Knowledge about the human papillomaviruses (HPV) types in anal cancers in some world regions is scanty. Here we describe the HPV DNA prevalence and type distribution in a series of invasive anal cancers and anal intraepithelial neoplasias (AIN) grades 2/3 from 24 countries. We analyzed 43 AIN 2/3 cases and 496 anal cancers diagnosed from 1986 to 2011. After histopathological evaluation of formalin-fixed paraffin-embedded samples, HPV DNA detection and genotyping was performed using SPF-10/DEIA/LiPA25 system (version 1). A subset of 116 cancers was further tested for p16INK4a expression, a cellular surrogate marker for HPV-associated transformation. Prevalence ratios were estimated using multivariate Poisson regression with robust variance in cancer dataset. HPV DNA was detected in 88.3% of anal cancers (95%CI:85.1–91.0%) and in 95.4% of AIN 2/3 (95%CI:84.2–99.4%). Among cancers, the highest prevalence was observed in warty-basaloid subtype of squamous cell carcinomas, in younger patients and in North American geographical region. There were no statistically significant differences in prevalence by gender. HPV16 was the most frequent HPV type detected in both cancers (80.7%) and AIN 2/3 lesions (75.4%). HPV18 was the second most common type in invasive cancers (3.6%). p16INK4a overexpression was found in 95% of HPV DNA positive anal cancers. In view of HPV DNA results and high proportion of p16INK4a overexpression, infection by HPV is most likely to be a necessary cause for anal cancers in both men and women. The large contribution of HPV16 reinforces the potential impact of HPV vaccines in the prevention of these lesions.

Fifty-nine isolates of Staphylococcus aureus and a single strain of Staphylococcus intermedius were typed by arbitrarily primed PCR (AP-PCR). To study reproducibility and discriminatory abilities, AP-PCR was carried out in seven laboratories with a standardized amplification protocol, template DNA isolated in a single institution, and a common set of three primers with different resolving powers. The 60 strains could be divided into 16 to 30 different genetic types, depending on the laboratory. This difference in resolution was due to differences in technical procedures (as shown by the deliberate introduction of experimental variables) and/or the interpretation of the DNA fingerprints. However, this did not hamper the epidemiologically correct clustering of related strains. The average number of different genotypes identified exceeded those of the more traditional typing strategies (F. C.

Mycoplasma pneumoniae and viruses in acute respiratory tract infections in children were studied during the winter of 1992-1993 in Antwerp, Belgium. M. pneumoniae was diagnosed in nasopharyngeal aspirates by culture and polymerase chain reaction (PCR). For this, amplification of a fragment of the PI adhesin gene in samples prepared by two methods was compared in two laboratories, and in one laboratory, a fragment of the 16S rRNA gene was amplified. The sensitivity of culture versus PCR was 61.5%. Provided a specific internal control is used, sample preparation by freeze-boiling combined with PCR for the PI gene and amplicon detection by visual inspection of the electrophoresis gel can be recommended, although maximal results are obtained after hybridization. M. pneumoniae was present in 0.5% of patients <2 years old and 6.9% of patients >2. M. pneumoniae was second to respiratory syncytial virus or detected equally in lower respiratory infections.

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The taxonomic affiliation of Campylobacter hyoilei was reevaluated by examining a variety of phenotypic and genotypic criteria. Whole-cell protein electrophoresis and a comparison of 66 phenotypic characters revealed that reference strains of C. hyoilei were indistinguishable from Campylobacter coli strains. These data were confirmed by a DNA-DNA hybridization level of 67% between the type strains of the two species. Several species-specific assays based on PCR amplification or probe hybridization further substantiated that C. coli strains and C. hyoilei strains are indistinguishable. It is therefore concluded that C. hyoilei and C. coli represent the same species and that the former name should be regarded as a junior synonym of the latter name. The taxonomic structure and relationships of the family Campylobacteraceae have been unravelled by an integrated polyphasic approach (40,41,44,49). As in many other lineages of the class Proteobacteria, results from rRNA homology experiments formed the framework used to revise the classification and nomenclature of campylobacters (17, 31, 36, 41, 44). Assignment of taxa to the genus Campylobacter and to the related genera Arcobacter and Helicobacter is primarily based on rRNA similarity data, in accordance with the present view of classification (namely, that natural relationships between bacteria [55] should be reflected where possible). Although definitely among the most valuable taxonomic tools, rRNA sequence analysis is not the appropriate method for resolving every problem in bacterial classification. The resolution of 16s rRNA sequence analysis for closely related species (organisms sharing more than 97% of their 16s rRNA sequences) has been shown to be low (5, 11, 35). For such organisms, DNA-DNA hybridization experiments are essential for species demarcation , and guidelines have been presented by an ad hoc committee (54). However, the interpretation of DNA-DNA hybridization results is often not straightforward as the threshold values for species delimitation vary among taxa and data obtained in different laboratories or with different hybridiza-tion methods often do not correlate (46). In the present study, we evaluated the criteria used to assign 12 porcine isolates to the new species Campylobacter hyoilei (1). Remarkably, strains classified as C. hyoilei and Campy-lobactel-coli were reported to produce exactly the same band patterns in several DNA probe hybridization assays, and the phenotypic data used to differentiate C. hyoilei from C. coli were at variance with other published data (1, 3, 27). MATERIALS AND METHODS Strains used. The strains used and their sources are listed in Table 1. Bacte-riological purity was checked by plating and examining living and Gram-stained cells. Polyacrylamide gel electrophoresis of whole-cell proteins. All of the strains examined were grown on Mueller-Hinton agar (catalog no. CM 337; Oxoid, Ltd., Basingstoke, United Kingdom) supplemented with 5% (vol/vol) horse blood and were incubated at 36 to 37°C in a microaerobic atmosp...