Prevalence of oral HPV in the adult sample population in Sydney

BACKGROUND

Oropharyngeal squamous cell carcinomas are increasing in incidence. Risk factors include sexual behaviour, high-risk oral HPV infection and poor oral hygiene. We aimed to provide initial information on the prevalence and assess the feasibility of testing in dental settings.

METHODS

Patients ≥18 years old attending dental clinics in Sydney, Australia, were recruited, oral hygiene assessed, and 10 mL saline oral rinses obtained. Rinses were tested for HBG and HPV by PCR. Participants completed demographic and behavioural questionnaires.

RESULTS

The mean age was 48 years, of whom 131 (43.6%) were male. HPV genotypes, one each of 16, 66, 51, 35 and 58 in five participants, and 18 and 52 in one participant, were detected in six samples (2.0%), all men. Oral sex was reported by 89 (67.9%) male participants. One participant (4.3%) of the 23 with poor OH had at least one HPV genotype detected.

DISCUSSION

With dental patients willing to provide rinse samples and disclose potentially sensitive information, we found the hrHPV prevalence of 2%. Given large proportions of the general population attending dental clinics regularly, dentists may be ideally placed to screen for oropharyngeal carcinoma and contribute to the currently limited knowledge of oral HPV prevalence in Australian adults. © 2022 Australian Dental Association.

New Detection of Locally Acquired Japanese Encephalitis Virus Using Clinical Metagenomics, New South Wales, Australia

In the context of an emerging Japanese encephalitis outbreak within Australia, we describe a novel locally acquired case in New South Wales. A man in his 70s had rapidly progressive, fatal meningoencephalitis, diagnosed as caused by Japanese encephalitis virus by RNA-based metagenomic next-generation sequencing performed on postmortem brain tissue.

Meningococcal and pneumococcal carriage in Hajj pilgrims: findings of a randomized controlled trial

BACKGROUND

Intense congestion during the Hajj pilgrimage amplifies the risk of meningococcal carriage and disease, and there have been many meningococcal outbreaks reported amongst pilgrims. Thus, a strict vaccination policy is enforced by the host country and either polysaccharide or conjugate quadrivalent meningococcal vaccines are mandatory. However, unlike conjugate vaccines, the polysaccharide vaccine is not thought to reduce pharyngeal carriage of meningococci.

METHODS

A single-blinded, randomized, controlled trial amongst pilgrims from Saudi Arabia and Australia during the Hajj seasons of 2016-2017 was conducted to compare MenACWY-Conjugate vaccine with MenACWY-Polysaccharide vaccine, to determine if the conjugate vaccine is more effective in reducing asymptomatic carriage of meningococci, and whether the effect may be long-standing. Oropharyngeal swabs were obtained pre-, immediately post- and 6-11 months following completion of Hajj and tested for the presence of meningococci.

RESULTS

Amongst 2000 individuals approached, only 1146 participants aged 18-91 (mean 37.6) years agreed to participate and were randomized to receive either the polysaccharide (n = 561) or the conjugate (n = 561) vaccine, 60.8% were male, and 93.5% were from Saudi Arabia. Amongst oropharyngeal swabs obtained before Hajj, only two (0.2%) tested positive for Neisseria meningitidis. Similarly, meningococci were identified in only one sample at each of the post-Hajj and late follow-up visits. None of the carriage isolates were amongst the serogroups covered by the vaccines. A post hoc analysis of the third swabs revealed that 22.4% of all participants (50/223) were positive for Streptococcus pneumoniae nucleic acid.

CONCLUSION

The low overall carriage rate of meningococci found amongst Hajj pilgrims in 2016 and 2017 demonstrates a successful vaccination policy, but neither supports nor refutes the superiority of meningococcal conjugate ACWY vaccine over the polysaccharide vaccine against carriage. Although an association could not be established in this study, molecular epidemiology would help to establish the role of Hajj in facilitating transmission of pneumococci and inform vaccination policy.

Prevalence of rectal Mycoplasma genitalium and macrolide resistance in men who have sex with men attending Sydney Sexual Health Centre

Background Sexually transmissible infections (STIs) have been increasing in men who have sex with men (MSM) in recent years; however, few studies have investigated the prevalence or antimicrobial resistance in rectal Mycoplasma genitalium in this group. This study aimed to determine the prevalence and predictors of rectal M. genitalium in MSM attending an urban sexual health service in Sydney, Australia, namely the Sydney Sexual Health Centre (SSHC), as well as estimate the rate of macrolide resistance.

