Comparing Polymerase Chain Reaction Testing of Nasopharyngeal Swab and Lower Respiratory Tract Specimens for the Diagnosis of Pneumocystis jirovecii Pneumonia

Using nasopharyngeal (NP) swab samples instead of lower respiratory tract specimens for polymerase chain reaction (PCR) to diagnose Pneumocystis jirovecii pneumonia (PJP) may be better tolerated and improve diagnostic accessibility. In this 2-year Australian retrospective cohort study of patients with clinically suspected PJP, P jirovecii PCR on NP swab samples had perfect specificity but low sensitivity (0.66).

The improving state of Q fever surveillance. A review of Queensland notifications, 2003-2017

Q fever is a notifiable zoonotic disease in Australia, caused by infection with Coxiella burnetii. This study has reviewed 2,838 Q fever notifications reported in Queensland between 2003 and 2017 presenting descriptive analyses, with counts, rates, and proportions. For this study period, Queensland accounted for 43% of the Australian national Q fever notifications. Enhanced surveillance follow-up of Q fever cases through Queensland Public Health Units was implemented in 2012, which improved the data collected for occupational risk exposures and animal contacts. For 2013-2017, forty-nine percent (377/774) of cases with an identifiable occupational group would be considered high risk for Q fever. The most common identifiable occupational group was agricultural/farming (31%). For the same period, at-risk environmental exposures were identified in 82% (961/1,170) of notifications; at-risk animal-related exposures were identified in 52% (612/1,170) of notifications; abattoir exposure was identified in 7% of notifications. This study has shown that the improved follow-up of Q fever cases since 2012 has been effective in the identification of possible exposure pathways for Q fever transmission. This improved surveillance has highlighted the need for further education and heightened awareness of Q fever risk for all people living in Queensland, not just those in previously-considered high risk occupations.

Influenza vaccine efficacy in young children attending childcare: A randomised controlled trial

AIM

Influenza causes a substantial burden in young children. Vaccine efficacy (VE) data are limited in this age group. We examined trivalent influenza vaccine (TIV) efficacy and safety in young children attending childcare.

METHODS

A double-blind, randomised controlled trial in children aged 6 to <48 months was conducted with recruitment from Sydney childcare centres in 2011. Children were randomised to receive two doses of TIV or control hepatitis A vaccine. Efficacy was evaluated against polymerase chain reaction-confirmed influenza using parent-collected nose/throat swabs during influenza-like-illness. Safety outcomes were assessed during 6 months of follow-up.

RESULTS

Fifty-seven children were allocated to influenza vaccine and 67 to control; all completed the study. The influenza attack rate was 1.8 vs 13.4% in the TIV and control groups, respectively; VE 87% (95%CI: 0-98%). For children aged 24 to <48 months, 0 vs 8 (18.6%) influenza infections occurred in the TIV and control groups respectively, giving a VE of 100% (16-100%). Efficacy was not shown in children 6 to <24 months, probably due to insufficient power. Injection site and systemic adverse events were mostly mild to moderate with no significant differences, apart from more mild diarrhoea following dose 2 in TIV recipients (11.8 vs 0%).

CONCLUSIONS

Influenza vaccine appeared efficacious in the subgroup of children aged 24 to <48 months, although caution is required due to the small number of participants. There were no serious adverse events and most parents would vaccinate again. Influenza vaccination in a childcare setting could be valuable and a larger confirmatory study would be helpful.

Temporal Changes in BEXSERO® Antigen Sequence Type Associated with Genetic Lineages of Neisseria meningitidis over a 15-Year Period in Western Australia

Neisseria meningitidis is the causative agent of invasive meningococcal disease (IMD). The BEXSERO^® vaccine which is used to prevent serogroup B disease is composed of four sub-capsular protein antigens supplemented with an outer membrane vesicle. Since the sub-capsular protein antigens are variably expressed and antigenically variable amongst meningococcal isolates, vaccine coverage can be estimated by the meningococcal antigen typing system (MATS) which measures the propensity of the strain to be killed by vaccinated sera. Whole genome sequencing (WGS) which identifies the alleles of the antigens that may be recognised by the antibody response could represent, in future, an alternative estimate of coverage. In this study, WGS of 278 meningococcal isolates responsible for 62% of IMD in Western Australia from 2000–2014 were analysed for association of genetic lineage (sequence type [ST], clonal complex [cc]) with BEXSERO^® antigen sequence type (BAST) and MATS to predict the annual vaccine coverage. A hyper-endemic period of IMD between 2000–05 was caused by cc41/44 with the major sequence type of ST-146 which was not predicted by MATS or BAST to be covered by the vaccine. An increase in serogroup diversity was observed between 2010–14 with the emergence of cc11 serogroup W in the adolescent population and cc23 serogroup Y in the elderly. BASTs were statistically associated with clonal complex although individual antigens underwent antigenic drift from the major type. BAST and MATS predicted an annual range of 44–91% vaccine coverage. Periods of low vaccine coverage in years post-2005 were not a result of the resurgence of cc41/44:ST-146 but were characterised by increased diversity of clonal complexes expressing BASTs which were not predicted by MATS to be covered by the vaccine. The driving force behind the diversity of the clonal complex and BAST during these periods of low vaccine coverage is unknown, but could be due to immune selection and inter-strain competition with carriage of non-disease causing meningococci.

