Use of pulsed-field agarose gel electrophoresis to size genomes of Campylobacter species and to construct a SalI map of Campylobacter jejuni UA580

Peritonitis Due to Stenotrophomonas Maltophilia in Patients Undergoing Chronic Peritoneal Dialysis

The occurrence of cases of Stenotrophomonas maltophilia peritonitis in chronic peritoneal dialysis (PD) patients prompted a review of our experience with this condition. A search of microbiology records revealed seven episodes of S. maltophilia peritonitis in 7 patients in 1996 — 3.8% of all PD patients — compared to no cases in 1994 and 1995 ( p = 0.01). Patients ranged in age from 16 to 64 years; there were 3 males and 4 females. Six of seven episodes of peritonitis were community acquired and one was hospital acquired. No temporal clustering of cases was seen. Patients were from different urban and rural communities. Patients used the same commercially supplied dialysate fluid, different dialysis techniques, and were taught a no-touch technique for connection. Treatment of peritonitis required removal of the Tenckhoff catheter in 4 of 7 cases. Fingerprinting of six available isolates by polymerase chain reaction using primers derived from the conserved region of the 16/23Sr RNA gene sequence and pulsed field gel electrophoresis revealed all to be unique strains. A case-control study comparing 7 S. maltophilia cases to 21 PD controls showed case patients to be younger and more likely to be on immuno-suppressive therapy. We conclude that S. maltophilia has emerged as an important cause of peritonitis in our continuous ambulatory PD population. Evidence to date suggests community acquisition with no evidence of a common source.

Campylobacter: from microbiology to prevention

In last years, Campylobacter spp has become one of the most important foodborne pathogens even in high-income countries. Particularly, in Europe, Campylobacteriosis is, since 2005, the foodborne disease most frequently notified and the second in USA, preceded by the infection due to Salmonella spp. Campylobacter spp is a commensal microorganism of the gastrointestinal tract of many wild animals (birds such as ducks and gulls), farm animals (cattle and pigs) and companion animals (such as dogs and cats) and it is responsible for zoonoses. The transmission occurs via the fecal-oral route through ingestion of contaminated food and water. The disease varied from a watery diarrhea to a severe inflammatory diarrhea with abdominal pain and fever and can be burdened by some complications. The main recognized sequelae are Guillain-Barré Syndrome (GBS), the Reactive Arthritis (REA) and irritable bowel syndrome (IBS). Recently, many cases of Campylobacter spp isolated from human infections, showed an important resistance to various antibiotics such as tetracyclines and fluoroquinolones. For these reasons, the prevention of this infection plays an essential role. Many preventive measures exist to limit the transmission of the pathogens and the subsequent disease such as the health surveillance, the vaccination of the poultry and the correct food hygiene throughout the entire production chain. A global surveillance of Campylobacteriosis is desirable and should include data from all countries, including notifications of cases and the microbiological data typing of strains isolated from both human and animal cases.

Analysis of Genomic Diversity among Helicobacter pylori Strains Isolated from Iranian Children by Pulsed Field Gel Electrophoresis

OBJECTIVE

Presence of genomic diversity among Helicobacter pylori (H. pylori) strains have been suggested by numerous investigators. Little is known about diversity of H. pylori strains isolated from Iranian children and their association with virulence of the strains. Our purpose was to assess the degree of genomic diversity among H. pylori strains isolated from Iranian-children, on the basis of vacA genotype, cagA status of the strains, sex, age as well as the pathological status of the patients.

METHODS

Genomic DNA from 44 unrelated H. pylori strains isolated during 1997-2009, was examined by pulse-field gel electrophoresis (PFGE). Pathological status of the patients was performed according to the modified Sydney-system and genotype/status of vacA/cagA genes was determined by PCR. PFGE was performed using XbaI restriction-endonuclease and the field inversion-gel electrophoresis system.

FINDINGS

No significant relationship was observed between the patterns of PFGE and the cagA/vacA status/genotype. Also no relationship was observed between age, sex, and pathological status of the children and the PFGE patterns of their isolates. Similar conclusion was obtained by Total Lab software. However, more relationship was observed between the strains isolated in the close period (1997-2009, 2001-2003, 2005-2007, and 2007-2009) and more difference was observed among those obtained in the distant periods (1997 and 2009).

CONCLUSION

H. pylori strains isolated from children in Iran are extremely diverse and this diversity is not related to their virulence characteristics. Occurrence of this extreme diversity may be related to adaptation of H. pylori strains to variable living conditions during transmission between various host individuals.

Detection, identification and quantification of Campylobacter jejuni, coli and lari in food matrices all at once using multiplex qPCR

BACKGROUND

Thermotolerant Campylobacter jejuni, coli and lari are recognized as leading food-borne pathogens causing an acute bacterial enteritis worldwide. Due to narrow spectrum of their biochemical activity, it is very complicated to distinguish between individual species. For reliable risk assessment, proper incidence evaluation or swift sample analysis regarding individual species, a demand for simple and rapid method for their distinguishing is reasonable. In this study, we evaluated a reliable and simple approach for their simultaneous detection, species identification and quantification using multiplex qPCR.

RESULTS

Species specific primers and hydrolysis probes are directed to hippuricase gene of C. jejuni, serine hydroxymethyltransferase gene of C. coli and peptidase T gene of C. lari. Efficiencies of reactions were 90.85% for C. jejuni, 96.97% for C. coli and 92.89% for C. lari. At 95.00% confidence level and when cut off is set to 38 cycles, limits of detection are in all cases under 10 genome copies per reaction which is very appreciated since it is known that infectious doses are very low.

CONCLUSIONS

Proposed assay was positively validated on different food matrices (chicken wing rinses, chicken juice and homogenized fried chicken strips). No inhibition of PCR reaction occurred. Assay was evaluated in accordance with MIQE handbook.

Pulsed-field gel electrophoresis typing of Campylobacter fetus subsp. fetus from sheep abortions in the Hawke's Bay region of New Zealand

AIM

To type Campylobacter isolates from sheep abortions from the Hawke's Bay region of New Zealand.

METHODS

Campylobacter isolates were collected from aborted sheep fetuses from commercial farms in the Hawke's Bay region. Information on the Campylobacter vaccination status of flocks in the study was collected. Isolates were identified to species level using standard phenotypic tests, then typed using pulsed-field gel electrophoresis (PFGE).