METHODS

A prospective cross-sectional analysis was conducted of rectally asymptomatic MSM having a rectal swab collected as part of their routine care. Participants self-collected a rectal swab to be tested for M. genitalium and completed a 14-item questionnaire that provided information on behavioural risk factors. The prevalence of rectal M. genitalium was determined and multivariate analysis was performed to assess the associations for this infection. Positive specimens then underwent testing for macrolide-resistant mutations (MRMs) using the ResistancePlus MG assay (SpeeDx, Eveleigh, NSW, Australia).

RESULTS

In all, 742 patients were consecutively enrolled in the study. The median age was 31 years (interquartile range 27-39 years), with 43.0% born in Australia. Overall, 19.0% of men were bisexual, 22.9% were taking pre-exposure prophylaxis (PrEP) and 4.3% were HIV positive. The prevalence of rectal M. genitalium was 7.0% (95% confidence interval (CI) 5.3-9.1) overall and 11.8% in those taking PrEP. On multivariate analysis, PrEP use was significantly associated with having rectal M. genitalium (odds ratio 2.01; 95% CI 1.09-3.73; P = 0.01). MRMs were detected in 75.0% (36/48; 95% CI 60.4-86.4%) of infections.

CONCLUSION

Rates of rectal M. genitalium infection were high among asymptomatic MSM attending SSHC and MRMs were detected in 75% of infections. PrEP use was found to be significantly associated with rectal M. genitalium infection. These data contribute to the evidence base for screening guidelines in MSM.

BK polyomavirus: a review of the virology, pathogenesis, clinical and laboratory features, and treatment

BK polyomavirus (BKPyV) is a non-enveloped, circular dsDNA virus with a genome of approximately 5100 base pairs. It can be divided into four major genotypes, but the effects of different genotypes on clinical disease are uncertain. Primary BKPyV infection is generally acquired asymptomatically in childhood. It establishes low-level persistence in many tissues, particularly the genitourinary tract. Reactivation can lead to severe disease including BKPyV-associated nephropathy confirmed by renal biopsy, hemorrhagic cystitis and meningoencephalitis. Nucleic acid amplification testing of blood and urine is the main diagnostic and prognostic test for BKPyV infection. The treatment of BKPyV infection has concentrated on reduction in immunosuppressive therapy. Recent studies suggest that antiviral drugs have demonstrated only modest benefit, but adoptive T-cell therapies offer potential advances.

Surveillance of Australian Hajj pilgrims for carriage of potentially pathogenic bacteria: Data from two pilot studies

AIM

To estimate the pharyngeal carriage rate of Neisseria meningitidis (N. meningitidis), Streptococcus pneumoniae (S. pneumoniae) and Staphylococcus aureus (S. aureus) among Australian Hajj pilgrims.

METHODS

In 2014, surveillance was conducted in two phases among Australian Hajj pilgrims: The first phase during Hajj in Mina, and the second phase soon after returning home to Australia. Nasopharyngeal or oropharyngeal swabs were taken from participants then tested, firstly by nucleic acid testing, and also by standard culture.

RESULTS

Of 183 participants recruited in the first phase, 26 (14.2%) tested positive for S. pneumoniae; 4 had received pneumococcal conjugate vaccine (PCV13). Only one tested positive for N. meningitidis (W). Of 93 2^nd phase samples cultured, 17 (18.3%) grew S. aureus, all methicillin sensitive, 2 (2.2%) grew N. meningitidis (on subculture; one serotype B, one negative), and 1 (1%), from an unvaccinated pilgrim, grew S. pneumoniae.

CONCLUSION

Relatively high carriage of S. pneumoniae and little meningococcal carriage was found. This indicates the importance of a larger study for improved infection surveillance and possible vaccine evaluation.

Treatment and outcomes of polymerase chain reaction-confirmed early syphilis

Background Syphilis is resurgent among gay and bisexual men (GBM) despite effective treatment and widely available diagnostic serology. The polymerase chain reaction assay for Treponema pallidum (TP-PCR) is available, but little is known about the clinical features and outcomes for patients testing positive by TP-PCR.

METHODS

Clinical data were collected from four medical practices for patients recording a positive TP-PCR result between 2004 and 2011. Demographic, serological, treatment and reinfection details were obtained. Results were stratified by HIV status and whether treatment conformed to international guidelines.

