[Show abstract][Hide abstract] ABSTRACT: The Clinical and Laboratory Standards Institute recommends consideration of blaZ gene testing for cases of serious Staphylococcus aureus infection. Conventional PCR methods have demonstrated superior sensitivity and specificity to phenotypic tests. To our knowledge,
this is the first description of real-time PCR detection of the blaZ gene.
Preview · Article · Jan 2014 · Journal of clinical microbiology
[Show abstract][Hide abstract] ABSTRACT: Dust mites produce bacteriolytic enzymes, one of which belongs to the NlpC/P60 superfamily comprising bacterial and fungal proteins. Whether this enzyme is derived from the mite or from mite-associated microbes is unclear. To this end, the bacteriology of mites per se, and carpet and mattress dust from a group of asthmatic children and their parents was investigated. Dust from parents' and children's mattresses yielded significantly more colony forming units compared with dust from their corresponding carpets. Zymography demonstrated some dusts contained bacteriolytic enzymes, and in nine of the twelve dust samples from three of five houses examined, a prominent bacteriolytic band was obtained that corresponded to the mite band, although in one home, other lytic bands were detected. Fifty bacterial isolates were obtained from surface-sterilised, commercially obtained Dermatophagoides pteronyssinus. 16S rRNA, tuf and rpoB gene sequencing of nine Gram-positive isolates identified them as Bacillus cereus, B. licheniformis, Staphylococcus aureus, S. epidermidis, S. capitis and Micrococcus luteus, known human skin commensals. 16S rRNA sequence homologies of four of the nine isolates identified as B. licheniformis formed a distinct phylogenetic cluster. All species secreted lytic enzymes during culture although the lytic profiles obtained differed between the rods and the cocci, and none of the bands detected corresponded to those observed in dust or mites. In conclusion, mites harbour a variety of bacterial species often associated with human skin and house dusts contain bacteriolytic enzymes that may be mite-derived. The identification of a novel cluster of B. licheniformis isolates suggests an ecological adaptation to laboratory-reared D. pteronyssinus. It remains to be determined whether the previously described mite-associated 14 K lytic enzyme is derived from a microbial source.
No preview · Article · Jun 2013 · Experimental and Applied Acarology
[Show abstract][Hide abstract] ABSTRACT: Background: Branchial cleft cysts (brCC) can resemble level 2 nodal cystic metastatic squamous cell carcinomas (mSCC). mSCC in this location often arise from an HPV-associated oropharyngeal primary. P16 immunohistochemistry (IHC) is used as a surrogate marker for infection by oncogenic HPV in this setting and can be combined with HPV PCR to identify this subset of mSCC. Aim: (1) Evaluate the usefulness of p16 IHC and HPV PCR in the separation of brCC and mSCC. (2) Assess how different PCR techniques perform in this setting. Methods: 54 brCC and 35 mSCC with cell blocks were assessed. 15/35 (42.8%) mSCC were oropharyngeal in origin. P16 IHC was scored by three pathologists. HPV detection was carried out by multiplex nested PCR (nPCR) and a newer multiplex tandem PCR (tPCR) technique. Results: No brCC had >=20% p16 positive cells in contrast to 17/35 (48.6%) mSCC; 12/17 (70.6%) were oropharyngeal in origin. tPCR identified HPV DNA in 20/54 (37%) brCC and 24/35 (68.6%) mSCC; 15/24 (62.5%) were oropharyngeal in origin. nPCR identified HPV DNA in 1/54 (1.8%) brCC and 14/27 (51.8%) mSCC; 10/14 (71.4%) were oropharyngeal in origin. No HPV PCR+ brCC were p16+ (>=20% cells staining). P16+ was present in 17/24 (70.8%) tPCR HPV+ mSCC and 13/14 (92.8%) nPCR HPV+ mSCC. 10/13 (76.9%) p16+/nPCR HPV+ mSCC and 12/17 (70.6%) p16+/tPCR HPV+ mSCC were of oropharyngeal origin. Conclusions: (1) tPCR in isolation is not useful in separating brCC and mSCC; (2) dual p16/nPCR HPV DNA+ has the highest predictive value for mSCC from the oropharynx; (3) more experience is required with tPCR in this clinical setting given the high rate of HPV DNA detection in brCC.
[Show abstract][Hide abstract] ABSTRACT: Objectives:
This study examines the prognostic significance of hypoxia inducing factor-1α (HIF-1α) expression in relation to human papillomavirus (HPV) status in oropharyngeal squamous cell carcinoma (SCC).