RESULTS

Eighty-one C. fetus subsp. fetus isolates were cultured from aborted sheep fetuses from 25 farms and four C. jejuni isolates were cultured from fetuses from three farms. The C. fetus subsp. fetus isolates were classified into six PFGE groups. A single pulsed-field type predominated amongst isolates from 19 of the 25 farms. The C. jejuni isolates comprised two types.

CONCLUSIONS

A range of C. fetus subsp. fetus PFGE types was identified, and one type, B1, was found most frequently. Campylobacter fetus subsp. fetus was only isolated from samples from sheep that had not been vaccinated with C. fetus subsp. fetus vaccine that season.

Morphologic, genetic, and biochemical characterization of Helicobacter magdeburgensis, a novel species isolated from the intestine of laboratory mice

BACKGROUND

The presence of enterohepatic Helicobacter species (EHS) is commonly noted in mouse colonies. These infections often remain unrecognized but can cause severe health complications or more subtle host immune perturbations and therefore can confound the results of animal experiments. The aim of this study was to isolate and characterize a putative novel EHS that has previously been detected by PCR screening of specific-pathogen-free mice.

MATERIALS AND METHODS

 Biochemical analysis of enzyme activities (API campy), morphologic investigation (Gram-staining and electron microscopy) and genetic analyses (16SrRNA and 23SrRNA analyses, DNA fingerprinting, restriction fragment polymorphisms, and pulsed-field gel electrophoresis) were used to characterize isolated EHS. Genomic DNA fragments were sequenced to develop a species-specific PCR detection assay.

RESULTS

Scanning electron microscopy revealed the presence of spiral-shaped EHS, which varied in length (2.5-6 μm) and contained single monopolar or single bipolar sheathed flagella. The bacteria were grown under anaerobic conditions, preferably on agar plates containing serum or blood. The 16SrRNA, genetic, and biochemical analyses indicated the identification of a novel EHS species, named Helicobacter magdeburgensis. We also examined the genome content using pulsed-field gel electrophoresis. Based on the pattern produced by two restriction enzymes, BamIII and KspI, the genome size was determined to be about 1.7-1.8 Mbp.

CONCLUSION

We isolated and characterized a novel EHS species, H. magdeburgensis, morphologically, biochemically, and genetically. These results are important for future studies on the prevalence and pathophysiologic relevance of such infections. Our PCR assay can be used to detect and discriminate H. magdeburgensis from other Helicobacter species.

Transmission ofCampylobacterspp. in a poultry slaughterhouse and genetic characterisation of the isolates by pulsed-field gel electrophoresis

1. Contamination of retail products with Campylobacter spp. during the slaughter of poultry is a well-known problem of product hygiene. Mechanical evisceration often leads to intestinal rupture and discharge of gut contents, which can contain zoonotic and human pathogens. Processes along the slaughter line cause aerosols and airborne droplets, containing bacterial loads. 2. To estimate the possible transmission routes of intestinal Campylobacter, 36 measurements of the bioaerosol (Andersen sampler and SKC BioSampler), 30 cloacal (of three flocks), 10 equipment and 4 sedimentation samples were tested for the presence of Campylobacter species. 3. The results imply that, in addition to contaminated equipment, which was Campylobacter-positive in 80% of cases, aerosols with peak values of 4.0 x 10(4) (test series 1) and 1.4 x 10(4) (test series 2) CFU/m3 also provide a potential vector for horizontal transmission. 4. To explore the genetic similarities of isolates from different origins, 18 isolates recovered from air, 26 cloacal, 8 equipment and 4 sedimentation isolates were analysed by pulsed-field gel electrophoresis (PFGE), using the restriction enzymes Sma I and Sal I. The similarity of cloacal isolates with isolates from equipment, air and sediment, suggest that the contamination is of intestinal origin. 5. There were direct links between Campylobacter-positive flocks and the presence of the same strains in the aerosol of the slaughter hall. Air as a potential source for microbial transmission must be taken into account.

Campylobacter spp. subtype analysis using gel-based repetitive extragenic palindromic-PCR discriminates in parallel fashion to flaA short variable region DNA sequence analysis

AIMS

The repetitive extragenic palindromic-PCR (rep-PCR) subtyping technique, which targets repetitive extragenic DNA sequences in a PCR, was optimized for Campylobacter spp. These data were then used for comparison with the established genotyping method of flaA short variable region (SVR) DNA sequence analysis as a tool for molecular epidemiology.

METHODS AND RESULTS

Uprime Dt, Uprime B1 or Uprime RI primers were utilized to generate gel-based fingerprints from a set of 50 Campylobacter spp. isolates recovered from a variety of epidemiological backgrounds and sources. Analysis and phenogram tree construction, using the unweighted pair group method with arithmetic mean, of the generated fingerprints demonstrated that the Uprime Dt primers were effective in providing reproducible patterns (100% typability, 99% reproducibility) and at placing isolates into epidemiological relevant groups. Genetic stability of the rep-PCR Uprime Dt patterns under nonselective, short-term transfer conditions revealed a Pearson's correlation approaching 99%. These same 50 Campylobacter spp. isolates were analysed by flaA SVR DNA sequence analysis to obtain phylogenetic relationships.

CONCLUSIONS

The Uprime Dt primer-generated rep-PCR phenogram was compared with a phenogram generated from flaA SVR DNA sequence analysis of the same isolates. Comparison of the two sets of resulting genomic relationships revealed that both methods segregated isolates into similar groups.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results indicate that rep-PCR analysis performed using the Mo Bio Ultra Clean Microbial Genomic DNA Isolation Kit for DNA isolation and the Uprime DT primer set for amplification is a useful and effective tool for accurate differentiation of Campylobacter spp. for subtyping and epidemiological analyses.

Genotyping of Campylobacter spp. from retail meats by pulsed-field gel electrophoresis and ribotyping

AIMS

To determine the genetic relatedness of Campylobacter spp. from retail meat products, and compare the discriminatory power of pulsed-field gel electrophoresis (PFGE) and automatic ribotyping.

