Clinical evaluation of a GP5+/6+-based luminex assay having full high-risk human papillomavirus genotyping capability and an internal control.

The LMNX genotyping kit HPV GP (LMNX) is based on the clinically validated GP5+/6+ PCR, with a genotyping readout as an alternative for the more established enzyme immunoassay (EIA) detection of 14 targeted high-risk human papillomavirus (HPV) types. LMNX is additionally provided with an internal control probe. Here, we present an analysis of the clinical performance of the LMNX using a sample panel and infrastructure provided by the international VALGENT (Validation of Genotyping Tests) project. This panel consisted of cervical specimens from approximately 1,000 women attending routine screening, "enriched" with 300 women with abnormal cytology. Cases were defined as women classified with cervical intraepithelial neoplasia (CIN) grade 2+ (CIN2+) (n = 102) or CIN3+ (n = 55) within the previous 18 months. Controls were women who had normal cytology results over two subsequent screening rounds at a 3-year interval (n = 746). The GP5+/6+-PCR EIA (EIA) was used as a comparator assay and showed sensitivities of 94.1% and 98.2% for CIN2+ and CIN3+, respectively, with a clinical specificity of 92.4% among women aged ≥ 30 years. The LMNX demonstrated clinical sensitivities of 96.1% for CIN2+ and of 98.2% for CIN3+ and a clinical specificity of 92.6% for women aged ≥ 30 years. The LMNX and EIA were in high agreement (Cohen's kappa = 0.969) for the detection of 14 hrHPVs in aggregate, and no significant difference was observed (McNemar's P = 0.629). The LMNX internal control detected 0.6% inadequate specimens. Based on our study results, we consider the LMNX, similarly to the EIA, useful for HPV-based cervical cancer screening.

Human papillomavirus infection and squamous cell carcinoma of the conjunctiva.

BACKGROUND: Squamous cell carcinoma of the conjunctiva (SCCC) is associated with HIV-related immunosuppression, but human papillomavirus virus (HPV) is also suspected to have a role. We carried out a case-control study to assess the role of cutaneous and mucosal HPV types in SCCC, conjunctival dysplasia, and their combination (SCCC/dysplasia) in Uganda. METHODS: We compared HPV prevalence in frozen biopsies from 94 SCCC cases (79 of whom were found to be HIV-positive), 39 dysplasia cases (34 HIV-positive), and 285 hospital controls (128 HIV-positive) having other eye conditions that required surgery. Highly sensitive PCR assays that detect 75 HPV types were used. Odds ratios (ORs) and 95% confidence intervals (CIs) were computed, adjusting for, or stratifying by age, sex, and HIV status. RESULTS: Cutaneous HPV types were detected in 45% of SCCC cases, 41% of dysplasia cases and 11% of controls. Human papillomavirus virus 5 and 8 were the most common types in SCCC, and most often occurred in combination with other types. Associations were observed between SCCC/dysplasia and detection of both single (OR=2.3; 1.2-4.4) and multiple (OR=18.3; 6.2-54.4) cutaneous HPV types, and were chiefly based on findings in HIV-positive patients. Cutaneous HPV infections were rarely observed among HIV-negative patients and the association with SCCC/dysplasia was not significant (OR=2.4; 0.6-9.6) among them. Squamous cell carcinoma of the conjunctiva/dysplasia risk and mucosal HPV types were not associated in either HIV-positive or HIV-negative patients. CONCLUSIONS: We detected cutaneous HPV types in nearly half of SCCC/dysplasia cases and often multiple types (HPV5 and 8 being most common). The role of HIV (confounder or strong enhancer of cutaneous HPV carcinogenicity) is still uncertain.

Comparison of three genotyping methods to identify Chlamydia trachomatis genotypes in positive men and women.

