiological tool for the characterization of the H antigen of E. coli pathotypes. The PCR-RFLP technique is capable of guiding the determination of the H antigen and could partially replace seroagglutination. With the determination of the molecular profiles of alleles from strains obtained in epidemiological studies, new patterns will be described for ETEC strains or other E. coli pathotypes, thus permitting widespread use of this technique to characterize fliC genes and determine the H antigen of E. coli strains.     

Evidence for acquisition of the lipooligosaccharide biosynthesis locus in Campylobacter jejuni GB11, a strain isolated from a patient with Guillain-Barré syndrome, by horizontal exchange

Campylobacter jejuni GB11, a strain isolated from a patient with Guillain-Barré syndrome, has been shown to be genetically closely related to the completely sequenced strain C. jejuni NCTC 11168 by various molecular typing and serotyping methods. However, we observed that the lipooligosaccharide (LOS) biosynthesis genes strongly diverged between GB11 and NCTC 11168. We sequenced the LOS biosynthesis locus of GB11 and found that it was nearly identical to the class A LOS locus from the C. jejuni HS:19 Penner serotype strain (ATCC 43446). Analysis of the DNA sequencing data showed that a horizontal exchange event involving at least 14.26 kb had occurred in the LOS biosynthesis locus of GB11 between galE (Cj1131c in NCTC 11168) and gmhA (Cj1149 in NCTC 11168). Mass spectrometry of the GB11 LOS showed that GB11 expressed an LOS outer core that mimicked the carbohydrate portion of the gangliosides GM1a and GD1a, similar to C. jejuni ATCC 43446. The serum from the GB11-infected patient was shown to react with the LOS from both GB11 and ATCC 43446 but not with that from NCTC 11168. These data indicate that the antiganglioside response in the GB11-infected patient was raised against the structures synthesized by the acquired class A LOS locus.     

Deoxyribonucleic acid restriction digest patterns in Campylobacter species: a comparison with Penner serotype

Diversity, based on restriction fragment length polymorphism (RFLP) analysis, was studied in 48 strains of Campylobacter, comprising 27 chicken and 21 human strains of C. jejuni and C. coli, using genomic Southern hybridisation. Restriction digests of chromosomal DNA were prepared by treating with HaeIII and probed using a C. jejuni DNA probe. Nineteen distinct hybridisation patterns were identified, and differences in hybridisation pattern between members of the two species, and in individual strains of the same species, were seen. The method described proved more discriminatory than the Penner serotype, as strains from the same serotype were distinguished. The relative simplicity of the patterns obtained, together with the apparent diversity identified among individual strains and species, suggests that DNA fingerprinting using the C. jejuni DNA probe could be a useful identification method in epidemiological studies of Campylobacter infection in Nigeria.     

Comparison of the Penner and Lior methods for serotyping Campylobacter spp.

We compared two Campylobacter serotyping systems by using 1,405 isolates of Campylobacter collected from human, animal, and environmental sources during epidemiologic investigations and special studies. We found 96.1% of isolates to be typable by the Penner method for heat-stable antigens, which involved the use of an indirect hemagglutination technique, and 92.1% of isolates to be typable by the Lior method for heat-labile antigens, which involved the use of a slide agglutination technique and absorbed antisera. Absorbed antisera were not required for the Penner method, making that method less difficult to implement. The Lior method was simpler to perform and gave more rapid results than did the Penner method. Cultures frequently reacted in multiple antisera with the Penner method, whereas multiple reactions were rare with the Lior method. Thus, results were easier to interpret with the Lior system. Strains of a single serotype in one system were sometimes found to be multiple serotypes in the other system; hence, the two methods have the potential to be complementary. Both systems were comparable in serotyping isolates from human and nonhuman sources and for evaluating the relationship of strains collected during outbreak investigations.     

Complete genotyping of mucosal human papillomavirus using a restriction fragment length polymorphism analysis and an original typing algorithm.

