Insertion sequence IS200 fingerprinting of Salmonella typhi: an assessment of epidemiological applicability.

When Pst I-generated digests of genomic DNA from each of the type strains of 49 of the Vi phage types of Salmonella typhi were probed with a PCR-amplified IS200 gene probe, all strains were found to possess at least 11 IS200 elements carried on fragments in the range 24.2-1.2 kb. Fourteen fingerprints were identified but two patterns designated IS200Sty1 and IS200Sty2 predominated. In one strain, a plasmid-mediated IS200 element was identified. When IS200 fingerprinting was applied to epidemiologically-unrelated strains of S. typhi isolated in Ecuador, 3 patterns were identified in 10 strains belonging to 9 different phage types. It is concluded that Vi phage typing remains the method of choice for the primary differentiation of S. typhi but that IS200 fingerprinting may be of limited use in laboratories which do not have access to phage typing.     

Grouping of Salmonella enterica serotype Montevideo strains by ribotyping and IS200 profiling

One-hundred and twenty-one isolates of Salmonella enterica serotype Montevideo, representing different biotypes and incidents of infection detected in the UK between 1977 and 1995, were analysed by EcoRI ribotyping, PvuII ribotyping and IS200 fingerprinting. Among the isolates examined, 7 EcoRI ribotypes, 5 PvuII ribotypes and 55 IS200 profile types were recognized and 4 arbitrary groups defined. All 33 isolates of biotype 2d belonged to EcoRI/PvuII ribotype 1/1 and IS200 lineage A and comprised Group I. The other 88 isolates of biotype 10di and its variants were assigned to Groups II-IV. All 27 isolates in Group II were of EcoRI/PvuII ribotype 2/2 and IS200 lineage B. Among the 43 isolates in Group III, 42 of which were of EcoRI/PvuII ribotype 3/3, IS200 analysis identified 38 profiles in lineages C-I. Six EcoRI/PvuII ribotypes and 8 IS200 profiles, mostly in lineages C-E, were recognized among the 18 isolates in Group IV. The combined use of biotyping and ribotyping, and to some extent IS200 profiling, has enhanced our understanding of the clonal structure of serotype Montevideo and provides a basis for further study.     

Molecular typing of Salmonella serotype Thompson strains isolated from human and animal sources

One-hundred-and-thirteen isolates of Salmonella serotype Thompson from diverse sources in seven countries were characterized by PvuII ribotyping and IS200 fingerprinting. Ten PvuII ribotypes were observed. The predominant PvuII ribotype 1 represented a major clone of world-wide distribution but was not found in Australia; PvuII ribotypes 2 and 3 represented minor clones. HincII ribotyping discriminated subtypes within PvuII ribotype 1: HincII ribotype 1 was distributed widely but HincII ribotype 2 was found mainly in Scottish isolates. None of 101 isolates of PvuII ribotypes 1-3 contained copies of IS200. All 12 isolates of PvuII ribotypes 4-10 were from Australia and 7 of them contained copies of IS200 of 5 different profiles. These results suggest the existence of at least two lineages of Salmonella Thompson with a different geographical distribution. The finding that most isolates from man and poultry in Scotland belonged to the same ribotype (PvuII 1/HincII 2) and were IS200-negative suggests that poultry is an important source of human infection in Scotland.     

Ciprofloxacin-resistant Salmonella enterica Typhimurium and Choleraesuis from pigs to humans, Taiwan