Materials and methods:
Clinical details on 233 oropharyngeal SCCs were extracted from institutional databases. Recurrence in any form or death from any cause was recorded for a median of 51 months after diagnosis. HIF-1α expression was evaluated by semiquantitative immunohistochemistry and HPV status was determined by HPV E6-targeted multiplex real-time PCR and p16 immunohistochemistry. Determinants of recurrence and mortality hazards were modeled using Cox regression with censoring at dates of last follow-up.
The HIF-1α positivity rate was 58.8%. HIF-1α positivity was associated with higher T category (T3/T4 vs. T1/T2, 64.2% vs. 48.4%, p=0.001) and lower grade (Grade 1-2 vs. 3, 62% vs. 46.9%, p=0.001). There was no significant association between HIF-1α expression and HPV status. After adjustment for clinico-pathological variables, HPV status but not HIF-1α was a strong predictor of outcome. The combination of HPV and HIF-1α was not a prognostic variable but the worst outcomes were seen in those with HPV negative and HIF-1α positive cancers. There was no statistically significant evidence of an interaction between HPV and HIF-1α.
The degree of hypoxia as measured by HIF-1α expression does not differ between HPV positive and HPV negative cancers. The role of hypoxia in HPV negative oropharyngeal cancer warrants further investigation.
[Show abstract][Hide abstract] ABSTRACT: Background and purpose:
Human papillomavirus (HPV) causes up to 70 % of oropharyngeal cancers (OSCC). HPV positive OSCC has a more favorable outcome, thus HPV status is being used to guide treatment and predict outcome. Combination HPV DNA/p16(ink4) (p16) testing is commonly used for HPV status, but there are no standardized methods, scoring or interpretative criteria. The significance of discordant (HPV DNA positive/p16 negative and HPV DNA negative/p16 positive) cancers is controversial. In this study, 647 OSCCs from 10 Australian centers were tested for HPV DNA/p16 expression. Our aims are to determine p16 distribution by HPV DNA status to inform decisions on p16 scoring and to assess clinical significance of discordant cancers.
HPV DNA was identified using a multiplex tandem HPV E6 polymerase chain reaction (PCR) assay and p16 expression by semiquantitative immunohistochemistry.
p16 distribution was essentially bimodal (42 % of cancers had ≥ 70 % positive staining, 52 % <5 % positive, 6 % between 5 and 70 %). Cancers with 5 to <50 % staining had similar characteristics to the p16 negative group, and cancers with 50 to <70 % staining were consistent with the ≥ 70 % group. Using a p16 cut-point of 50 %, there were 25 % HPV DNA positive/p16 negative cancers and 1 % HPV DNA negative/p16 positive cancers. HPV DNA positive/p16 negative cancers had outcomes similar to HPV DNA negative/p16 negative cancers.
50 % is a reasonable cut-point for p16; HPV DNA positive/p16 negative OSCCs may be treated as HPV negative for clinical purposes; HPV DNA/p16 testing may add no prognostic information over p16 alone.
No preview · Article · Dec 2012 · Annals of Surgical Oncology
[Show abstract][Hide abstract] ABSTRACT: Background
Despite the association with more advanced nodal stage, patients with human papillomavirus (HPV) positive oropharyngeal cancers have better outcomes. We examined whether the HPV can modify the effect of known prognostic factors in tonsillar cancer.Patients and methodsA total of 489 patients from 10 centres were followed up for recurrence or death for a median of 3.2 years. Determinants of the rate of locoregional recurrence, death from tonsillar cancer and overall survival were modelled using Cox regression.ResultsThe prognostic value of T and N stages were modified by HPV as indicated by statistically significant interaction terms. After adjusting for age, gender and treatment, T stage appeared relevant only for HPV-positive cancers (where a higher T stage was associated with worse outcomes). There was some evidence that N stage was a more relevant prognostic factor for HPV-negative than -positive cancers. There was no evidence that the HPV modifies the effect of age, gender or grade on outcomes.Conclusions
This study suggests that the prognostic significance of the conventional staging system in tonsillar cancer is modified by HPV.
[Show abstract][Hide abstract] ABSTRACT: Acute lower respiratory tract infections (ALRI) commonly result in fatal outcomes in the young children of Papua New Guinea (PNG). However, comprehensive studies of the viral aetiology of ALRI have not been conducted in PNG for almost 30 years.
To determine the viruses associated with ALRI among children living in the PNG highlands using sensitive molecular detection techniques.