Chlamydia trachomatis (Ct) comprises 3 serogroups and 19 serovars. Different genotyping methods are available to differentiate between the serovars. The aim of this study was to evaluate the sensitivity and discriminatory power of three genotyping methods, respectively Omp1 sequencing, the Ct Detection and genoTyping (DT) assay and the pmpH real-time PCR discriminating an LGV infection from a non-LGV infection. In total, 50 Aptima Combo 2 (AC2) Ct positive samples were selected and tested with the 3 genotyping methods. The Ct-DT assay detected 3 double Ct infections that caused a non interpretable result by Omp1 sequencing, while Omp1 sequencing has a higher discriminatory power that gave additional information about Ct genovariants. All three methods detected the 6 LGV samples. Although the pmpH real-time PCR detected all LGV infections, a substantial amount (24%) of non-LGV infections were missed. The sensitivity compared to AC2 Ct detection was 80% (95% CI 67-89%) for the Ct-DT assay, 72% (95% CI 58-83%) for Omp1 sequencing and 64% (95% CI 50-76%) for the pmpH real-time PCR. In conclusion, the Ct-DT assay is appropriate for serovar distribution studies, epidemiological studies and differentiation between an LGV and non-LGV Ct infection, while Omp1 sequencing is more appropriate for phylogenetic studies. The pmpH real-time PCR is suitable as second assay to differentiate between an LGV and non-LGV infection, but not as primary detection assay, due to its low sensitivity for non-LGV strains.

Helicobacter species in cancers of the gallbladder and extrahepatic biliary tract.

Helicobacter species have been found in human bile and biliary tract (BT) tissue and are suspected to cause BT diseases, including gallbladder and extrahepatic cancers, collectively referred to in this work as BT cancers. We conducted a literature review of the epidemiological evidence linking the presence of Helicobacter species in bile or BT biopsies to BT cancers and benign diseases. Reports showed great variability with respect to study methods. Nine studies of BT cancers were identified, all with 30 or fewer BT cancers; eight included cancer-free control subjects and used polymerase chain reaction (PCR) as a means of Helicobacter species detection. In four of these studies, Helicobacter species were detected in patients with BT cancer significantly more frequently than in controls, at least when controls without BT diseases were used. In two studies, no Helicobacter species were detected in either cases or controls. Helicobacter species were also often detected in benign BT diseases such as gallstone disease or chronic cholecystitis. As our current knowledge relies on a few small studies that showed substantial differences, larger studies and more standardised protocols for detecting DNA and antibodies against Helicobacter species are needed to investigate a potential association with BT cancer.

Helicobacter genotyping and detection in peroperative lavage fluid in patients with perforated peptic ulcer.

INTRODUCTION AND OBJECTIVES: Certain Helicobacter pylori genotypes are associated with peptic ulcer disease; however, little is known about associations between the H. pylori genotype and perforated peptic ulcer (PPU). The primary aim of this study was to evaluate which genotypes are present in patients with PPU and which genotype is dominant in this population. The secondary aim was to study the possibility of determining the H. pylori status in a way other than by biopsy. MATERIALS AND METHODS: Serum samples, gastric tissue biopsies, lavage fluid, and fluid from the nasogastric tube were collected from patients operated upon for PPU. By means of PCR, DEIA, and LIPA the presence of the "cytotoxin associated gene" (cagA) and the genotype of the "vacuolating cytotoxin gene" were determined. RESULTS: Fluid from the nasogastric tube was obtained from 25 patients, lavage fluid from 26 patients, serum samples from 20 patients and biopsies from 18 patients. Several genotypes were found, of which the vacA s1 cagA positive strains were predominant. Additionally, a correlation was found between the H. pylori presence in biopsy and its presence in lavage fluid (p=0.015), rendering the latter as an alternative for biopsy. Sensitivity and specificity of lavage fluid analysis were 100% and 67%, respectively. CONCLUSION: This study shows the vacA s1 cagA positive strain is predominant in a PPU population. The correlation found between the H. pylori presence in biopsy and its presence in lavage fluid suggests that analysis of the lavage fluid is sufficient to determine the H. pylori presence. Risks associated with biopsy taking may be avoided.