We evaluated the disk susceptibility data of 671 nontyphoid Salmonella isolates collected from different parts of Taiwan from March 2001 to August 2001 and 1,261 nontyphoid Salmonella isolates from the National Taiwan University Hospital from 1996 to 2001. Overall, ciprofloxacin resistance was found in 2.7% (18/671) of all nontyphoid Salmonella isolates, in 1.4% (5/347) of Salmonella enterica serotype Typhimurium and in 7.5% (8/107) in S. enterica serotype Choleraesuis nationwide. MICs of six newer fluoroquinolones were determined for the following isolates: 37 isolates of ciprofloxacin-resistant (human) S. Typhimurium (N = 26) and Choleraesuis (N = 11), 10 isolates of ciprofloxacin-susceptible (MIC <1 mg/mL) (human) isolates of these two serotypes, and 15 swine isolates from S. Choleraesuis (N = 13) and Typhmurium (N = 2) with reduced susceptibility to ciprofloxacin (MIC >0.12 microg/mL). Sequence analysis of the gryA, gyrB, parC, parE, and acrR genes, ciprofloxacin accumulation, and genotypes generated by pulsed-field gel electrophoresis with three restriction enzymes (SpeI, XbaI, and BlnI) were performed. All 26 S. Typhimurium isolates from humans and pigs belonged to genotype I. For S. Choleraesuis isolates, 91% (10/11) of human isolates and 54% (7/13) of swine isolates belonged to genotype B. These two genotypes isolates from humans all exhibited a high-level of resistance to ciprofloxacin (MIC 16-64 mg/mL). They had two-base substitutions in the gyrA gene at codons 83 (Ser83Phe) and 87 (Asp87Gly or Asp87Asn) and in the parC gene at codon 80 (Ser80Arg, Ser80Ile, or Ser84Lys). Our investigation documented that not only did these two S. enterica isolates have a high prevalence of ciprofloxacin resistance nationwide but also that some closely related ciprofloxacin-resistant strains are disseminated from pigs to humans.     

Live attenuated Salmonella enterica serovar Choleraesuis vaccine vector displaying regulated delayed attenuation and regulated delayed antigen synthesis to confer protection against Streptococcus suis in mice

Salmonella enterica serotype Choleraesuis (S. Choleraesuis) and Streptococcus suis (S. suis) are important swine pathogens. Development of a safe and effective attenuated S. Choleraesuis vaccine vector would open a new window to prevent and control pig diseases. To achieve this goal, the mannose and arabinose regulated delayed attenuated systems (RDAS), Δpmi and ΔP_crp::TT araC P_BAD crp, were introduced into the wild type S. Choleraesuis strain C78-3. We also introduced ΔrelA::araC P_BAD lacI TT to achieve regulated delayed antigen synthesis and ΔasdA to constitute a balanced-lethal plasmid system. The safety and immunogenicity of the resulted RDAS S. Choleraesuis strain rSC0011 carrying 6-phosphogluconate dehydrogenase (6-PGD) of S. suis serotype 2 (SS2) were evaluated in vitro and in vivo. Compared with the wild type parent strain C78-3 and vaccine strain C500, a live attenuated S. Choleraesuis vaccine licensed for piglet in China, the results showed that the survival curves of the vaccine strain rSC0011 were similar to those of strains C78-3 and C500 at the early stage of infection, but lower than those of C78-3 and higher than those of C500 at the later stage in both porcine alveolar macrophages and peripheral porcine monocytes. The LD₅₀ of the RDAS strains rSC0011 by oral route in mice was close to that of C500 and 10,000-fold higher than that of C78-3. Similar results were achieved by intraperitoneal (i.p.) route, suggesting that the RDAS strains rSC0011 achieved similar attenuation as C500. However, the RDAS strain rSC0011 was superior to C500 in colonization of Peyer's patches. Adult mice orally immunized with strain rSC0011 carrying a plasmid expression 6-phosphogluconate dehydrogenase (6-PGD) gene from SS2 developed strong immune responses against 6-PGD and Salmonella antigens, and conferred high protection against i.p. challenge with SS2.     

IS200 fingerprint of Salmonella enterica serotype Typhimurium human strains isolated in Sardinia.

A collection of Salmonella enterica serotype Typhimurium human strains isolated in Northern Sardinia (Italy) was examined for the insertion sequence IS200, phage type, antibiotic profile, ribotyping polymorphisms and plasmid profile. All clinical isolates studied contained from 4 to 10 copies of the IS200 element. IS200 permitted to discriminate Typhimurium strains and to identify five IS200 types, some of them circulating in Sardinia at least since 1900. Strains belonging to phage DT104 predominated and correlated with a specific IS200 pattern.     

The use of PCR ribotyping for typing strains ofListeria spp.