BACKGROUND: Due to the differences in the oncogenic activity of human papillomaviruses (HPV), it is clinically important to accurately identify HPV types in a simple and time effective manner. OBJECTIVES: We aimed at developing a straightforward and cost-effective assay to individually identify all mucosal HPVs, based on the amplification of L1 gene using MY09/11 primers, and subsequent restriction fragment length polymorphism (RFLP) analysis. STUDY DESIGN: We made use of bioinformatic tools to analyze all published DNA sequences of 49 mucosal HPV types for PstI, HaeIII, DdeI and RsaI restriction sites. Based on the RFLP patterns, we have designed an original genotyping algorithm. RESULTS: Each HPV type presented a distinct RFLP pattern, which was visually distinguishable on polyacrylamide gels. A set of 27 pre-selected patient samples of known HPV types was confirmed positive for the same HPV type using this RFLP assay. Furthermore, in a random and blind HPV typing experiment performed in 30 untyped clinical samples, RFLP data consistently matched DNA sequencing results. CONCLUSIONS: Our polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method, using 4 restriction enzymes (PstI, HaeIII, DdeI, RsaI) and an original genotyping algorithm, allows discrimination of all individual mucosal HPV types in single infections, and even detection of multiple infections. This assay gives complementary information to commercially available methods, and may also be financially advantageous, particularly when financial resources are scarce.     

Genome Sequence-Based Fluorescent Amplified Fragment Length Polymorphism of Campylobacter jejuni, Its Relationship to Serotyping, and Its Implications for Epidemiological Analysis

The published genome sequence of Campylobacter jejuni strain NCTC 11168 was used to model an accurate and highly reproducible fluorescent amplified fragment length polymorphism (FAFLP) analysis. Predicted and experimentally observed amplified fragments (AFs) generated with the primer pair HindIII+A and HhaI+A were compared. All but one of the 61 predicted AFs were reproducibly detected, and no unpredicted fragments were amplified. This FAFLP analysis was used to genotype 74 C. jejuni strains belonging to the nine heat-stable (HS) serotypes most prevalent in human disease in England and Wales. The 74 C. jejuni strains exhibited 60 FAFLP profiles, and cluster analysis of them yielded a radial tree showing genetic relationships between and within 13 major clusters. Some clusters were related, and others were unrelated, to a single HS serotype. For example, all strains belonging to serotypes HS6 and HS19 grouped into corresponding single genotypic clusters, while strains of serotypes HS11 and HS18 each grouped into two genotypic clusters. Strains of HS50, the most prevalent serotype infecting humans, were found both in one large (multiserotype) cluster complex and dispersed throughout the tree. The strain genotypes within each FAFLP cluster were characterized by a particular combination of AFs, and among the cluster there were additional differential AFs. Identification of such AFs could act as a search tool to look for potential associations with disease or animal hosts, when applied to large number of human isolates. Genome-sequence based FAFLP, thus, has the potential to establish a genetic database for epidemiological investigations of Campylobacter.     

Biotype and Lior serogroup distribution of enteric Campylobacter isolated from children in Bangui (Central African Republic), and comparison with Penner serotypes

The new extended biotyping scheme of Lior as well as the slide agglutination technique were applied to 209 strains of enteric Campylobacter isolated from children in Bangui (Central African Republic). Three biotypes of C. jejuni and 2 biotypes of C. coli were identified among the strains; 31.1% were C. jejuni I, 11% C. jejuni II, 2.4% C. jejuni III, 44% C. coli I and 11.5% C. coli II. We were able to serotype 71.3% of the strains with 20 immune sera prepared against strains of Campylobacter isolated previously; 63% of the strains were distributed among the ten most common serogroups. No significant difference was observed in the distribution of biotypes or serogroups between strains from healthy and diarrhoeic children. Comparison of Lior serogroups with Penner serotypes showed that different Penner serotypes may correspond to a Lior serogroup and vice versa.