Functional analysis of iceA1, a CATG-recognizing restriction endonuclease gene in Helicobacter pylori.

iceA1 in Helicobacter pylori is a homolog of nlaIIIR, which encodes the CATG-specific restriction endonuclease NlaIII in Neisseria lactamica. Analysis of iceA1 sequences from 49 H.pylori strains shows that a full-length NlaIII-like ORF is present in 10 strains, including CH4, but in other strains, including strain 60190, the ORFs are truncated due to a variety of mutations. Our goal was to determine whether iceA1 can encode a NlaIII-like endonuclease. Overexpression in Escherichia coli of iceA1 from CH4, but not from 60190, yielded NlaIII-like activity, indicating that the full-length iceA1 is a functional endonuclease gene. Repair of the iceA1 frameshift mutation in strain 60190 and its expression in E.coli yielded functional NlaIII-like activity. We conclude that iceA1 in CH4 is a functional restriction endonuclease gene, while iceA1 in 60190 is not, due to a frameshift mutation, but that its repair restores its restriction endonuclease activity.

[Vaccination against human papillomavirus for the prevention of cervical cancer]. / Vaccinatie tegen Humaan papillomavirus ter preventie van baarmoederhalskanker.

Persistent infections with high-risk Human papillomavirus (HPV) can lead to cervical cancer. This fact could imply that vaccination against HPV could prevent this disease. Such vaccines could be aimed at the prevention of HPV infections or the treatment of infections, cervical intraepithelial neoplasia (CIN) and cervical cancer. There are two prophylactic candidate vaccines against the high risk HPV types 16 and 18, which appear to be safe and effective in preventing incidental and persistent HPV infections. Phase III studies should reveal whether these vaccines will also have long-term effects by preventing the development of CIN and eventually cervical cancer. The introduction of such an HPV vaccine in the Netherlands, its cost-effectiveness and introduction into the existing national vaccination programmes needs to be studied. The vaccination of girls before they become sexually active seems to be the most effective approach, although older women can also profit from prophylactic vaccination. The current community-based screening, possibly complemented by an HPV test, needs to be continued to identify and treat presently HPV-infected women. In a population with an existing community-based screening program for cervical cancer, a vaccine preventing persisting infection with high-risk HPV will further reduce the incidence of HPV-related cervical cancer.

Genetic organization and heterogeneity of the iceA locus of Helicobacter pylori.

The genetic organization and sequence heterogeneity of the iceA locus of Helicobacter pylori was studied, and the existence of two distinct gene families, iceA1 and iceA2, at this locus was confirmed. iceA1 has significant sequence homology to nlaIIIR, encoding an endonuclease in Neisseria lactamica, but the similarity at the protein level is limited, due to frameshift mutations of iceA1 in most H. pylori strains. In only five of the 19 iceA1 strains studied, a full-length open reading frame (ORF), capable of encoding a 228aa protein, with 52% homology to NlaIII was observed. The region upstream of iceA2 is highly variable in length, containing up to 15 copies of 8bp tandem repeats. iceA2 can encode proteins of 24, 59, 94, or 129 amino acids, consisting of 14 and 10aa domains, conserved in all iceA2 strains, flanking 0, 1, 2, or 3 copies of a 35aa cassette. This 35aa cassette consists of domains of 13, 16 and 6aa, respectively. The 13aa and 6aa domains are highly conserved, but the 16aa domain exists in two variants. In total, five distinct iceA2 subtypes were defined. Database searches did not reveal any homologous sequences. Recombinant IceA1 and IceA2 proteins were expressed in Escherichia coli, confirming the predicted ORFs. Genotype-specific PCR primers permitted iceA genotyping in 318 (99. 1%) of a worldwide collection of 321 H. pylori strains. The conserved sizes of the amplification products confirmed the worldwide distribution of discrete variants of iceA1 and iceA2.