METHODS AND RESULTS

A total of 378 Campylobacter isolates recovered from 159 raw meats (130 chicken, 25 turkey, three pork and one beef) sampled from 50 retail grocery stores of four supermarket chains in the Maryland suburban area from August 1999 to July 2000 were analysed by PFGE with SmaI, 120 isolates of which were also characterized by ribotyping with PstI using RiboPrinter system. A total of 148 unique PFGE patterns were identified, 91 of which were present in multiple Campylobacter isolates and 24 in multiple meat samples. Nineteen Campylobacter clones with identical PFGE patterns recurred frequently (up to nine times) throughout the sampling period. Comparing ribotyping with PFGE, we identified 44 PFGE patterns and 22 RiboGroups among the 120 isolates tested. Multiple PFGE patterns within one RiboGroup were commonly observed, as well as multiple RiboGroups within one PFGE pattern.

CONCLUSIONS

Although Campylobacter present in retail meats were genetically diverse, certain clones persisted in poultry meats. PFGE had a greater discriminatory power than ribotyping, and the two methods were complementary in genotyping Campylobacter.

SIGNIFICANCE AND IMPACT OF THE STUDY

Genomic DNA fingerprinting of Campylobacter confirmed diverse and recurrent Campylobacter clones in the retail meats, which provides additional data for a better understanding of the epidemiological aspect of Campylobacter infection.

Diversity within the Campylobacter jejuni type I restriction-modification loci

The type I restriction-modification (hsd) systems of 73 Campylobacter jejuni strains were characterized according to their DNA and amino acid sequences, and/or gene organization. A number of new genes were identified which are not present in the sequenced strain NCTC 11168. The closely related organism Helicobacter pylori has three type I systems; however, no evidence was found that C. jejuni strains contain multiple type I systems, although hsd loci are present in at least two different chromosomal locations. Also, unlike H. pylori, intervening ORFs are present, in some strains, between hsdR and hsdS and between hsdS and hsdM. No definitive function can be ascribed to these ORFs, designated here as rloA-H (R-linked ORF) and mloA-B (M-linked ORF). Based on parsimony analysis of amino acid sequences to assess character relatedness, the C. jejuni type I R-M systems are assigned to one of three families: 'IAB', 'IC' or 'IF'. This study confirms that HsdM proteins within a family are highly conserved but share little homology with HsdM proteins from other families. The 'IC' hsd loci are >99 % identical at the nucleotide level, as are the 'IF' hsd loci. Additionally, whereas the nucleotide sequences of the 'IAB' hsdR and hsdM genes show a high degree of similarity, the nucleotide sequences of the 'IAB' hsdS and rlo genes vary considerably. This diversity suggests that recombination between 'IAB' hsd loci would lead not only to new hsdS alleles but also to the exchange of rlo genes; five C. jejuni hsd loci are presumably the result of such recombination. The importance of these findings with regard to the evolution of C. jejuni type I R-M systems is discussed.

Genotypic analysis of strains of mutans streptococci by pulsed-field gel electrophoresis

The species and serotypes of various strains of S. mutans and S. sobrinus were characterized by pulsed-field gel electrophoresis after the genomic DNA from the various strains had been digested with five restriction enzymes (EcoR I, Xba I, Hind III, Sfi I and BssH II) separately. Among these restriction enzymes, BssH II was very useful for the characterization of species and serotypes and, in particular, digestion discriminated between serotypes d and g. The restriction patterns obtained from the genomic DNA of isolates isolated from children's saliva were essentially identical to those from the genomic DNA of the standard laboratory strains. Patterns of BssH II digests of the genomic DNA of 10 isolates identified as S. sobrinus were characteristic of serotype g of the standard laboratory strains. Our results indicate that digestion with BssH II and subsequence analysis by pulsed-field gel electrophoresis should be useful for the characterization of species and serotypes and for epidemiological studies of mutans streptococci.

Isolation and characterisation of Arcobacter butzleri from meat

A survey was conducted to determine the prevalence of Arcobacter in ground chicken, pork, beef and lamb meats. Meat samples were enriched in Arcobacter broth (AB) containing cefoperazone, amphotericin and teicoplanin (CAT) supplement. Samples were screened for the presence of Arcobacter spp. using a multiplex polymerase chain reaction (PCR) followed by isolation on blood and selective agar. Arcobacter butzleri was the only species of Arcobacter isolated from 35% of 88 samples of ground meats. A. butzleri was more frequently isolated from poultry (73%) than pork (29%), beef (22%) or lamb (15%) samples. No significant differences were found in the isolation rates and from the different regions sampled. Isolates were characterised by pulsed-field gel electrophoresis (PFGE) using SacII, EagI and SmaI restriction endonucleases. A number of isolates with indistinguishable PFGE fingerprints were found to be epidemiologically related, which may indicate cross-contamination of common types of Arcobacter from different meat species or between meat species. The public health significance of Arcobacter in ground meat needs to be determined.

Chromosome mapping in lactic acid bacteria

The chromosome structure of lactic acid bacteria has been investigated only recently. The development of pulsed-field gel electrophoresis (PFGE) combined with other DNA-based techniques enables whole-genome analysis of any bacterium, and has allowed rapid progress to be made in the knowledge of the lactic acid bacteria genome. Lactic acid bacteria possess one of the smallest eubacterial chromosomes. Depending on the species, the genome sizes range from 1.1 to 2.6 Mb. Combined physical and genetic maps of several species are already available or close to being achieved. Knowledge of the genomic structure of these organisms will serve as a basis for future genetic studies. Macrorestriction fingerprinting by PFGE is already one of the major tools for strain differentiation, identification of individual strains, and the detection of strain lineages. The genome data resulting from these studies will be of general application strain improvement.

Phenotypic and molecular characterization of bovine Campylobacter fetus strains isolated in Brazil

The objective of the present study was to characterize the phenotypic and molecular aspects of Campylobacter fetus strains isolated from bovine herds with reproductive problems. Thirty-one Brazilian field isolates, together with one reference strain of each subspecies of C. fetus, were analyzed. The strains were submitted to phenotypic identification followed by subspecies characterization using the polymerase chain reaction (PCR) and numeric evaluation of restriction fragment length polymorphism (RFLP) separated by pulsed-field gel electrophoresis (PFGE). Phenotypically, 4 isolates (12.1%) were classified as C. fetus subsp. fetus, and 29 isolates (87.9%) were classified as C. fetus subsp. venerealis. However, according to molecular analysis, only 1 isolate (3.0%) was classified as C. fetus subsp. fetus (the reference strain), whereas 32 isolates (97.0%) were considered C. fetus subsp. venerealis. SalI digestion of C. fetus genomic DNA, obtained from the 33 strains, yielded 7-10 DNA fragments ranging in size from 40 to 373kb, with 12 distinct patterns. Furthermore, the numeric analysis by neighbor-joining of the DNA from the 33 strains resulted in a dendrogram in which 2 distinct groups were identified. It was concluded that phenotypic characterization of C. fetus subspecies might lead to erroneous classification of field isolates. Although RFLP-PFGE is a powerful and reliable technique to characterize C. fetus, it has the inconvenience of being time consuming and laborious. Whereas PCR, besides providing rapid results, was found to be reliable and convenient for the characterization of field isolates of C. fetus.