Pernasal swabs were collected routinely between 1 week and 18 months of age and also during episodes of ALRI, as part of a neonatal pneumococcal conjugate vaccine trial. A tandem multiplex real-time PCR assay was used to test for a comprehensive range of respiratory viruses in samples collected from 221 young children. Picornavirus typing was supported by DNA sequence analysis.
Recognized pathogenic respiratory viruses were detected in 198/273 (73%) samples collected from children with no evidence of ALRI and 69/80 (86%) samples collected during ALRI episodes. Human rhinoviruses (HRV) species A, B and C were detected in 152 (56%) samples from non-ALRI children and 50 (63%) samples collected during ALRI episodes. Partial structural region sequences for two new species C rhinoviruses were added to the GenBank database. ALRI was associated with detection of adenovirus species B (p<0.01) or C (p<0.05), influenza A (p<0.0001) or respiratory syncytial virus (p<0.0001). Multiple viruses were detected more often during ALRI episodes (49%) than when children displayed no symptoms of ALRI (18%) (p<0.0001).
The burden of infection with respiratory viruses remains significant in young children living in the PNG highlands.
Full-text · Article · May 2012 · Journal of clinical virology: the official publication of the Pan American Society for Clinical Virology
[Show abstract][Hide abstract] ABSTRACT: Both bacteria and viruses play a role in the development of acute otitis media, however, the importance of specific viruses is unclear. In this study molecular methods were used to determine the presence of nucleic acids of human rhinoviruses (HRV; types A, B, and C), respiratory syncytial viruses (RSV; types A and B), bocavirus (HBoV), adenovirus, enterovirus, coronaviruses (229E, HKU1, NL63, and OC43), influenza viruses (types A, B, and C), parainfluenza viruses (types 1, 2, 3, 4A, and 4B), human metapneumovirus, and polyomaviruses (KI and WU) in the nasopharynx of children between 6 and 36 months of age either with (n = 180) or without (n = 66) a history of recurrent acute otitis media and in 238 middle ear effusion samples collected from 143 children with recurrent acute otitis media. The co-detection of these viruses with Streptococcus pneumoniae, nontypeable Haemophilus influenzae, and Moraxella catarrhalis was analyzed. HRV (58.3% vs. 42.4%), HBoV (52.2% vs. 19.7%), polyomaviruses (36.1% vs. 15.2%), parainfluenza viruses (29.4% vs. 9.1%), adenovirus (25.0% vs. 6.1%), and RSV (27.8% vs. 9.1%) were detected significantly more often in the nasopharynx of children with a history of recurrent acute otitis media compared to healthy children. HRV was predominant in the middle ear and detected in middle ear effusion of 46% of children. Since respiratory viruses were detected frequently in the nasopharynx of both children with and without a history of recurrent acute otitis media, the etiological role of specific viruses in recurrent acute otitis media remains uncertain, however, anti-viral therapies may be beneficial in future treatment and prevention strategies for acute otitis media.
No preview · Article · Nov 2011 · Journal of Medical Virology
[Show abstract][Hide abstract] ABSTRACT: Genotypic characterization of 215 Aeromonas strains (143 clinical, 52 environmental, and 20 reference strains) showed that Aeromonas aquariorum (60 strains, 30.4%) was the most frequently isolated species in clinical and water samples and could be misidentified as
Aeromonas hydrophila by phenotypic methods.
Full-text · Article · Jun 2011 · Journal of clinical microbiology
[Show abstract][Hide abstract] ABSTRACT: Background: Human papillomavirus (HPV) infection is implicated as an aetiological factor in head and neck squamous carcinomas (HNSCC), especially in the tonsils of the oropharyngeal region. This study investigates the frequency of HPV infection, p16 and p53 tumour profile and mutations in epidermal growth factor receptor (EGFR), Kirsten RNA Associated Rat Sarcoma 2 Virus (KRAS) and B-Raf proto-oncogene serine/threonine protein kinase (BRAF) genes in tonsillar and non-tonsillar HNSCCs and correlates with clinical outcome and histopathological parameters in previously unstudied cohort of patients.
Methods: A retrospective clinical study was performed utilising the demographic data and pathological specimens from 60 out of 726 head and neck cancer patients. Smoking and alcohol history, tumour staging, treatment and outcomes were recorded. Histopathology and immunochemistry for p16 and p53 was performed and HPV DNA was detected with polymerase chain reaction. Genomic DNA from all cancers were analysed for somatic mutations of EGFR, BRAF and KRAS genes.