The potential of PCR ribotyping for discriminating between and within various species ofListeria, as well as strains ofListeria monocytogenes was examined. In total, 49 strains ofListeria monocytogenes and 12 isolates ofListeria spp. were analyzed. The genomic DNA isolated from these strains was subjected to PCR amplification in the regions between 16S and 5S rRNA. Amplifications were performed with both low and high concentrations of Taq polymerase. Length polymorphisms in the amplified DNA products enabled distinction between various strains of Listeria spp. and between various serotypes ofL. monocytogenes. Six composite profiles for serotype 4b strains, 8 for l/2a strains and 11 for l/2b strains, were observed. In addition, several different PCR ribotyping strategies were evaluated. Restriction fragment length polymorphisms of the spacer region between the 16S and 23S rRNA genes of 16 strains ofL. monocytogenes were not observed, except for two isolates. PCR ribotyping analysis displayed promise as an alternative to traditionalL. monocytogenes molecular typing methods.     

Regulated delayed attenuation enhances the immunogenicity and protection provided by recombinant Salmonella enterica serovar Typhimurium vaccines expressing serovar Choleraesuis O-polysaccharides

Regulated delayed attenuation is a well-studied strategy for retaining the immunogenicity of Salmonella-vectored vaccines. In this study, this strategy was used to optimize two previously constructed recombinant Salmonella enterica serovar Typhimurium vaccines expressing S. Choleraesuis O-polysaccharides (OPS). The novel vaccine strains SLT31 (Δasd ΔrmlB-rfbP ΔP_crp::T araC P_BAD) and SLT33 (Δasd ΔrfbP ΔpagL::T araC P_BAD rfbP ΔP_crp::T araC P_BAD) were constructed by replacement of the native crp promoter with the arabinose-dependent araC P_BAD promoter. As controls, two vaccine strains with direct crp mutations were also constructed, namely, SLT30 (Δasd ΔrmlB-rfbP Δcrp) and SLT32 (Δasd ΔrfbP ΔpagL::T araC P_BAD rfbP Δcrp). Then, the ability to deliver the heterologous S. Choleraesuis OPS on the Asd⁺ plasmid pCZ1 to the mouse immune system was evaluated in the strains with or without regulated delayed attenuation. The SLT30 (pCZ1) and SLT31 (pCZ1) strains expressed only the heterologous OPS, while the SLT32 (pCZ1) and SLT33 (pCZ1) strains co-expressed the homologous and heterologous OPS. The strain SLT31 (pCZ1) or SLT33 (pCZ1), which exhibited regulated delayed attenuation, colonized mouse tissues significantly better and stimulated stronger antibody responses against S. Choleraesuis LPS post immunization than the SLT30 (pCZ1) or SLT32 (pCZ1) strain. Immunization with SLT31 (pCZ1) or SLT33 (pCZ1) resulted in a significant reduction in bacterial loads in mouse tissues and a greater degree of protection against a lethal S. Choleraesuis dose compared with the effects observed after SLT30 (pCZ1) or SLT32 (pCZ1) immunization (100% vs. 80% or 70% vs. 50%, respectively). In addition, all four vaccines conferred complete protection against S. Typhimurium challenge. Overall, our study demonstrates that regulated delayed attenuation via an araC P_BAD-regulated crp gene can enhance the cross-protection by Salmonella-vectored vaccines expressing heterologous OPS, and strain SLT31 (pCZ1) is a good candidate vaccine for preventing both S. Typhimurium and S. Choleraesuis infections.     

Leishmania in the Old World: 4. The distribution of L. donovani sensu lato zymodemes

Isoenzyme profiles of 67 stocks of Leishmania donovani sensu lato from across the Old World were compared with those of reference strains of L. donovani sensu stricto, L. infantum, L. major, L. tropica and L. aethiopica using starch-gel electrophoresis of 13 enzymes (GPI, GD, ES, PGM, PEPD, NH, ASAT, ALAT, PK, MPI, 6PGD, SOD, MDH). 12 zymodemes were seen. Isolates from man, Canis familiaris, Vulpes vulpes, Rattus rattus, Arvicanthis sp. and Phlebotomus martini were examined. Several zymodemes comprised stocks from man and C. familiaris, two of which also included wild animal isolates. Isolates from cases of post-kala-azar dermal leishmaniasis and visceral leishmaniasis were indistinguishable. L. donovani s.l., including L. donovani s.s. and L. infantum, formed a coherent group with a striking degree of enzymic homogeneity. Only one enzyme pattern was held in common with the L. tropica and L. aethiopica reference strains and two with the L. major reference strain enzyme profile.     