Transmission of Campylobacter hyointestinalis from a pig to a human

We report on a case of human gastroenteritis caused by the pathogen Campylobacter hyointestinalis. Recurrent watery diarrhea and intermittent vomiting were the most significant symptoms of the previously healthy patient. Whole-cell protein electrophoresis and 16S rRNA gene sequencing were used to identify this Campylobacter species. Investigation of the patient's surroundings led to the recovery of a second C. hyointestinalis strain originating from porcine feces. Subsequent typing of the human and the porcine isolates by pulsed-field gel electrophoresis revealed similar macrorestriction profiles, indicating transmission of this pathogen.

Rapid pulsed-field gel electrophoresis protocol for subtyping of Campylobacter jejuni

We developed a rapid pulsed-field gel electrophoresis (PFGE) protocol for subtyping Campylobacter isolates based on the standardized protocols used by PulseNet laboratories for the subtyping of other food-borne bacterial pathogens. Various combinations of buffers, reagents, reaction conditions (e.g., cell suspension concentration, lysis time, lysis temperature, and restriction enzyme concentration), and electrophoretic parameters were evaluated in an effort to devise a protocol that is simple, rapid, and robust. PFGE analysis of Campylobacter isolates can be completed in 24 to 30 h using this protocol, whereas the most widely used current protocols require 3 to 4 days to complete. Comparison of PFGE patterns obtained in six laboratories showed that subtyping results obtained using this protocol are highly reproducible.

Specificities of eleven different DNA methyltransferases of Helicobacter pylori strain 26695

Methyltransferases (MTases) of procaryotes affect general cellular processes such as mismatch repair, regulation of transcription, replication, and transposition, and in some cases may be essential for viability. As components of restriction-modification systems, they contribute to bacterial genetic diversity. The genome of Helicobacter pylori strain 26695 contains 25 open reading frames encoding putative DNA MTases. To assess which MTase genes are active, strain 26695 genomic DNA was tested for cleavage by 147 restriction endonucleases; 24 were found that did not cleave this DNA. The specificities of 11 expressed MTases and the genes encoding them were identified from this restriction data, combined with the known sensitivities of restriction endonucleases to specific DNA modification, homology searches, gene cloning and genomic mapping of the methylated bases m(4)C, m(5)C, and m(6)A.

Purification, characterization and sequence analysis of Omp50,a new porin isolated from Campylobacter jejuni

A novel pore-forming protein identified in Campylobacter was purified by ion-exchange chromatography and named Omp50 according to both its molecular mass and its outer membrane localization. We observed a pore-forming ability of Omp50 after re-incorporation into artificial membranes. The protein induced cation-selective channels with major conductance values of 50-60 pS in 1 M NaCl. N-terminal sequencing allowed us to identify the predicted coding sequence Cj1170c from the Campylobacter jejuni genome database as the corresponding gene in the NCTC 11168 genome sequence. The gene, designated omp50, consists of a 1425 bp open reading frame encoding a deduced 453-amino acid protein with a calculated pI of 5.81 and a molecular mass of 51169.2 Da. The protein possessed a 20-amino acid leader sequence. No significant similarity was found between Omp50 and porin protein sequences already determined. Moreover, the protein showed only weak sequence identity with the major outer-membrane protein (MOMP) of Campylobacter, correlating with the absence of antigenic cross-reactivity between these two proteins. Omp50 is expressed in C. jejuni and Campylobacter lari but not in Campylobacter coli. The gene, however, was detected in all three species by PCR. According to its conformation and functional properties, the protein would belong to the family of outer-membrane monomeric porins.

Computer-assisted analysis and epidemiological value of genotyping methods for Campylobacter jejuni and Campylobacter coli

For epidemiological tracing of the thermotolerant Campylobacter species C. jejuni and C. coli, reliable and highly discriminatory typing techniques are necessary. In this study the genotyping techniques of flagellin typing (flaA typing), pulsed-field gel electrophoresis (PFGE), automated ribotyping, and amplified fragment length polymorphism (AFLP) fingerprinting were compared. The following aspects were compared: computer-assisted analysis, discriminatory power, and use for epidemiological typing of campylobacters. A set of 50 campylobacter poultry isolates from The Netherlands and neighboring countries was analyzed. Computer-assisted analysis made cluster analysis possible and eased the designation of different genotypes. AFLP fingerprinting was the most discriminatory technique, identifying 41 distinct genotypes, while PFGE identified 38 different types, flaA typing discriminated 31 different types, and ribotyping discriminated 26 different types. Furthermore, AFLP analysis was the most suitable method for computer-assisted data analysis. In some cases combining the results of AFLP fingerprinting, PFGE, and flaA typing increased our ability to differentiate strains that appeared genetically related. We conclude that AFLP is a highly discriminatory typing method and well suited for computer-assisted data analysis; however, for optimal typing of campylobacters, a combination of multiple typing methods is needed.

Viability and DNA maintenance in nonculturable spiral Campylobacter jejuni cells after long-term exposure to low temperatures

Survival of Campylobacter jejuni at 4 and 20 degrees C was investigated by using cellular integrity, respiratory activity, two-dimensional (2D) protein profile, and intact DNA content as indicators of potential viability of nonculturable cells. Intact DNA content after 116 days, along with cellular integrity and respiring cells, was detected for up to 7 months at 4 degrees C by pulsed-field gel electrophoresis. Most changes in 2D protein profiles involved up- or down-regulation.

Bacterial fingerprinting by flow cytometry: bacterial species discrimination

BACKGROUND

A flow cytometric measurement (FCM) technique has been developed to size DNA fragments. Individual fragments of a restriction digest of genomic DNA, stained with an intercalating dye, are passed through an ultrasensitive cytometer. The measured fluorescence intensity from each fragment is proportional to the fragment length.

