- Volume 59, Issue 11, 2010

The hsp60 gene sequences were determined for 121 strains of Gram-negative anaerobic rods, including the genera Bacteroides, Barnesiella, Butyricimonas, Odoribacter, Parabacteroides, Paraprevotella, Porphyromonas, Prevotella and Tannerella. The mean pairwise hsp60 gene sequence similarity (73.8–97.1 %) between species in each genus, except for the genus Tannerella that comprises one species, was significantly less than that of the 16S rRNA gene sequence (88.3–96.3 %). Only pairwise hsp60 gene sequence similarity (97.1 %) of the genus Paraprevotella was higher than that of the 16S rRNA gene sequence (93.8 %). Each genus formed a distinct clade in the phylogenetic analysis of the hsp60 gene sequence as well as the 16S rRNA gene sequence. The phylogenetic analysis indicated a higher evolutionary rate for the hsp60 gene sequence than the 16S rRNA gene sequence, especially in the genera Porphyromonas and Prevotella. This study suggests that the hsp60 gene is a useful alternative phylogenetic marker for the identification and classification of a broad range of Gram-negative anaerobic rods.

A simple paper smear (PS) method for dry collection and storage of cervical specimens was employed to develop an easy multiplex (MPX) PCR for simultaneous detection of generic human papillomaviruses (HPVs) as well as typing of the high-risk HPV-16 and -18, the two clinically most important HPV genotypes, which are responsible for more than 80 % of cervical cancers. Multiplexing was performed with a small amount of DNA eluted by boiling from a single PS punch in a single tube and using a mixture of four pairs of primers specific for the HPV L1 consensus sequence, HPV-16, HPV-18 and the β-globin gene. Sixty HPV-positive biopsies and corresponding PS specimens from cervical cancer patients as well as cervical smears from 100 healthy women with or without abnormal cytology were collected both as PSs and in PBS. Detection of HPV DNA from cervical biopsies collected in PBS and corresponding cervical scrapes on a PS or in PBS by conventional and MPX-PCR showed a concordance of 100 % and adequacy of 93 %. A similar comparative study in cervical scrapes from normal women also revealed 100 % concordance. The technique was validated in a multicentric study at four different national laboratories. PSs collected by different centres showed variable adequacy (73–82 %) but the use of multiple PS discs for DNA extraction significantly increased the adequacy. Integration of PSs with MPX-PCR for the detection and typing of HPVs is a highly convenient, efficient, simple and cost-effective method for large-scale clinico-epidemiological studies and is also suitable for HPV vaccine monitoring programmes in resource-poor settings.

In this study, PCR–RFLP analysis (PRA) targeting hsp65 and rpoB gene regions was evaluated for the identification of mycobacterial species isolated from Malaysian patients. Overall, the hsp65 PRA identified 92.2 % of 90 isolates compared to 85.6 % by the rpoB PRA. With 47 rapidly growing species, the hsp65 PRA identified fewer (89.4 %) species than the rpoB PRA (95.7 %), but with 23 slow-growing species the reverse was true (91.3 % identification by the hsp65 PRA but only 52.5 % by the rpoB PRA). There were 16 isolates with discordant PRA results, which were resolved by 16S rRNA and hsp65 gene sequence analysis. The findings in this study suggest that the hsp65 PRA is more useful than the rpoB PRA for the identification of Mycobacterium species, particularly with the slow-growing members of the genus. In addition, this study reports 5 and 12 novel restriction patterns for inclusion in the hsp65 and rpoB PRA algorithms, respectively.

Clostridium difficile infection is an increasing problem in hospitals worldwide, mainly due to the recent emergence of a hypervirulent C. difficile strain. C. difficile PCR ribotyping, based on size variation of the 16S–23S rRNA intergenic spacer region (16S–23S ISR), is widely used in Europe for molecular epidemiological investigation. The mechanism underlying the 16S–23S ISR size variations in the genome of C. difficile is currently not completely understood. To elucidate this mechanism, isolates of six different PCR ribotypes were analysed by cloning and sequencing the 16S–23S ISR. A direct repeat, IB, of 9 bp was detected up to five times in the 16S–23S ISR in all 47 clones investigated. Thirty-five clones displayed differences either by ribotype or by nucleotide sequence. The sequences of the 16S–23S ISR of C. difficile showed a uniformly organized structure, composed of a tRNAAla gene and spacers of 33 and 53 bp separated by the 9 bp direct repeat IB. The results of the study support the hypothesis that this composition is responsible for the length variations seen in the 16S–23S ISR, and indicate that these length variations result from slipped-strand mispairing and intra- and possibly interchromosomal homologous recombination.

Acanthamoeba keratitis (AK) is a corneal disease caused by members of a genus of free-living amoebae and is associated predominantly with contact lens (CL) use. This study reports 16 cases of culture-proven AK diagnosed in northern Italy. Genotype identification was carried out with a PCR assay based on sequence analysis of the 18S rRNA gene, and sensitivity and specificity were evaluated in comparison with traditional parasitological techniques. A 405 bp region of the 18S rRNA gene (ASA.S1) including diagnostic fragment 3 (DF3) was amplified using the genus-specific primers JDP1 and JDP2. Genotype assignment was based on phenetic analysis of the ASA.S1 subset of the nuclear small-subunit rRNA gene sequence excluding the highly variable DF3 region. Phylogenetic analysis was also performed on the sequences obtained. All patients complained of monolateral infection; 11 (68.75%) admitted improper CL disinfection. In 14/16 (87.5 %) subjects, corneal scrapings were stained with calcofluor white and haematoxylin and eosin and, in ten cases (62.5 %), microscopy was positive for Acanthamoeba cysts. In vitro culture on 3 % non-nutrient agar plates was obtained in all cases (100 %), whereas cloning and axenic growth were positive for 14 amoebic stocks (87.5 %). PCR analysis had 100 % sensitivity and specificity compared with in vitro axenic culture, showing positive amplification from 15 isolates. All Acanthamoeba strains belonged to the T4 genotype, the main AK-related genotype worldwide. These results confirmed the importance of a complete diagnostic protocol, including a PCR assay, for the clinical diagnosis of AK on biological samples. Genotyping allowed inclusion of all isolates in the T4 group, thus demonstrating the prevalence of this genotype in northern Italy.