Further characterization of a 58 kDa Plasmodium berghei phosphoprotein as a cochaperone.

Molecular chaperones are important for proper protein folding during protein biogenesis. This report describes a protein from Plasmodium berghei which is 30% identical and 40% similar to a recently described mammalian cochaperone, or heat shock protein 70 interacting protein. The P. berghei cochaperone accumulates throughout the trophozoite stage and decreases during the schizont stage. The stage specific expression is consistent with its presumed role in protein folding or protein-protein interactions. The largest difference between the Plasmodium and mammalian sequences is a more extensive domain of imperfect glycine-glycine-methionine-proline (GGMP) tandem repeats in the parasite's cochaperone sequence. Immunofluorescence studies show that the protein is an abundant cytosolic protein of the parasite. However, antibodies raised against the GGMP repeat domain, which is also found in other parasite chaperones, react with both the parasite and host erythrocyte membrane. The reactivity with the host membrane suggests that the parasite exports molecular chaperones into the infected erythrocyte.

Hepatitis C virus genotyping by means of 5'-UR/core line probe assays and molecular analysis of untypeable samples.

To test the theoretical possibility of 5'-UR mistyping between hepatitis C virus subtypes 1a and 1b, we combined a 5'-UR/Core line probe assay (LiPA) with a nested PCR system and retested 183 sera, previously genotyped as type 1a or 1b and originating mainly from Western Europe. Eight percent of these were found to be wrongly subtyped. Based on this method, 3 additional subtypes of type 1 were discovered (1d-1f). Randomly selected European type 2 sera (n = 18) were tested with a similar type 2 5'-UR/Core LiPA. They were unexpectedly found to belong to subtype 2c in the majority of cases. Among serum samples originating from South-East Asia, several additional genotypes (7a, 7c, 7d, and 9a) were detected which had 5'-UR sequence motifs indistinguishable from genotype 1. Based on 13,203 pairwise comparisons in the 340-bp NS5B region, classification into types, subtypes, and isolates was obtained in 99.8% of all cases by using the phylogenetic border value of 0.328 for subtypes/types and 0.127 for isolates/subtypes; and evidence for a 10th major type of HCV was provided. Combination of all available HCV sequence data from the 447-bp Core/E1 region and the NS5B 340-bp and 222-bp regions provided evidence for the existence of 10 types, including 50 subtypes. Previously, extensive studies involving genotypes 1a, 1b, 2a, and 2b indicated the importance of HCV subtyping in interferon treatment and progression of chronic liver disease. The herein described expansion in the number of HCV types and subtypes should help improve diagnosis, treatment and possibly prophylaxis of hepatitis C liver disease.

Detection of Helicobacter pylori virulence-associated genes.

Helicobacter pylori is an important human pathogen and persistent colonization of the human gastric mucosa can cause severe gastrointestinal diseases. The bacterium should not be considered as a uniform organism, but as a population of closely related and yet genetically diverse bacteria. Several genes of H. pylori (such as vacA and cagA) have been identified as being virulence-associated and may have important clinical and epidemiological implications. Assessment of virulence-associated genes of H. pylori should be included in clinical and epidemiological studies as well as therapeutic trials, in order to stratify between patient groups, harboring H. pylori strains with particular virulence genotypes. Molecular determination of antibiotic resistance will be especially useful for treatment studies. Together with our increasing knowledge about the human genome, typing of H. pylori will facilitate the management of gastroenterological pathologies.

Molecular detection and genotyping of human papillomavirus.

Human papillomavirus infections are associated with the development of cervical neoplasia. Human papillomavirus is a group of heterogeneous viruses, comprising many genotypes, which can be divided into high-risk and low-risk types, depending on their association with disease. Therefore, accurate molecular diagnostic tools are required for detection and identification of human papillomavirus. Monitoring of human papillomavirus infection is necessary for adequate patient management and follow-up during treatment. This review describes the different molecular methods available for human papillomavirus detection and identification of genotypes.