北京、广东、宁夏三地结核分支杆菌DNA指纹的应用研究

目的 分析“北京家族”结核分支杆菌,从分子流行病学角度探讨北京、广东及宁夏三地结核分支杆菌的分布特征。方法 采用Gel compare4．1软件对来自三地的206株结核分支杆菌的插入序列IS6110 DNA指纹图谱进行数字化,经互联网与世界结核分支杆菌DNA指纹库进行相似性比较;同时应用该软件对上述菌株行聚类分析;构建标准的结核分支杆菌Spoligotyping(间隔区寡核苷酸分型法)DNA指纹方法;用χ^2检验比较不同组别肺结核病人临床分离菌株成簇率的差别,同时计算相对危险度(OR)。结果 206株结核分支杆菌的IS6110 DNA指纹图谱与DNA指纹图谱库相比较,未发现相同者。56．8％(117／206)的结核分支杆菌IS6110 DNA指纹相似值在1．00—0．65之间,且它们的Spo1igotyping指纹图谱均与“北京家族”结核分支杆菌相一致;分组统计显示：男性组与女性组、年龄≥42岁组与＜42岁组成簇率之间差异有显著性(P＜0．05),OR值为男性4．43,95％CI：0．94—28．76;＜42岁为5．06,95％CI：1．00—34．34。其他各组之间差异无显著统计学意义(P＞0．05)。结论 “北京家族”结核分支杆菌在三地呈较高水平的流行;结核分支杆菌在男性和＜42岁人群中的传播频率较女性和≥42岁人群为高,且男性和＜42岁可能是三地结核病近期传播的危险因素。利用结核分支杆菌的DNA指纹图谱和互联网技术,可以实现结核分支杆菌传染源全球范围的追踪。     

Genotype analysis of human blood isolates of Campylobacter jejuni in England and Wales.

Genomic profiles were obtained for 76 strains of Campylobacter jejuni isolated from bacteraemic patients in England and Wales over the period 1981-94. Genotyping was performed by restriction fragment length polymorphism (RFLP) analysis using a random cloned DNA probe, and by ribotyping with a PCR-generated C. jejuni 16S ribosomal DNA probe. Phenotypic characterization was achieved by heat-stable (HS) and heat-labile (HL) serogrouping, and Preston phagetyping and biotyping. The blood isolates were genomically heterogenous, with 24 RFLP/16S profiles occurring within the 76 strains. Forty-four percent of isolates belonged to one of three RFLP/16S genotypes, reflecting the patterns seen in faecal isolates, except that genotypes usually associated with the HS 1 antigen were uncommon. The two most prevalent genotypes, characteristic of HS 2 and HS 4 strains, showed similarity by cluster analysis. Further evidence was seen of associations between phenotypic and genotypic characters within some HS serogroups. Chromosomal profiling by RFLP analysis does not indicate that particular genotypes have a predisposition to invade the bloodstream.     

Molecular subtyping by genome and plasmid analysis of Campylobacter jejuni serogroups O1 and O2 (Penner) from sporadic and outbreak cases of human diarrhoea.

Ribosomal RNA gene patterns, randomly amplified polymorphic genomic DNA (RAPD) profiles and plasmid profiles were used to discriminate between 28 strains of Campylobacter jejuni serogroups O1 and O2 (Penner). Most isolates were biotype I (Lior). The strains were representative isolates from a UK school outbreak of enteritis (7 cases) and from 21 sporadic human cases of enteritis in 4 countries. The molecular techniques discriminated to various degrees between strains in each of the serogroups. The outbreak strains were homogeneous in most molecular features but a variety of types was detected amongst the isolates from the sporadic cases. Five groups of two or more strains with identical ribopatterns were identified and within each, strains from different patients were homogenous with respect to serogroup. RAPD profile typing based on numerical analysis generally matched ribotyping. Plasmid profiling overall gave least discrimination but was useful in separating some strains similar in other features. We concluded that optimal discrimination of C. jejuni could best be achieved using a combination of phenotypic and genotypic properties. Hae III ribotyping was the single most discriminatory and reproducible technique investigated. Several strains of C. jejuni from sporadic infections had similar molecular profiles which have potential for general typing purposes.     