Chlamydiosis is a zoonotic disease in birds caused by Chlamydophila psittaci, an obligate intracellular bacterium. There are seven known avian outer-membrane protein A genotypes, A–F and E/B. The importance of genotyping lies in the fact that certain genotypes tend to be associated with certain hosts and a difference in virulence. Genotype B is the most prevalent in pigeons, but the more virulent genotypes A and D have also been discovered. The current study assessed the prevalence of C. psittaci in 32 Belgian homing-pigeon facilities and in 61 feral pigeons captured in the city of Ghent, Belgium. Additionally, zoonotic transmission of C. psittaci was investigated in the homing-pigeon facilities. Homing pigeons were often infected, as at least one of the lofts was positive in 13 of the 32 (40.6 %) pigeon breeding facilities. Genotypes B, C and D were detected. Zoonotic transmission was discovered in 4 of the 32 (12.5 %) pigeon fanciers, revealing genotype D in two of them, whilst genotyping was unsuccessful for the other two human pharyngeal swabs. This study clearly demonstrates the possible risk of C. psittaci zoonotic transmission from homing pigeons. Pigeon fanciers often (37.5 %) used antibiotics for prevention of respiratory disease. Because of the risk of developing drug-resistant strains, regular use of antimicrobial drugs must be avoided. This study is believed to be the first to detect C. psittaci in Belgian feral pigeons. The prevalence rate in the city of Ghent was extremely low, which is beneficial for public health.

Bacterial occurrence in treated root canals, even in patients without post-treatment apical periodontitis, raises the possibility that factors other than mere bacterial presence can be determinants for a favourable outcome of endodontic treatment. Because these factors may be related to the bacterial communities colonizing the root canal, including virulence, density and interactions, the objective of this study was to compare the community structures found in root-canal-treated teeth with (12 samples) and without (11 samples) apical periodontitis lesions by means of a PCR-denaturing gradient gel electrophoresis fingerprinting approach. Results confirmed a polymicrobial composition even in treated patients without post-treatment disease. A large microbial community diversity was observed for treated teeth both with or without disease, but no specific pattern was detected for diseased teeth. Nevertheless, the number of bands from samples with apical periodontitis lesions was statistically significantly higher (P=0.04) than that from samples collected from root-canal-treated teeth without post-treatment apical periodontitis. Furthermore, predominant bands in samples from patients with apical disease were also observed.

Iliopsoas abscess is usually secondary to the spread of infection from a contiguous focus. Primary disease is uncommon, except in children where Staphylococcus aureus is the main pathogen. We report a 60-year-old woman who developed a primary iliopsoas abscess as a result of haematogenous spread of Capnocytophaga sputigena from a palatal fistula and chronic sinusitis due to previous treatment for nasopharyngeal carcinoma. Pyomyositis due to unusual and fastidious Gram-negative bacilli should be considered in patients with head and neck tumours who have previously received radiotherapy.

Vancomycin-resistant Enterococcus faecium (VRE) infection is a rare event in paediatric patients and often occurs under immunosuppression or after surgical intervention. We report what we believe to be the first paediatric case of ventriculitis due to VRE (in a 2-month-old infant) to be successfully treated with combined intravenous (i.v.) and intraventricular chloramphenicol after failure of i.v. linezolid and intraventricular gentamicin.

Chronic meningococcaemia is an unusual clinical presentation of Neisseria meningitidis infection. We describe the case of a patient, who presented with total IgA deficiency and partial IgM deficiency with a low switched memory B cells count, suggestive of a borderline form of common variable immunodeficiency (CVID). The role of IgA in the protection against Neisseria meningitidis, and the link between IgA deficiency and CVID are discussed.

Mycobacterium bovis is a pathogen of cattle. The unpasteurized milk of affected cattle is a source of infection in humans. Despite the screening of cattle and the pasteurization of milk, M bovis has not been eradicated. A high index of clinical suspicion is needed in symptomatic patients with a history of possible exposure. At risk groups include animal workers, farmers, meat packers, vets and zoo keepers. Humans are usually infected by the aerosol route. We present two cases of human bovine tuberculosis. One was a presumptive case and the second was a confirmed case. Both responded well to antituberculous therapy. In the confirmed case, there was evidence of transmission to the partner living in the same house. Rifampicin prophylaxis was given to the exposed case. The M. bovis from the confirmed case was isoniazid resistant, in addition to having the well known resistance to pyrazinamide. Isoniazid resistance has been described before in those who are immunocompromised. We describe it in an immunocompetent patient.

The spread of antimicrobial resistance among members of the Enterobacteriaceae is a significant clinical threat. We report the treatment of pan-resistant Klebsiella pneumoniae bacteraemia with combination tigecycline and colistin in a 49-year-old male and review available therapeutic options. Despite a poor prognosis, the patient recovered, but remains colonized with the pan-resistant isolate.