METHODS

The isolation of bacterial genomic DNA and digestion by restriction enzymes were performed inside an agarose plug. Rare cutting enzymes were employed to produce a manageable number of DNA fragments. Electroelution was used to move the DNA fragments from the agarose plug into a solution containing polyamines to protect the DNA from shear-induced breakage. The DNA was stained with the bisintercalating dye thiazole orange homodimer and introduced into our ultrasensitive flow cytometer. A histogram of the fluorescence intensities (fingerprint) was constructed.

RESULTS

Gram-positive Bacillus globigii and gram-negative bacteria Escherichia coli and Erwinia herbicola were distinguished by the fingerprint pattern of restriction fragments of their genomic DNA. DNA sizes determined by FCM are in good agreement with pulsed-field gel electrophoresis (PFGE) analysis. Flow cytometry requires only picogram quantities of purified DNA and takes less than 10 min for data collection and analysis. When the total sample preparation time is included, the analysis times for PFGE and FCM are similar ( approximately 3 days).

CONCLUSIONS

FCM is an attractive technique for the identification of bacterial species. It is more sensitive and potentially much faster than PFGE.

Identification of the enteropathogens Campylobacter jejuni and Campylobacter coli based on the cadF virulence gene and its product

Campylobacter jejuni and Campylobacter coli are common causes of gastroenteritis in humans. Infection with C. jejuni or C. coli is commonly acquired by eating undercooked chicken. The goal of this study was to develop specific detection assays for C. jejuni and C. coli isolates based on the cadF virulence gene and its product. The cadF gene from C. jejuni and C. coli encodes a 37-kDa outer membrane protein that promotes the binding of these pathogens to intestinal epithelial cells. A fragment of approximately 400 bp was amplified from 38 of 40 (95%) C. jejuni isolates and 5 of 6 (83.3%) C. coli isolates with primers designed to amplify an internal fragment of the cadF gene. PCR was then used to amplify Campylobacter DNA from store-bought chickens. A 400-bp band was amplified from 26 of the 27 chicken carcasses tested by the PCR-based assay. The CadF protein was detected in every C. jejuni and C. coli isolate tested, as judged by immunoblot analysis with a rabbit anti-C. jejuni 37-kDa serum. In addition, methanol-fixed samples of whole-cell C. jejuni and C. coli were detected with the rabbit anti-37-kDa serum by using an indirect-immunofluorescence microscopy assay. These findings indicate that the cadF gene and its product are conserved among C. jejuni and C. coli isolates and that a PCR assay based on the cadF gene may be useful for the detection of Campylobacter organisms in food products.

Characterization of Helicobacter felis by pulsed-field gel electrophoresis, plasmid profiling and ribotyping

BACKGROUND

Helicobacter felis, an organism naturally infecting both canine and feline gastric mucosa, has been largely used as in animal models to study the ecology and treatment of human Helicobacter pylori infections. H. felis has not yet been studied at the genetic level.

METHODS

The aims of this study were to modify an in situ DNA isolation method suitable for H. felis and, by the use of pulsed-field gel electrophoresis (PFGE), plasmid profiling, and ribotyping, to determine the degree of genetic variation among H. felis strains isolated from cats and dogs from various geographic locations, and to determine the genome size of H. felis. Furthermore, the ability of these new H. felis strains to colonize mice was tested.

RESULTS

Most H. felis strains were distinguishable from each other, and 20 distinct PFGE types were detected. Four pairs of strains within a country and animal species produced identical patterns. All strains tested were found to carry several plasmids and plasmid profiling was equally discriminatory to PFGE. Ribotyping was not able to discriminate all the strains.

CONCLUSIONS

The genome size of H. felis was found to be approximately 1.6 Mb.

The diverse and dynamic structure of bacterial genomes

Bacterial genome sizes, which range from 500 to 10,000 kbp, are within the current scope of operation of large-scale nucleotide sequence determination facilities. To date, 8 complete bacterial genomes have been sequenced, and at least 40 more will be completed in the near future. Such projects give wonderfully detailed information concerning the structure of the organism's genes and the overall organization of the sequenced genomes. It will be very important to put this incredible wealth of detail into a larger biological picture: How does this information apply to the genomes of related genera, related species, or even other individuals from the same species? Recent advances in pulsed-field gel electrophoretic technology have facilitated the construction of complete and accurate physical maps of bacterial chromosomes, and the many maps constructed in the past decade have revealed unexpected and substantial differences in genome size and organization even among closely related bacteria. This review focuses on this recently appreciated plasticity in structure of bacterial genomes, and diversity in genome size, replicon geometry, and chromosome number are discussed at inter- and intraspecies levels.

Macrorestriction analysis of Desulfurella acetivorans and Desulfurella multipotens

The genomes of the phylogenetically and physiologically unique bacteria Desulfurella acetivorans DSM 5264T and D. multipotens DSM 8415T were characterized and compared by pulsed field gel electrophoresis (PFGE). Macrorestriction patterns made of large PFGE separated DNA fragments were generated by digesting the genomic DNAs of both strains with the rare cutting restriction endonucleases ApaI, AscI, EagI, RsrII, SacII, SalI as well as with the intron encoded endonuclease I-CeuI. The sum of calculated fragment sizes from digests of the first six enzymes yielded estimates for the chromosome sizes of D. acetivorans with a mean of 1939.0 +/- 26.0 kb and for D. multipotens with a mean of 1864.0 +/- 23.0 kb. Within the patterns obtained from EagI and RsrII cleavages the apparent differences could be attributed to DNA insertion or deletion and to point mutation. The single, circular chromosomes of the two strains contain two copies of 23S rRNA genes each. Different extrachromosomal elements were detected in both strains.