Epidemiology of Salmonella typhimurium: ribosomal DNA analysis of strains from human and animal sources.

Salmonella typhimurium is the most frequently identified serovar of Salmonella in Italy. This serovar is characterized by the widespread dissemination among human and non-human sources of phenotypically and genetically well-differentiated clones. In this study 457 strains of S. typhimurium isolated in Italy in the years 1982-91 from human and animal sources were submitted to characterization by the rDNA fingerprinting technique. Application of this typing method, after digestion of chromosomal DNA with HincII endonuclease, confirmed the greatest genetic differentiation of clones of S. typhimurium, allowing reliable identification of 45 rDNA patterns linked into 9 major clusters. rDNA pattern clusters or ribotypes specific to man were not recognized, whereas some rDNA patterns were characteristically related to ducks, pigeons and pet birds. The ribotyping results for isolates from animal hosts suggest that pig and cattle are the main source of human infection.     

Antigenic and genomic analysis of a Borrelia burgdorferi sensu stricto strain isolated from Ixodes ricinus ticks in Alto Adige-South Tyrol, Italy

A Borrelia burgdorferi sensu lato strain isolated from Ixodes ricinus ticks in Alto Adige-South Tyrol (Northern Italy) was analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of whole cell proteins, Western immunoblotting analysis (WBA) with polyclonal and monoclonal antibodies, and pulsed-field gel electrophoresis (PFGE). The isolate named BZ6 was identified as belonging to the genospecies B. burgdorferi sensu stricto on the basis of its protein profile and its reactivity with monoclonal and polyclonal antibodies. The PFGE study performed with the two rare-cutting restriction enzymes MluI and SmaI confirmed the SDS-PAGE and WBA characterizations, but showed a genetic diversity between the isolate and two out of the three B. burgdorferi sensu stricto strains used in this study as controls, the American type strain B31 and the locally isolated strain BZ1. No difference in the PFGE patterns between the isolate BZ6 and the Swiss strain IRS was noted. Our findings show the value of PFGE analysis for classifying B. burgdorferi sensu lato isolates and for revealing their genetic diversity, and its usefulness for epidemiological investigations.     

Genomic fingerprints of Staphylococcus aureus of bovine origin by polymerase chain reaction-based DNA fingerprinting.

Staphylococcus aureus (n = 75) isolated from mammary secretions of cows with subclinical and clinical mastitis from several geographic locations in the USA were examined using polymerase chain reaction-based DNA fingerprinting. DNA fingerprints were produced using a synthetic oligonucleotide primer (5''GTAACGCC3'') to produce a distinct spectrum of amplified DNA fragments facilitating a high degree of resolution for differentiating S. aureus strains. PCR-based DNA fingerprinting grouped the 75 S. aureus isolates into 19 distinct profiles. The technique differentiated closely related strains within and between geographic locations. Findings suggest that certain types are found across geographic regions suggesting a common clonal type. Within herd data suggest heterogeneity among subclinical and clinical isolates of S. aureus strains. Compared to existing typing methods, PCR-based DNA fingerprinting is easy to perform and interpret. Use of PCR-based DNA fingerprinting may allow for a more detailed investigation of the epidemiology of S. aureus mastitis in dairy cows.     

Genotypic and phenotypic analysis of Streptococcus uberis isolated from bovine mammary secretions.

