- Volume 56, Issue 3, 2007

Penicillium marneffei is a dimorphic fungus endemic in southeast Asia. The incidence of P. marneffei infection has increased greatly in this region with the spread of human immunodeficiency virus, but the infection routes and pathogenic mechanisms of P. marneffei remain poorly understood. P. marneffei is an opportunistic human pathogen exhibiting a temperature-dependent dimorphic switch. At 25 °C it grows as filamentous hyphae, whilst at 37 °C it forms uninucleate yeast cells and divides by fission. Dimorphic fungal pathogenicity is frequently associated with the dimorphic switch, but the mechanism that regulates the switch has remained obscure. In this report, two-dimensional difference gel electrophoresis was used to investigate the proteins expressed differentially in the yeast and mycelial phases of a wild-type isolate of P. marneffei. Among thousands of protein molecules displayed, more than 500 showed differential expression between the two phases. In particular, 26 proteins were identified using matrix-assisted laser desorption/ionization time-of-flight MS. Expression of catalase-peroxidase, isocitrate lyase, Hsp90, binding protein and cytochrome P-450 increased significantly in the yeast phase, whereas levels of poly(A) polymerase and SNF22 were reduced.

This study investigated the comparative performance of the Amplicor assay and an in-house semi-automated, multiplex real-time PCR for the diagnosis of genital chlamydial infection. Four different assays, the COBAS Amplicor CT test (Amplicor PCR), in-house real-time PCR (IHRT-PCR), in-house nested cryptic plasmid PCR and in-house nested major outer membrane protein PCR, were performed on genital swabs from 1000 consecutive patients attending a genitourinary medicine clinic. The samples were designated true positive if Chlamydia trachomatis DNA was detected by at least two of the four above-mentioned assays while a sample was defined as true negative if C. trachomatis DNA was detected in only one or none of the assays. By this criterion, there were 129 true positive and 871 true negative samples for C. trachomatis DNA in this cohort. Amplicor PCR designated 144 samples positive: 128 (89 %) of 144 samples were true positive and 16 (11 %) were false positive. IHRT-PCR detected 126 of 129 true positive samples and did not generate any false positive results. The sensitivity of IHRT-PCR was comparable with, and specificity was higher than, Amplicor PCR for the diagnosis of genital chlamydial infection.

In this study a real-time PCR assay using self-quenched primers labelled with a single fluorophore for the detection of Aeromonas salmonicida was developed. Probe specificity was confirmed by amplification of 16 A. salmonicida strain templates and by the lack of a PCR product with 26 non-A. salmonicida strains. With a pure culture of A. salmonicida, the assay was linear over a range of 0.5 pg to 50 ng and was able to detect 16 c.f.u. per reaction. A similar sensitivity was observed in DNA extracted from a mixture of A. salmonicida and fish tissue. Results using artificially inoculated tissues and diseased fish from outbreaks indicated that the assay can provide sensitive species-specific detection and quantification of A. salmonicida in fish tissue.

Variability in the genes for toxin A, toxin B and other pathogenicity locus regions is well known and is the basis for the distribution of Clostridium difficile strains into variant toxinotypes. Previous data have indicated that some C. difficile strains have a non-functional truncated form of the binary toxin (CDT) locus. This study analysed variability in the CDT locus and the presence of deleted tcdC genes in C. difficile strains. A total of 146 strains were screened, including known variant toxinotypes and non-variant A+B+ (toxinotype 0) and A−B− C. difficile strains. In all of the strains studied, only two forms of the CDT locus were found: a full-length 4.3 kb fragment encoding the functional binary toxin or a truncated 2.3 kb fragment. Whilst the full-length CDT locus was found almost exclusively in variant toxinotypes, the truncated form was detected in 79 % of toxinotype 0 strains. Non-toxinogenic A−B− strains with a truncated version were not found and only rarely possessed the full-length CDT locus (A−B−CDT+ strains). Four different forms of the tcdC gene were found; three represented deleted versions and typically were found in toxinotypes III–VII, XI, XIV–XVI and XXIV.

An outbreak of Legionnaires' disease at a long-term care facility in Ontario, Canada from September to October 2005 resulted in the death of 23 residents and the illness of 112 other people. In response, molecular methods were developed to detect Legionella pneumophila in clinical lung samples and to subtype isolates from clinical and environmental samples. The targeted genetic loci included Legionella-specific virulence determinants (mip, icmO, sidA and lidA) and core bacterial determinants (ftsZ, trpS and dnaX). An established amplified fragment length polymorphism typing method provided the first indication of genetic relatedness between strains recovered from clinical samples and strains cultured from environmental samples taken from the outbreak site. These associations were verified using the European Working Group for Legionella Infections sequence-based typing protocol targeting the flaA, pilE, asd, mip, mompS and proA loci. These molecular typing methods confirmed the outbreak source as a contaminated air conditioning cooling tower.