New strategies on molecular biology applied to microbial systematics

Systematics is the study of diversity of the organisms and their relationships comprising classification, nomenclature and identification. The term classification or taxonomy means the arrangement of the organisms in groups (rate) and the nomenclature is the attribution of correct international scientific names to organisms and identification is the inclusion of unknown strains in groups derived from classification. Therefore, classification for a stable nomenclature and a perfect identification are required previously. The beginning of the new bacterial systematics era can be remembered by the introduction and application of new taxonomic concepts and techniques, from the 50's and 60's. Important progress were achieved using numerical taxonomy and molecular taxonomy. Molecular taxonomy, brought into effect after the emergence of the Molecular Biology resources, provided knowledge that comprises systematics of bacteria, in which occurs great evolutionary interest, or where is observed the necessity of eliminating any environmental interference. When you study the composition and disposition of nucleotides in certain portions of the genetic material, you study searching their genome, much less susceptible to environmental alterations than proteins, codified based on it. In the molecular taxonomy, you can research both DNA and RNA, and the main techniques that have been used in the systematics comprise the build of restriction maps, DNA-DNA hybridization, DNA-RNA hybridization, sequencing of DNA sequencing of sub-units 16S and 23S of rRNA, RAPD, RFLP, PFGE etc. Techniques such as base sequencing, though they are extremely sensible and greatly precise, are relatively onerous and impracticable to the great majority of the bacterial taxonomy laboratories. Several specialized techniques have been applied to taxonomic studies of microorganisms. In the last years, these have included preliminary electrophoretic analysis of soluble proteins and isoenzymes, and subsequently determination of deoxyribonucleic acid base composition and assessment of base sequence homology by means of DNA-RNA hybrid experiments beside others. These various techniques, as expected, have generally indicated a lack of taxonomic information in microbial systematics. There are numberless techniques and methodologies that make bacteria identification and classification study possible, part of them described here, allowing establish different degrees of subspecific and interspecific similarity through phenetic-genetic polymorphism analysis. However, was pointed out the necessity of using more than one technique for better establish similarity degrees within microorganisms. Obtaining data resulting from application of a sole technique isolatedly may not provide significant information from Bacterial Systematics viewpoint.

Cloning and characterization of a Campylobacter jejuni 72Dz/92 gene encoding a 30 kDa immunopositive protein, component of the ABC transport system; expression of the gene in avirulent Salmonella typhimurium

Three gene libraries of Campylobacter jejuni 72Dz/92 DNA were prepared using lambda gt11, pSupercos and pWSK129 cloning vectors. Screening of the libraries with Escherichia coli absorbed antiserum generated against whole C. jejuni revealed several immunoreactive clones of apparent molecular masses 19, 28, 30 and 50 kDa. The most commonly isolated clones expressed 30 kDa protein. The nucleotide sequence of the 1768 bp C. jejuni DNA yielded one complete (ORF2) and two partial open reading frames (ORF1 and ORF3). ORF2 encoded CjaA protein exhibits relevant overall homology to several prokaryotic solute binding proteins (family 3), components of the ABC transport system, while the product of the truncated ORF3 (CjaB protein) shows extensive homology to Gram-negative bacterial proteins, members of the sugar transporter family. The genetic organization of the putative cjaAB operon was studied. The cjaA gene fragment (616 bp) was amplified from three C. jejuni strains isolated from patients with acute bloody diarrhea, whereas it was not amplified from strains which caused acute diarrhea with no blood in the stools. The gene was introduced into avirulent Salmonella typhimurium vaccine strain where it is expressed at a reasonably high level.

Microtitre plate riboprobe system for detection of ultrasonicated Campylobacter jejuni genomic DNA

Microtitre plate nucleic acid probe hybridization systems were developed for the detection of thermophilic Campylobacter and Campylobacter jejuni. Specific RNA probes obtained by in vitro transcription of DNA templates synthesized by polymerase chain reaction using two sets of specific primers incorporating bacteriophage T7 promoter sequences were immobilized on a microtitre plate. The hybridizations were carried out on samples of genomic DNA sheared by ultrasonication. Optimum conditions for the ultrasonic treatment were determined in order to obtain the highest degree of hybridization with immobilized RNA probe. Finally, detection of RNA-DNA hybrids in the wells was accomplished by an immunoenzymatic assay using a monoclonal anti-RNA-DNA hybrid antibody. This rapid, simple hybridization and immunoenzymatic assay system will facilitate the detection of Campylobacter in foods and clinical samples.

Expanded genomic map of Campylobacter jejuni UA580 and localization of 23S ribosomal rRNA genes by I-CeuI restriction endonuclease digestion

The genomic map of Campylobacter jejuni UA580 was expanded and more precisely constructed using I-CeuI, Sal/I and SmaI restriction endonucleases in conjunction with pulsed-field gel electrophoresis (PFGE). The presence of three fragments after digestion with I-CeuI confirmed the presence of three copies of the 23S ribosomal rRNA (rrl) gene. The genome size of Campylobacter jejuni UA580 was determined to be 1725 +/- 5.9 kbp by I-CeuI with fragment sizes of 1053 +/- 4.4, 361 +/- 2.7 and 311 +/- 3.6 kbp. Analysis of a PCR product from C. jejuni UA580 23S rRNA gene showed that I-CeuI did cut within the gene. The precise locations of the three genes were determined using I-CeuI with two copies of the 23S and 5S rRNA genes located separately from the 16S rRNA gene whereas the third copy of the 23S and 5S rRNA genes had a closer linkage to a 16S rRNA gene copy. Homologous gene probes were used to map additional genes and allowed the realignment of a few previously mapped genes on the chromosome. Other strains of C. jejuni were also cut into three fragments with I-CeuI, which generated variable PFGE patterns.

Interactions between Campylobacter jejuni and lipids

We previously showed that motility plays several key roles in Campylobacter jejuni pathogenesis, including increasing the efficiency of C. jejuni attachment to host epithelial cells. To further characterize C. jejuni attachment, we first examined the role of carbohydrates. Experiments with Chinese hamster ovary (CHO) cell mutants with defined defects in complex carbohydrate biosynthesis revealed that oligosaccharide sequences probably play a subordinate role in C. jejuni attachment to eukaryotic cells. Simple sugars such as mannose, fucose, glucose, N-acetylglucosamine, maltose, and galactose also did not significantly alter the binding of C. jejuni to CHO cells. Thin-layer chromatography overlay analysis with lipids extracted from CHO cells suggested that C. jejuni binds to lipids. Lipid binding was further investigated using a receptor-based enzyme-linked immunosorbent assay. Hydrophobic interactions were determined to play a minor role in binding, since tetramethylurea, a strong inhibitor of hydrophobic interactions, did not significantly decrease binding between C. jejuni and lipids. The interaction was dissected further by comparing the binding of C. jejuni to lipids and their derivatives. The results showed that binding was greatest to the entire lipid structure and decreased in affinity when portions of the lipid were removed. Thin-layer chromatography overlay analysis showed that lipids with unsaturated fatty acids were bound with the highest affinity. Our results suggest that C. jejuni may interact with lipids in host cell membranes. However, lipids only partially inhibited C. jejuni binding to CHO cells, suggesting that multiple interactions occur between the bacteria and host cells.