Polymerase chain reaction for the detection of Helicobacter pylori in formaldehyde-sublimate fixed, paraffin-embedded gastric biopsies.

To improve morphologic detail and immunohistochemical staining, mercuric chloride-containing fixatives such as formaldehyde-sublimate (FS) has been widely used as an alternative for neutral buffered formalin. FS-fixed, paraffin-embedded tissue, however, is considered to be an unreliable source of DNA. We used an adapted DNA-extraction method for FS-fixed, paraffin-embedded tissue. In all cases tested we obtained amplifiable DNA with polymerase chain reaction (PCR), after FS-fixation and after fixation in neutral buffered formalin as well. A PCR assay for the 16S-rRNA region of Helicobacter pylori was developed amplifying a fragment of 145 bp. The specificity of this PCR assay was tested on a range of different microorganisms. PCR was performed on 46 archival FS-fixed paraffin-embedded gastric biopsies. The results were compared with histologic examination and with immunohistochemical detection using a polyclonal antibody against H. pylori. Both PCR and immunohistochemistry are very sensitive methods for the detection of H. pylori. A PCR offers the possibility of additional subtyping in archival FS-fixed, paraffin-embedded tissue.

Genotyping of Helicobacter pylori strains in formalin-fixed or Formaldehyde-sublimate-fixed paraffin-embedded gastric biopsy specimens.

Different genotypes of Helicobacter pylori can play a role in the development of atrophic gastritis, peptic ulcer disease, and gastric carcinomas. In this study the authors developed polymerase chain reaction assays for the detection and identification of vacA (s- and m-regions), cagA, and iceA genotypes of H. pylori in formalin-fixed or formaldehyde-sublimate-fixed paraffin-embedded gastric biopsy specimens. Polymerase chain reaction products were analyzed by reverse hybridization on a line-probe assay. Complete genotyping was achieved in 26 of 28 samples (93%), and multiple genotypes, indicating the presence of multiple strains, were detected in nine samples (32%). This genotyping method offers the possibility for long-term retrospective studies on H. pylori genotypes and gastric pathology in the same archival gastric tissue specimens.

Risk factors for HCV infection in two haemodialysis units in The Netherlands.

BACKGROUND: In order to assess risk factors for HCV infection during haemodialysis, all patients receiving haemodialysis for more than 6 months in two separate units in the Netherlands were studied retrospectively. METHODS: Antibodies to HCV, HCV-RNA and HCV genotypes were determined. Risk factors were identified by analysis of an extensive collection of clinical data. RESULTS: In unit A, 8 out of 75 (11%) patients and in unit B 4 out of 122 (3%) patients had antibodies to HCV. Eleven out of the 12 anti-HCV-positive patients had detectable HCV-RNA. Genotyping showed the presence of 4 different genotypes in unit A (1, 1a, 2b, and 3a). Three patients in unit B were infected with the same genotype (1b), where one of these patients was also infected with genotype 1a. One patient in unit B did not have detectable HCV-RNA. The risk of acquiring a HCV infection in unit A was associated with the number of blood transfusions. However, in unit B this risk was associated with the duration of dialysis. Other factors such as the number of surgical procedures were not associated with HCV infection. CONCLUSIONS: Blood transfusions and the dialysis process itself are important and independent risk factors for HCV transmission in dialysis patients. Surgical events do not appear to be important risk factors. However, relative risks may vary considerably between different dialysis centres.

[Nosocomial transmission of hepatitis C virus in a Dutch dialysis center]. / Nosocomiale transmissie van het hepatitis-C-virus in een Nederlands dialysecentrum.