This study describes a multiplex PCR assay for the detection of antibiotic resistance genes and the SXT element in Vibrio cholerae. Conditions were optimized to amplify fragments of sulII (encoding sulfamethoxazole resistance), dfrA1 (O1-specific trimethoprim resistance), dfr18 (O139-specific trimethoprim resistance), strB (streptomycin B resistance) and the SXT element simultaneously in one PCR. This multiplex PCR was evaluated on 142 V. cholerae isolates and the results correlated with the phenotypic antibiotic data obtained using a disc diffusion assay and a colony blot assay. Thus this one-step PCR can be used as a simple, rapid and accurate method for identification of antibiotic resistance profiles and could be used for the surveillance of the spread of antibiotic resistance determinants in epidemiological and environmental studies.

Previous results in the laboratory of the authors showed that Saccharomyces cerevisiae strain 905, isolated during ‘cachaça’ production, was able to colonize and survive in the gastrointestinal tract of germ-free and conventional mice, and to protect these animals against oral challenge with Salmonella enterica serotype Typhimurium or Clostridium difficile. In the present work, the effects of S. cerevisiae 905 on the translocation of Salm. Typhimurium (mesenteric lymph nodes, Peyer's patches, spleen, liver) as well as on the immune system (number of Küpffer cells, immunoglobulin production, clearance of Escherichia coli B41) were evaluated in gnotobiotic and/or conventional mice. The treatment with the yeast reduced significantly the translocation of Salm. Typhimurium to liver in gnotobiotic animals and to all the organs tested in conventional mice. The number of Küpffer cells per 100 hepatocytes in liver was significantly higher (P<0.05) in yeast mono-associated mice (52.9±15.7) than in germ-free controls (38.1±9.0). Probably as a consequence, clearance of E. coli B41 from the bloodstream was more efficient in yeast mono-associated animals when compared to germ-free mice. Higher levels (P<0.05) of secretory IgA in intestinal content and of IgA and IgM in serum were observed in yeast mono-associated mice when compared to germ-free group. Concluding, the protection against pathogenic bacteria observed in a previous study was probably due to a modulation of both local and systemic immunity of mice treated with S. cerevisiae 905.

Conventional methods for determining drug susceptibility of Mycobacterium tuberculosis require several weeks to obtain results, limiting their usefulness; automated methods and those based on molecular biology techniques have been able to reduce the turnaround time, but their high cost and need for sophisticated equipment restrict their use in developing countries. The goal of the present study was to evaluate the diagnostic accuracy of a rapid (3–4 days) low-cost test based on the use of mycobacteriophage D29 to determine the susceptibility of strains of M. tuberculosis to rifampicin (RIF) and isoniazid (INH). Results obtained show that susceptibility testing for RIF has a high diagnostic accuracy as compared to the standard indirect proportion method on Löwenstein–Jensen medium (sensitivity 100 % and specificity 98 %). Given the association between the resistance to RIF and INH, which define multidrug resistance (MDR), this test seems suitable for rapid detection of MDR tuberculosis strains (κ=0.978). Susceptibility testing for INH using mycobacteriophage D29 had a good but lower diagnostic accuracy as compared to the standard method (sensitivity 80.4 % and specificity 80.8 %); the test would then be of limited usefulness in the management of tuberculosis patients. Further studies to determine the relationship of mycobacteriophage D29 tests to in vivo correlates of sensitivity to specific antituberculosis drugs are warranted.

The aim of this study was to determine the extent of EMRSA-15 spread in hospitals in Singapore. Molecular analysis of 197 non-duplicate meticillin-resistant Staphylococcus aureus (MRSA) isolates collected from five acute care public hospitals in Singapore in May 2005 revealed that 66 (33.5 %) were EMRSA-15 while 121 (61.4 %) belonged to the endemic multidrug-resistant ST239 clone. Median and mode vancomycin MIC for both major clones of health-care-associated MRSA were relatively high at 2.0 μg ml−1. Subsequent laboratory surveillance data collected from the first half of 2006 confirmed increasing numbers of the EMRSA-15 clone – ranging from 25.0 to 66.1 % of all MRSA isolated in local hospitals – replacing the ST239 clone island-wide.

The prevalence of Shiga toxin-producing Escherichia coli (STEC) and its characteristics were determined among hospitalized patients with diarrhoea and children with diarrhoea in an urban slum community of Dhaka city using sensitive culture and PCR methods. Stool samples were collected from 410 patients with diarrhoea enrolled in the 2 % surveillance system (every 50th patient attending the hospital with diarrhoeal disease is included) at the ICDDR,B hospital and from 160 children of 2–5 years of age with diarrhoea living in an urban slum in Dhaka, between September 2004 and April 2005. Shiga toxin genes (stx) were detected by multiplex PCR in the enrichment broth of nine samples (2.2 %) from hospitalized patients and 11 samples (6.9 %) from the community patients. STEC was isolated from five stool samples with positive PCR results using a colony patch technique. All five isolates were positive in the Vero cell assay and PCR fragments of stx genes were confirmed by sequencing. Two isolates were positive for the E. coli attaching-and-effacing (eae) gene and four were positive for the enterohaemolysin (hly EHEC) gene and enterohaemolysin production. The five isolates belonged to five different serotypes: O32 : H25, O2 : H45, O76 : H19, ONT : H25 and ONT : H19. It can be concluded that STEC is not a common pathogen in Bangladesh among hospitalized patients with diarrhoea nor among mild cases of diarrhoea in the community.