Identification methods for campylobacters, helicobacters, and related organisms

The organisms which are referred to as campylobacteria are associated with a diverse range of diseases and habitats and are important from both clinical and economic perspectives. Accurate identification of these organisms is desirable for deciding upon appropriate therapeutic measures, and also for furthering our understanding of their pathology and epidemiology. However, the identification process is made difficult because of the complex and rapidly evolving taxonomy, fastidious nature, and biochemical inertness of these bacteria. These problems have resulted in a proliferation of phenotypic and genotypic methods for identifying members of this group. The purpose of this review is to summarize the problems associated with identifying campylobacteria, critically appraise the methods that have been used for this purpose, and discuss prospects for improvements in this field.

DNA diversity among isolates of Campylobacter jejuni detected by PCR-based RAPD fingerprinting

A PCR-based randomly amplified polymorphic DNA method was used to amplify Campylobacter jejuni DNA using a single oligonucleotide primer derived from either a homologous source or from Mycoplasma gallisepticum. The method was able to detect the heterogeneity of amplified DNA from human, chicken and turkey sources and can be used as a tool to study the epidemiology of Campylobacter jejuni infection.

Physical and genetic map of the chromosome of the unicellular cyanobacterium Synechocystis sp. strain PCC 6803

A combined physical and genetic map of the cyanobacterium Synechocystis sp. strain PCC 6803 chromosome was constructed. An estimated genome size of 3.82 Mb was obtained by summing the sizes of 25 MluI or 40 NotI fragments seen by pulsed-field electrophoresis. The order of the restriction fragments was determined by using two independent experimental approaches: pulsed-field fragment hybridization and linking clone analysis. The relative positions of 30 known genes or gene clusters were localized.

Analysis of strains of Campylobacter fetus by pulsed-field gel electrophoresis

Campylobacter fetus chromosomal DNA from 21 strains was analyzed by pulsed-field gel electrophoresis. The fingerprint patterns generated with SmaI and SalI were distinctive. Using the profiles obtained by pulsed-field gel electrophoresis, we established the phylogenetic dendrogram of C. fetus to identify the genetic relationship of the strains.

Molecular subtyping scheme for serotypes HS1 and HS4 of Campylobacter jejuni

We describe a molecular subtyping scheme for two principal O (heat-stable [HS]) serotypes of Campylobacter jejuni, HS1 and the HS4 complex. A 16S rRNA gene-specific probe confirmed that almost all the C. jejuni strains had three copies of this gene, and strains could be assigned with complete typeability to 1 of 16 combined (Pst1 and HaeIII) 16S ribotypes. Macrorestriction profiles (mrps) consisting of up to 10 SmaI fragments from approximately 40 to approximately 480 kbp were resolved by pulsed-field gel electrophoresis (PFGE). There were 11 mrps among the HS1 strains and 9 mrps among HS4 strains which corresponded to valid types--they occurred in multiple isolates, hosts, places, and times. There were 14 additional single-strain mrp fingerprints in HS1 and 20 in HS4. PFGE exhibited complete typeability when formaldehyde fixation of cells was employed, and PFGE was generally more differential than ribotyping. The data presented elucidate a high-resolution genotypic subtyping scheme for these common subspecific phenotypes of C. jejuni, which is both coherent and efficient for epidemiological purposes.

Localization of the sapA gene on a physical map of Campylobacter fetus chromosomal DNA

We constructed a physical map of Campylobacter fetus TK(+) chromosomal DNA digested by either SmaI, SalI, or NotI using pulsed-field gel electrophoresis and Southern hybridization data. The genome size of C. fetus TK(+) is 2016kb, larger than that reported by the others. To locate the sapA gene, which encodes the surface array protein (SAP), on the physical map, we performed Southern hybridizations with probes based on the conserved region of the sapA gene. The results showed that more than seven copies of the conserved region were present on C. fetus chromosomal DNA and that the sapA gene was located on a limited number of fragments forming a cluster of genes. By comparing fingerprint patterns of strain TK(+) and strain TK(-), which lost the ability to produce SAP during culture on agar medium, an approximately 10kb deletion was observed in the fragments of strain TK(-). The results of Southern hybridization with two probes, one from the upstream region and the other from the variable region of sapA, suggest that the loss of SAP expression might not be the result of the loss of the sapA gene itself, but only a loss of its control systems.

High-frequency S-layer protein variation in Campylobacter fetus revealed by sapA mutagenesis

Campylobacter fetus utilizes paracrystalline surface (S-) layer proteins that confer complement resistance and that undergo antigenic variation to facilitate persistent mucosal colonization in ungulates. C. fetus possesses multiple homologues of sapA, each of which encode full-length S-layer proteins. Disruption of sapA by a gene targeting method (insertion of kanamycin (km) resistance) caused the loss of C. fetus cells bearing full-length S-layer proteins and their replacement by cells bearing a 50 kDa truncated protein that was not exported to the cell surface. After incubation of the mutants with serum, the survival rate was approximately 2 x 10(-2). Immunoblots of survivors showed that phenotypic reversion involving high-level production of full-length (98, 127 or 149 kDa) S-layer proteins had occurred. Revertants were serum resistant but caused approximately 10-fold less bacteraemia in orally challenged mice than did the wild-type strain. Southern hybridizations of the revertants showed rearrangement of sapA homologues and retention of the km marker. These results indicate that there exists high-frequency generation of C. fetus sapA antigenic variants, and that intracellular mechanisms acting at the level of DNA reciprocal recombination play key roles in this phenomenon.

Molecular characterization of a conserved 20-kilodalton membrane-associated lipoprotein antigen of Helicobacter pylori

Antisera raised in rabbits to whole cells of Helicobacter pylori recognized as a major antigen a protein with an apparent molecular weight of 20,000. The antigen was purified by differential solubilization with N-octyl-beta-D-glucopyranoside, urea, and sodium dodecyl sulfate followed by molecular sieving. The mass of the protein, Lpp20, was 18,283 Da as determined by mass spectrometry. The lpp20 gene encoding this protein was cloned in Escherichia coli by using the vector lambda EMBL3, and plasmid subclones expressed the full-length protein from the native H. pylori promoter. lpp20 was mapped to the same 358-kb NruI fragment as flaB. DNA sequence analysis showed that the gene was 525 bp long and encoded a 175-amino-acid protein with a molecular weight of 19,094 containing a 21-residue typical lipoprotein signal peptide and consensus prolipoprotein processing site. The mass of the deduced 154-residue mature protein was 16,865 Da. Growth of E. coli cells expressing the cloned H. pylori lpp20 gene in the presence of [3H]palmitic acid resulted in radiolabelled Lpp20 while treatment of the E. coli cells with globomycin caused accumulation of unprocessed Lpp20, consistent with Lpp20 being a lipoprotein. Lpp20 cofractionated with the cytoplasmic membrane fraction, although a proportion of the protein was also found in the outer membrane. A mutant generated by mutant-allele exchange displayed normal viability, showing that Lpp20 belonged to the nonessential class of lipoproteins.