OBJECTIVE: To describe the transmission of hepatitis C virus (HCV) in a dialysis centre in the Netherlands, to analyse risk factors and to redefine additional preventive measures. DESIGN: Descriptive. METHODS: The data of patients attending the dialysis centre of the Deventer Hospital, the Netherlands, who had participated in a national prospective survey on the epidemiology of HCV among Dutch dialysis patients, were examined. In addition, patients who developed signs of hepatic failure in the ensuing year were included in this study. To diagnose an HCV-infection serology as well as polymerase chain reaction were used. Genotyping and sequence analysis were used to assess phylogenetic relations. Infection control practices were audited. RESULTS: In the dialysis centre a cluster of four almost identical HCV isolates genotype 2a was found. Within a period of one year another cluster of four HCV-infected dialysis patients was detected in the same centre. These four isolates were almost identical to a fifth isolate, genotype 2b, found in the earlier study from another patient dialysing in the same unit. It was observed that possibly contaminating procedures were not strictly separated. Some of the shared medical equipment was not sterilised but only cleaned. Also blood-contaminated gloves might have played a role in the transmission of HCV. CONCLUSION: Nosocomial transmission plays an important role in the epidemiology of HCV in dialysis patients. Shared medical equipment and blood-contaminated gloves may constitute a potential route of transmission. There is a need for stringent implementation and regular auditing of infection control measures.

[The detection of melanoma metastases in sentinel nodes by polymerase chain reaction]. / Opsporing van metastasen van melanomen in schildwachtklieren met de polymerasekettingreactie.

OBJECTIVE: To investigate the possibility of detecting melanoma metastases using molecular biological techniques in patients with a primary malignant melanoma. DESIGN: Descriptive. SETTING: Reinier de Graaf Gasthuis Hospital Delft and diagnostic centre SSDZ Delft, the Netherlands. METHODS: A melanoma specific tyrosinase mRNA was amplified using the reverse transcriptase polymerase chain reaction (RT-PCR) technique. RESULTS: A total of 23 sentinel nodes derived from 9 patients were examined. In 14 sentinel nodes metastases were found using RT-PCR. In microscopic slides stained with haematoxylin and eosin (HE) melanoma metastases were found in 2 sentinel nodes of 2 patients. With immunohistochemistry melanoma metastases were found in the same 2 sentinel nodes. CONCLUSION: It is possible to detect melanoma metastases in sentinel nodes using molecular biological techniques.

Universal human papillomavirus genotyping by the digene HPV Genotyping RH and LQ Tests.

BACKGROUND: High-risk (hr)HPV testing plays an important role in primary cervical cancer screening. Subsequent hrHPV genotyping might contribute to better risk stratification. The majority of hrHPV tests do not include identification of individual hrHPV genotypes. OBJECTIVES: The digene HPV Genotyping RH Test (strip-based) and LQ Test (xMAP-based) allow genotyping of GP5+/6+ amplimers, but their probes target a region in the L1 ORF, which is also amplified by other broad-spectrum hrHPV assays, e.g., the Roche Amplicor HPV Test (Amplicor) and the Roche Linear Array. The goal was to test whether the RH Test and LQ Test can be used as an universal hrHPV genotyping test. STUDY DESIGN: Self-collected cervico-vaginal specimens (n=416) from an epidemiologic study were analyzed with Amplicor. The amplimers obtained were also tested with the RH Test and LQ Test for identification of 18 HPV types, including the 13 hrHPVs targeted by Amplicor. RESULTS: 197 specimens were positive by Amplicor, in which the RH Test and LQ Test identified one of the 13 hrHPVs in 94.4% and 98.0%, respectively. In 219 specimens remaining negative by Amplicor, the RH Test and LQ Test, performed on the Amplicor amplification products, still detected one of the 13 hrHPVs in 3.7% and 5.5%, respectively, and include identification of HPV53, 66, and 82. Overall, the RH and LQ Tests demonstrated high concordance with Amplicor for hrHPV detection (κ=0.908 and κ=0.923, respectively). CONCLUSIONS: The digene HPV Genotyping RH and LQ Tests can be directly used for amplimers generated by the Amplicor HPV Test.