Genotypic and phenotypic analysis of 42 strains of Streptococcus uberis isolated from mammary secretions of 17 cows collected at different periods of the lactation cycle and from episodes of clinical mastitis were performed. Seventeen restriction endonuclease fingerprint (REF) patterns and 12 bacteriocin-like inhibitory substance (BLIS) fingerprints were observed. REF identified and differentiated closely related strains of S. uberis isolated from mammary secretions collected from the same cow at different periods of the lactation cycle and from episodes of clinical mastitis. BLIS fingerprinting of S. uberis complemented REF results. REF and BLIS fingerprinting provided evidence concerning persistence of infection in the same quarter or different quarters of the mammary gland over different periods of the lactation cycle, and occurrence of infection with similar and dissimilar strains of S. uberis. Biochemical profiles could not identify closely related strains nor did they complement REF results. Antibiotic resistance patterns alone were of little value in differentiating closely related strains, but were identical with isolates having same REF pattern. None of the S. uberis strains was found to carry plasmids. REF and BLIS fingerprinting can be utilized effectively to differentiate closely related and unrelated strains of S. uberis isolated from bovine mammary secretions.     

Single-step polymerase chain reaction in the detection of Borrelia burgdorferi and the genome species in the Ixodes ricinus tick

The objective of the work to introduce screening PCR into the diagnosis of Borrelia burgdorferi sensu lato in the vector selection of the most suitable primer, derived from chromosomal DNA and detection of different genome species. The sensitivity of primers, described in the literature (LD, 16S, Wk, 5S-23S) was tested by different amounts of DNA strains of borrelias. The most sensitive primer--LD was used for detection of borrelias in the vector. Ticks were collected in municipal parks from 1995-1997. A total of 635 ticks were examined. The positivity of the group differs in individual years: 9.2% in 1995, 3.4% in 1996, and 4.5% in 1997. Adult ticks were markedly more infected than nymphs. Borrelia garinii prevails at the site, Borrelia burgdorferi sensu stricto was not detected so far. Mixed infection with Borrelia garinii/Borrelia afzelii was found in 1997 in one sample (female ticks). PCR is a sensitive and specific method suitable for assessment of the herd immunity of ticks with borrelias. It makes it possible to differentiate with a relatively high sensitivity individual genome species of Borrelia burgdorferi in the vector. Before its use the sensitivity of the reaction must be tested in the presence of tick DNA.     

Genetic diversity and major spoligotype families of drug-resistant Mycobacterium tuberculosis clinical isolates from different regions of Turkey.

To highlight the transmission rate and major phylogenetic clades of drug-resistant Mycobacterium tuberculosis isolates, a total of 200 drug-resistant strains isolated in four different regions of Turkey (Marmara n=81; Mediterranean n=39; Aegean n=42; East Anatolia n=38), were typed by spoligotyping and IS6110-restriction fragment length polymorphism (RFLP). The major spoligotyping-defined shared-types (STs) and corresponding lineages were, ST 41 (22.5%, LAM7-TUR), ST53 (19.5%, ill-defined T super-family), ST 50 (6.5%, Haarlem 3), ST 1261 (4.5%, LAM7-TUR), ST 47 (3.5%, Haarlem 1), as well as two STs that belonged to undefined clades (ST 284, 3%, and ST 2067, 2.5%). The global distribution of major M. tuberculosis lineages among drug-resistant strains was as follows: T super-family (29%), Latin-American & Mediterranean (33.5%), Haarlem (14%), and the S lineage (3%). A high number of strains (n=29, 14.5%) showed patterns that did not fall within major clades described so far. A combination of spoligotyping and IS6110-RFLP fingerprinting methods resulted in a final clustering rate of 38.5% and a recent transmission rate of 25.5%. Our results underline the highly diverse nature of drug-resistant tuberculosis in our study population, as well as its ongoing transmission with lineages that are specific to these regions, the most predominant being the LAM7-TUR lineage which shows an enhanced phylogeographical specificity for Turkey.     

Plasmid profile analysis of Portuguese Borrelia lusitaniae strains

Plasmid profiles of 2 Portuguese Borrelia lusitaniae strains, one isolated from a human patient and the other one from an Ixodes ricinus tick, were obtained by pulsed-field gel electrophoresis to evaluate the plasmid diversity in each strain. Overall, a maximum of 6 plasmids were detected that ranged from 19 kb to 76 kb, revealing completely different plasmid profiles from those previously described for other genospecies of B. burgdorferi sensu lato, the causative agents of Lyme borreliosis. The plasmid location of the ospA gene was investigated by hybridization, allowing its allocation to the plasmid of 70 kb instead of the 54 kb linear plasmid described for B. burgdorferi sensu stricto strains.