Bacterial genomics

During the last decade, great advances have been made in the study of bacterial genomes which is perhaps better described by the term bacterial genomics. The application of powerful techniques, such as pulsed-field gel electrophoresis of macro-restriction fragments of genomic DNA, has freed the characterisation of the chromosomes of many bacteria from the constraints imposed by classical genetic analysis. It is now possible to analyse the genome of virtually every microorganism by direct molecular methods and to construct detailed physical and gene maps. In this review, the various practical approaches are compared and contrasted, and some of the emerging themes of bacterial genomics, such as the size, shape, number and organisation of chromosomes are discussed.

Genome conservation in Helicobacter mustelae as determined by pulsed-field gel electrophoresis

Genomic DNA from 15 strains of Helicobacter mustelae was subjected to pulsed-field gel electrophoresis (PFGE) after digestion with PacI and SfiI. H. mustelae genome DNA appeared very similar in all strains examined, whether isolated from ferrets or mink or from animals bred in either the USA or in the UK. The H. mustelae genome size was estimated to be 1.7 Mb, similar in size to that of H. pylori. A minor difference in PacI PFGE pattern and genome size was observed between rifampicin-resistant and rifampicin-susceptible derivatives of H. mustelae F251. Another minor difference in genome pattern based on PFGE with SfiI was observed between an H. mustelae strain used to experimentally infect four ferrets which resulted in loss of an SfiI site in strains obtained from the newly infected ferrets. Thus, although minor differences in PFGE pattern were noted, H. mustelae lacks the genomic diversity observed in H. pylori.

Campylobacter fetus diarrhea in a Hutterite colony: epidemiological observations and typing of the causative organism

Following a case of Campylobacter fetus sepsis and meningitis in a 4-month-old female member of a Hutterite colony, an epidemiological investigation revealed at least 18 cases of diarrhea in other members of the colony. C. fetus was isolated from 7 of 15 fecal samples submitted from affected persons. A case control study suggested that persons who worked in the abattoir were 2.03 times more likely to have had diarrhea, but none of the risk factors studied were significant. The epicurve of the outbreak was inconclusive as to the likely mode of spread of C. fetus. All of the C. fetus strains isolated from the blood of the infant and from the fecal samples were the same by biochemical and antibiotic susceptibility tests. Pulsed-field gel electrophoresis showed that all isolates produced identical restriction endonuclease patterns and differed from other nonepidemiologically related strains of C. fetus.

Use of pulsed-field gel electrophoresis for epidemiological study of Bordetella pertussis in a whooping cough outbreak

We used pulsed-field gel electrophoresis (PFGE) of chromosomal DNA digested with XbaI to determine the distribution of different Bordetella pertussis strains from clinical isolates obtained during a large whooping cough outbreak that occurred in Alberta, Canada, from December 1989 to May 1991. Our initial study analyzed 28 clinical isolates, 14 from the city of Edmonton and 1 from each of 14 northern Alberta towns. These clinical isolates were randomly chosen over the course of the 18-month outbreak. The DNA profiles were more heterogeneous than anticipated and caused concern that PFGE was too sensitive a technique to characterize strains. Further analysis showed that this was not the case, as clusters of similar PFGE patterns were observed in strains isolated from the same outlying town. Identical PFGE patterns were also seen in clinical strains obtained from different members of the same family. Two PFGE pattern types, a and b, predominated in the outbreak, accounting overall for 44 of 70 B. pertussis strains tested. Results from isolates from outlying towns, however, indicated involvement of local strains rather than a single, highly infectious strain in the whooping cough outbreak in Alberta.

Campylobacter jejuni: specific oligonucleotides and DNA probes for use in polymerase chain reaction-based diagnosis

A 1189 base-pair long DNA fragment, VS1, was isolated from a Campylobacter jejuni CIP 70.2 cosmid library and was found to contain regions specific for this bacterial species. For detection and identification of C. jejuni, two oligonucleotides derived from the VS1 sequence were used as primers in polymerase chain reaction tests on genomic DNAs from 38 campylobacter and from 10 non-Campylobacter strains. A specific, 358 base-pair long DNA fragment was amplified only when C. jejuni DNA was used as a target. The detection limit of the amplification reaction was as low as 1.86 fg DNA, which is the equivalent of one C. jejuni genome.

Efficacy of filter types for detecting Campylobacter jejuni and Campylobacter coli in environmental water samples by polymerase chain reaction

A previously developed polymerase chain reaction (PCR) amplification of a target region in the flaA Campylobacter flagellin gene was evaluated and adapted for use with environmental water samples. The ability to detect Campylobacter jejuni or Campylobacter coli in seeded water samples was tested with various filters after concentration and freeze-thaw lysis of the bacterial cells. A nonradioactive probe for the amplified flagellin gene fragment detected as little as 1 to 10 fg of genomic DNA and as few as 10 to 100 viable C. jejuni cells per 100 ml of water filtered onto Fluoropore (Millipore Corp.) filters. No amplification was obtained with cellulose acetate filters, most likely because of binding of the DNA to the filter. Concentration and lysis of target cells on Fluoropore and Durapore (Millipore Corp.) filters allowed PCR to be performed in the same reaction tube without removing the filters. This methodology was then adapted for use with environmental water samples. The water supply to a broiler chicken production farm was suspected as the source of C. jejuni known to be endemic in grow-out flocks at the farm, despite the inability to culture the organisms by standard methods. The filtration-PCR method detected Campylobacter DNA in more than half of the farm water samples examined. Amplified campylobacter DNA was not detected in small volumes of regional surface water samples collected on a single occasion in February. The filtration-PCR amplification method provided a basis for detection of C. jejuni and C. coli in environmental waters with a high degree of specificity and sensitivity.