Results: 20 (33%) of 60 cases were tonsillar squamous carcinomas and 38 (66%) were non-tonsillar. 19 (95%) of the 20 tonsillar cancers and three (8%) of 38 non-tonsillar patients were patients who were HPV 16-positive. Nine (47%) of the 19 HPV 16-positive tonsillar cases were p16 positive. Gene mutations were rare. There was a statistically significant (P < 0.05) improved survival of patients with HPV positive tonsillar tumours, younger age and non-smokers.
Conclusion: Although limited in numbers, this study reinforces the role of HPV infection in HNSCC and its association with a more favourable clinical course in younger non-smokers worldwide. Gene mutation frequencies were low in all cancers tested and routine testing not recommended.
Full-text · Article · May 2011 · ANZ Journal of Surgery
[Show abstract][Hide abstract] ABSTRACT: Background / Purpose:
Human rhinoviruses (HRV) are the most common cause of respiratory infections worldwide. Recent advances in the molecular detection of respiratory viruses led to the identification of a new HRV group, HRV-C, which has been associated with more frequent and severe lower respiratory infections.As part of the Kalgoorlie Otitis Media Research Project (KOMRP), nasopharyngeal aspirates (NPAs) were to be collected routinely on seven occasions from 100 healthy Aboriginal and 180 healthy non-Aboriginal children before two years of age. HRV was the most frequently identified virus (19.6%) and was identified more often in specimens from Aboriginal than non-Aboriginal children.We now describe the prevalence of HRV groups and potential risk factors for HRV carriage in this population. This is the first study to describe the epidemiology of HRV groups among Aboriginal children.
HRV-A was more common than HRV-C among healthy children. HRV-C was associated with mild upper respiratory symptoms in both Aboriginal and non-Aboriginal children while HRV-A was not. Furthermore, HRV group carriage was associated with ethnicity, age, seasonality, bacterial carriage, exclusive breastfeeding, gestational smoking and maternal socio-economic factors.
[Show abstract][Hide abstract] ABSTRACT: There is increasing use of multiple molecular markers to predict prognosis in human cancer. Our aim was to examine the prognostic significance of cyclin D1 and retinoblastoma (pRb) expression in association with human papillomavirus (HPV) status in oropharyngeal squamous cell carcinoma. Clinical records and specimens of 226 patients with follow-up from 1 to 235 months postdiagnosis were retrieved. Tumor HPV status was determined by HPV E6-targeted multiplex real-time PCR/p16 semiquantitative immunohistochemistry and cyclin D1 and pRb expression by semiquantitative immunohistochemistry. Determinants of recurrence and mortality hazards were modeled using Cox regression with censoring at dates of last follow-up. The HPV-positivity rate was 37% (91% type 16). HPV was a predictor of recurrence, an event (recurrence or death) and death after adjustment for clinicopathological variables. There were inverse relationships between HPV status and cyclin D1 and pRb. On univariate analysis, cyclin D1 predicted locoregional recurrence, event and death and pRb predicted event and death. Within the HPV-positive group, after adjusting for clinicopathological factors, patients with cyclin D1-positive cancers had up to a eightfold increased risk of poor outcome relative to those with cyclin D1-negative tumors. However, within the HPV-negative group, there was only a very small adjusted increased risk. A combination of pRb and HPV did not provide additional prognostic information. Our data provide the first evidence that a combination of HPV and cyclin D1 provides more prognostic information in oropharyngeal cancer than HPV alone. If findings are confirmed, treatment based on HPV and cyclin D1 may improve outcomes.
Full-text · Article · Apr 2011 · International Journal of Cancer
[Show abstract][Hide abstract] ABSTRACT: AmpC β-lactamases (Bla(AmpC)) are an emerging group of antimicrobial resistance determinants. The lack of an agreed Bla(AmpC) detection method hinders investigation of their epidemiology and understanding of their clinical significance. This study compared the sensitivity and specificity of phenotypic methods of Bla(AmpC) detection in a collection of 246 Enterobacteriaceae with a diverse range of β-lactam resistance profiles. The Bla(AmpC) screening methods evaluated were based on cephamycin, ceftazidime and cefepime susceptibility. These were compared with Bla(AmpC) screening using conventional ESBL detection methods. The confirmatory methods evaluated were biologically based assays, inhibitor-based assays, an AmpC Etest and a rapid chromogenic assay. A multiplex nucleic acid amplification test and the three-dimensional enzyme extraction assay were used as reference methods. Bla(AmpC) activity was present in 74 isolates. The majority of the enzymes were plasmid-encoded and belonged to the CMY, DHA and EBC families. The screening methods had sensitivities between 47 and 99 % and specificities of 45-95 %. The performance of confirmatory tests varied widely, ranging in sensitivity from 19 % to 97 % and in specificity from 88 % to 100 %. Only the Tris-EDTA and MAST ID D68C disc tests had a sensitivity and a specificity above 90 %. Further investigation is needed to establish the most suitable enzyme substrates, inhibitor types, inhibitor concentrations and interpretative cut-offs in order to refine the inhibitor-based methods. A simple disc-based protocol using cefoxitin non-susceptibility as a screening tool, followed by the Tris-EDTA method for confirmation, detects Bla(AmpC) activity with 95 % sensitivity and 98 % specificity.