RESULTS

220 patients were positive for TP-PCR, of whom 92% were GBM. Seventeen (8.1%) were positive by TP-PCR before seroconversion. Almost one-third (32.1%) received treatment beyond that recommended in guidelines, and this was associated with HIV status (40.3% HIV positive vs 22.4% HIV negative, P<0.01). All but one patient with adequate follow up achieved serological cure. There was no significant difference in time to serological cure between the groups receiving standard therapy or enhanced therapy (95 vs 108 days; P=0.67) or between HIV positive and negative patients (93 vs 104 days, P=0.06). Nineteen patients were reinfected during follow up.

CONCLUSION

TP-PCR aids early diagnosis of syphilis and may be reactive before conventional serological tests. Treatment outcomes for TP-PCR-positive early infection were excellent, but a significant proportion of patients received non-standard therapy. Expanded use of syphilis PCR testing in at-risk populations is recommended since early identification and treatment is likely to be important in controlling the current epidemic in GBM.

Test performance characteristics of quantitative nucleic acid testing for polyomaviruses in kidney and kidney-pancreas transplant recipients

Screening for polyoma BK virus (BK) using nucleic testing (NAT) is recommended for kidney and kidney-pancreas transplant recipients, but the performance characteristics of quantitative BK NAT at different thresholds of plasma BK viral loads are unclear. We aim to evaluate the diagnostic accuracy of quantitative BK NAT as an add-on test to qualitative polyoma NAT for the diagnosis of BK virus-associated nephropathy (BKVAN) in kidney and kidney transplant recipients. We calculated the test sensitivity, specificity, and predictive values at the different thresholds of plasma BK viral load for BKVAN. At the recommended threshold of >1 × 10(3) serum BK copies/mL serum for test positivity, the sensitivity for BKVAN was 92.9% (95% confidence intervals [CI]: 66.1-99.8) and specificity 79.1% (95%: CI 67.4-88.1), with corresponding positive and negative predictive values of 42.0% (95% CI: 24.8-57.7%) and 98.6% (95% CI: 98.3-99.9%), respectively. The overall area under curve for the quantitative BK NAT was 0.92 (95% CI: 0.85-0.97). Quantitative BK NAT displays properties of high sensitivity and specificity that are fit for purpose as an add-on test to qualitative polyomavirus NAT for kidney and kidney-pancreas transplant recipients at risk of BKVAN.

Diagnosis of Barmah Forest virus infection by a nested real-time SYBR green RT-PCR assay

Barmah Forest virus (BFV) is a mosquito borne (+) ssRNA alphavirus found only in Australia. It causes rash, myalgia and arthralgia in humans and is usually diagnosed serologically. We developed a real-time PCR assay to detect BFV in an effort to improve diagnosis early in the course of infection. The limit of detection was 16 genome equivalents with a specificity of 100%. Fifty five serum samples from BFV-infected patients were tested by the PCR. 52 of 53 antibody-positive samples were PCR negative. Two culture-positive (neutralizing antibody negative) samples were positive on first round PCR, while one sample (IgM and neutralizing antibody strongly positive, IgG negative) was positive on second round PCR, suggesting that viral RNA is detectable and transiently present in early infection. PCR can provide results faster than culture, is capable of high throughput and by sequencing the PCR product strain variants can be characterized.

Real-time polymerase chain reaction for detection of Strongyloides stercoralis in stool

The use of real-time polymerase chain reaction (PCR) for detection of Strongyloides stercoralis in stool has recently been described. We compared five DNA extraction methods by using normal human stool spiked with Strongyloides ratti and tested by using a real-time PCR. The PowerSoil kit was found to be the best technique in terms of sensitivity and ease of use. The PCR detected DNA extracted from one spiked S. ratti larva diluted 10⁻². The PowerSoil kit was then used to extract DNA from 160 human survey samples. All culture positive specimens with a high and moderate larval load were identified by real-time PCR, but only 15% of specimens with low larval load were positive. Specificity was greater than 99%. The combination of the PowerSoil kit and real-time PCR reliably detected high to moderate larval numbers of S. stercoralis in stools but was less sensitive when the larval load was low.

Diagnostic accuracy of blood qualitative nucleic acid testing for polyomavirus-associated nephropathy in kidney recipients

AIM

Polyomavirus-associated nephropathy (PVAN) is an important cause of graft loss following kidney transplantation and may only be diagnosed with kidney transplant biopsy. Early detection may improve outcomes by enabling early intervention. Serum polyomavirus polymerase chain reaction (PVPCR) has been used to identify patients at risk of PVAN, but prior studies have not assessed all patients with negative PVPCR with transplant biopsy, potentially overestimating test performance.