A national multicentre cross-sectional study was undertaken on the correlates of hepatitis C virus (HCV) infection in a sample of inmates from eight Ghanaian prisons. A total of 1366 inmates from eight of the ten regional central prisons in Ghana were enrolled between May 2004 and December 2005. Subjects voluntarily completed a risk-factor questionnaire and provided blood specimens for unlinked anonymous testing for the presence of antibodies to HCV. These data were analysed using both univariate and multivariate techniques. The median age of participants was 36.5 years (range 16–84 years). Of the 1366 inmates tested, HCV seroprevalence was 18.7 %. On multivariate analysis, the independent determinants of HCV infection were being incarcerated for longer than the median time served of 36 months [odds ratio (OR) 5.8; 95 % confidence interval (95 % CI) 5.0–6.9], history of intravenous drug use (OR 4.5; 95 % CI 3.8–5.4) and homosexuality (OR 3.1; 95 % CI 2.5–3.9). Consistent with similar studies worldwide, the prevalence of HCV in prison inmates was higher than the general population in Ghana, suggesting probable transmission in prisons in Ghana through intravenous drug use and unsafe sexual behaviour.

Chlamydophila pneumoniae is an obligate intracellular respiratory pathogen that has been associated with pneumonia and chronic bronchitis, atherosclerosis, asthma and other chronic diseases in humans. However, C. pneumoniae is not restricted to humans, as originally thought, and can cause infections in several animal hosts. C. pneumoniae was isolated in cell culture from nine Western barred bandicoots (Perameles bougainville) from Australia. The sequences of five genomic regions were determined, including full-length sequences of the16S rRNA and ompA genes and the ygeD–urk intergenic spacer, and partial sequences of the 23S rRNA and rpoB genes. Sequence analysis of the entire 16S rRNA and ompA genes from bandicoot isolates demonstrated that they were 98.2–98.3 % similar to human isolates, 94.6–99.3 % similar to the equine biovar and almost identical, with 99.5–99.9 % similarity, to the koala biovar. Comparative genotyping of the variable domain 4 region of the ompA gene demonstrated that bandicoot isolates seemed to be identical to the animal genotype that has been recently identified in human carotid plaque specimens. Minor sequence polymorphism observed in ompA, 16S rRNA and rpoB genes of animal isolates, indicating genomic diversity within C. pneumoniae, may have important implications for diagnostic PCR assays leading to false negative results. Forty percent of selected published species-specific PCR assays were found to have sequence variability in primer and/or probe that might affect their performance in detecting bandicoot isolates of C. pneumoniae, or possibly other animal and human strains where minor sequence polymorphisms may be present. The data from this study support the previous observations that C. pneumoniae is not restricted to humans and may be widespread in an animal reservoir with a potential risk of transmission to humans.

The occurrence of 7 of the 11 known ssl genes that are found within the vSaα genomic island of Staphylococcus aureus and encode the novel Ssl family of exoproteins was examined in isolates from cows (42 isolates), goats (4 isolates), sheep (1 isolate), rabbits (3 isolates) and chickens (2 isolates). Based on seven S. aureus genome sequences for human strains NCTC 8325, N315, Mu50, COL, MRSA 252, MW2 and MSSA-476, and bovine strain RF122, along with the ssl reference gene sequences from strains NCTC 6571, FRI326 and NCTC 8325, ClustalW-generated alignments were used to design PCR primers for unique regions of the ssl genes that are present in the allelic variants of each, except for the ssl4 gene for which specific primers for the set2 and set9 allelic variants were designed individually. The genotypes of isolates were determined using random amplified polymorphic DNA (RAPD) typing. All of the animal-associated S. aureus isolates contained an ssl locus, but there were minor variations in the number of ssl genes present. Forty-nine of the animal isolates possessed a vSaα genomic island containing the ssl3 (set8), ssl5 (set3/set10), ssl7 (set1/set11), ssl8 (set12), ssl9 (set5/set13) and ssl10 (set4/set14) genes. One bovine and one goat isolate lacked the ssl3 gene. The ssl9 gene was absent in one bovine isolate. The goat isolate lacking the ssl3 gene was the only animal isolate that possessed the set2 allele of the ssl4 gene. PCR for the set9 allele of the ssl4 gene was inconclusive. Isolates that showed identical RAPD fingerprints had the same complement of ssl genes, but the ssl gene pattern was not RAPD-type specific. Southern blot hybridization showed similar ssl gene RFLPs in isolates of the same RAPD type.