Full-text · Article · Mar 2011 · Journal of Medical Microbiology
[Show abstract][Hide abstract] ABSTRACT: This study examines the prognostic significance of human papillomavirus (HPV) in patients with locally advanced oropharyngeal squamous cell carcinoma (SCC) treated primarily with surgery or definitive radiotherapy.
One hundred and ninety-eight patients with Stage 3/4 SCC were followed up for recurrence in any form or death from any cause for between 1 and 235 months after diagnosis. HPV status was determined using HPV E6-targeted multiplex real-time PCR/p16 immunohistochemistry. Determinants of recurrence and mortality hazards were modelled using Cox's regression with censoring at follow-up dates.
Forty-two per cent of cancers were HPV-positive (87% type 16). HPV predicted loco-regional control, event-free survival and overall survival in multivariable analysis. Within the surgery with adjuvant radiotherapy (n=110), definitive radiotherapy-alone (n=24) and definitive radiotherapy with chemotherapy (n=47) groups, patients with HPV-positive cancers were one-third or less as likely to have loco-regional recurrence, an event or to die of any cause as those with HPV-negative cancers after adjusting for age, gender, tumour grade, AJCC stage and primary site. The 14 patients treated with surgery alone were considered too few for multivariable analysis.
HPV status predicts better outcome in oropharyngeal cancer treated with surgery plus adjuvant radiotherapy as well as with definitive radiation therapy±chemotherapy.
Full-text · Article · Oct 2010 · British Journal of Cancer
[Show abstract][Hide abstract] ABSTRACT: A real-time reverse transcription PCR (rRT-PCR) assay was designed and evaluated for the detection of the point mutation in the influenza A N1 neuraminidase gene that results in a tyrosine to histidine substitution at amino acid position 275 (H275Y) causing resistance to oseltamivir, an antiviral neuraminidase inhibitor. The rRT-PCR assays detected the presence or absence of the H275Y mutation in 387/388 (99.7%) of clinical samples containing the pandemic influenza A/H1N1 2009 virus. The H275Y mutation was not detected in any of the community patient samples (0/132) but was detected in four hospitalized patients who had been treated with oseltamivir for several days. The sensitive rRT-PCR assays may be performed directly on patient specimens, can detect resistant virus at low levels, and therefore may provide early warning of developing resistance within individual patients or the wider population.
No preview · Article · Oct 2010 · Journal of virological methods
[Show abstract][Hide abstract] ABSTRACT: This study examines the prognostic significance of epidermal growth factor receptor (EGFR) expression in relation to human papillomavirus (HPV) status in oropharyngeal squamous cell carcinoma (SCC).
Pathological diagnosis of 270 oropharyngeal SCCs was verified by the study pathologist; clinical details were extracted from institutional databases. Recurrence in any form or death from any cause was recorded for a median of 2.5 (range: 0-19.3) years after diagnosis. HPV status was determined by HPV E6-targeted multiplex real-time PCR/p16 immunohistochemistry; EGFR expression was evaluated by semiquantitative immunohistochemistry. Determinants of recurrence and mortality hazards were modelled using Cox regression with censoring at dates of last follow-up.
Thirty-seven percent of cancers were HPV-positive (91% type 16). HPV was a predictor of loco-regional recurrence, event-free and overall survival after adjustment for clinicopathological variables and EGFR. Patients with EGFR-positive cancers were 5-fold more likely to have loco-regional failure relative to those with EGFR-negative cancers. Patients with HPV-negative/EGFR-positive cancers had an adjusted 13-fold increased risk of having a loco-regional failure, an almost 4-fold increased risk of having an event and more than a 4-fold increased risk of dying of any cause relative to those with HPV-positive/EGFR-negative cancers. There was weak evidence that the effects of EGFR on outcome were limited to patients with HPV-negative cancers.
HPV and EGFR are independent prognostic markers in oropharyngeal SCC. Combining testing for HPV and EGFR appears to provide additional prognostic information.
No preview · Article · Jul 2010 · European journal of cancer (Oxford, England: 1990)