METHODS

We assessed the diagnostic accuracy of qualitative PVPCR for detection of PVAN in a population undergoing protocol biopsies. We included all patients receiving kidney or kidney-pancreas transplants and followed at Westmead Hospital, Sydney, Australia, between May 2002 and March 2007, excluding those with graft loss prior to 1 month post transplant or without PVPCR testing in the first 12 months. We compared PVPCR to contemporaneous transplant biopsies assessed with light microscopy and immunohistochemistry.

RESULTS

Of the 257 included patients, 246 (96%) underwent biopsy within 30 days of PVPCR. Eight of 36 patients with positive PVPCR had PVAN and one of 210 patients with negative PVPCR had PVAN. The point prevalence of PVAN was therefore 3.7%, with PVPCR sensitivity 89% (95% CI 57% to 99%) and specificity 88%(95% CI 83% to 92%). The negative predictive value is 99.5% (95% CI 97.3% to 100.0%).

CONCLUSION

Qualitative PVPCR on serum is a reliable triage test for excluding the presence of PVAN. Screening for PVAN need not include biopsy in patients with negative PVPCR.

48. TREPONEMA PALLIDUM PCR: APPLICATION AND DIAGNOSTIC VALUE IN 2 CASES OF PRIMARY SYPHILIS

Epidemics of infectious syphilis have been ongoing in large cities in industrialised countries since the turn of the millennium. These epidemics have almost exclusively involved homosexually active men, with a disproportionately high rate among HIV infected individuals. Genital ulcerative disease, including syphilis, has a strong correlation with onward transmission of viral and bacterial sexually transmitted infections. Due to the lack of a culture system for Treponema pallidum, the causative organism of syphilis, other direct test methods are needed in the evaluation of skin lesions possibly due to syphilis. Dark ground microscopy was once commonly used by sexual health clinicians, but skills in this method have waned in recent years. Polymerase chain reaction (PCR) assays are being increasingly used in the diagnosis of infectious syphilis. We describe the use of a nucleic acid amplification assay for Treponema pallidum, which targets the 47 kilodalton gene, in the diagnosis of primary syphilis in 2 patients with genital lesions. The first patient was an HIV infected man who presented with an ulcer typical of a chancre but who denied any recent risk behaviour. The second was an HIV negative homosexually active man with an atypical genital lesion. In both cases, Treponema pallidum PCR was positive and serology was consistent with the diagnosis of primary syphilis. Conclusion/Recommendation: Appropriately validated Treponema pallidum nucleic acid amplification assays could replace dark ground microscopy and direct fluorescent antigen tests as a direct test for early infectious syphilis. It could be particularly useful in individuals who have treponemal skin lesions of atypical appearance.

Detection and discrimination of herpes simplex viruses, Haemophilus ducreyi, Treponema pallidum, and Calymmatobacterium (Klebsiella) granulomatis from genital ulcers

BACKGROUND

Genital ulcer disease (GUD) is commonly caused by pathogens for which suitable therapies exist, but clinical and laboratory diagnoses may be problematic. This collaborative project was undertaken to address the need for a rapid, economical, and sensitive approach to the detection and diagnosis of GUD using noninvasive techniques to sample genital ulcers.

METHODS

The genital ulcer disease multiplex polymerase chain reaction (GUMP) was developed as an inhouse nucleic acid amplification technique targeting serious causes of GUD, namely, herpes simplex viruses (HSVs), H. ducreyi, Treponema pallidum, and Klebsiella species. In addition, the GUMP assay included an endogenous internal control. Amplification products from GUMP were detected by enzyme linked amplicon hybridization assay (ELAHA).

RESULTS

GUMP-ELAHA was sensitive and specific in detecting a target microbe in 34.3% of specimens, including 1 detection of HSV-1, three detections of HSV-2, and 18 detections of T. pallidum. No H. ducreyi has been detected in Australia since 1998, and none was detected here. No Calymmatobacterium (Klebsiella) granulomatis was detected in the study, but there were 3 detections during ongoing diagnostic use of GUMP-ELAHA in 2004 and 2005. The presence of C. granulomatis was confirmed by restriction enzyme digestion and nucleotide sequencing of the 16S rRNA gene for phylogenetic analysis.

CONCLUSIONS

GUMP-ELAHA permitted comprehensive detection of common and rare causes of GUD and incorporated noninvasive sampling techniques. Data obtained by using GUMP-ELAHA will aid specific treatment of GUD and better define the prevalence of each microbe among at-risk populations with a view to the eradication of chancroid and donovanosis in Australia.