Estimating the prevalence of mixed-type gonococcal infections in Queensland, Australia

Background Mixed gonococcal infections within the one anatomical site have been recognised but questions remain over how often they occur. In this study, the aim was to estimate the prevalence of mixed gonococcal infections using novel real-time polymerase chain reaction (PCR) methods that were developed and validated, targeting the gonococcal porB gene.

METHODS

Neisseria gonorrhoeae strains were categorised into three different porB groups, based on sequence data derived from N. gonorrhoeae multi-antigen sequence typing (NG-MAST) analyses of local isolates. Specific PCR methods for each group were then developed and these PCR methods were used to test clinical samples (n=350) that were positive for gonorrhoea as determined by nucleic acid amplification test (NAAT) diagnostic screening.

RESULTS

Initial validation using isolates showed the group PCR methods proved 100% sensitive and 100% specific for their respective porB groups. When applied to the clinical specimens, 298/350 (85%) provided positive results by the group PCR methods. Of these, four specimens showed evidence of mixed infections, supported by subsequent DNA sequencing of the PCR products.

CONCLUSIONS

The data provide further evidence of mixed gonococcal infections at the same anatomical site, but show that such infections may be relatively infrequent (1.3%; 95% confidence interval 0.01-2.6%) in a general screening population.

A national quality assurance survey of Neisseria gonorrhoeae testing

The aims of this study were to (1) conduct a national survey of Neisseria gonorrhoeae identification by National Neisseria Network (NNN) reference laboratories contributing data to the Australian Gonococcal Surveillance Programme and (2) determine the prevalence in Australia of strains of N. gonorrhoeae lacking gene sequences commonly targeted by in-house PCR assays for confirmation of gonococcal nucleic acid amplification tests. Gonococcal clinical isolates referred to NNN laboratories for the first half of 2012 were screened using in-house real-time PCR assays targeting multicopy opa, porA pseudogene and cppB genes. There were 2455 clinical gonococcal isolates received in the study period; 98.6 % (2420/2455) of isolates harboured all three gene targets, 0.12 % (3/2455) were porA-negative, 0.04 % (1/2455) opa-negative and 1.14 % (28/2455) cppB-negative by PCR. Notably, no isolates were simultaneously negative for two targets. However, three isolates failed to be amplified by all three PCR methods, one isolate of which was shown to be a commensal Neisseria strain by 16S rRNA sequencing. Using PCR as the reference standard the results showed that (1) identification of N. gonorrhoeae isolates by NNN laboratories was highly specific (99.96 %) and (2) strains of N. gonorrhoeae lacking gene sequences commonly targeted by in-house PCR assays are present but not widespread throughout Australia at this point in time.

Experimentally induced blood-stage Plasmodium vivax infection in healthy volunteers

BACKGROUND

Major impediments to development of vaccines and drugs for Plasmodium vivax malaria are the inability to culture this species and the extreme difficulty in undertaking clinical research by experimental infection.

METHODS

A parasite bank was collected from a 49-year-old woman with P. vivax infection, characterized, and used in an experimental infection study.

RESULTS

The donor made a full recovery from malaria after collection of a parasite bank, which tested negative for agents screened for in blood donations. DNA sequence analysis of the isolate indicated that it was clonal. Two subjects inoculated with the isolate became polymerase chain reaction positive on days 8 and 9, with onset of symptoms and positive blood smears on day 14, when they were treated with artemether-lumefantrine, with rapid clinical and parasitologic response. Transcripts of the parasite gene pvs25 that is expressed in gametocytes, the life cycle stage infectious to mosquitoes, were first detected on days 11 and 12.

CONCLUSIONS

This experimental system results in in vivo parasite growth, probably infectious to mosquitoes. It offers the opportunity to undertake studies previously impossible in P. vivax that will facilitate a better understanding of the pathology of vivax malaria and development of antimalarial drugs and vaccines. Trial Registration. ANZCTR: 12612001096842.

Household transmission of respiratory viruses - assessment of viral, individual and household characteristics in a population study of healthy Australian adults

Background

Household transmission of influenza-like illness (ILI) may vary with viral and demographic characteristics. We examined the effect of these factors in a population-based sample of adults with ILI.

Methods

We conducted a prospective cohort study in community-dwelling Australian adults nested within an influenza vaccine effectiveness trial. On presentation with ILI, participants were swabbed for a range of respiratory viruses and asked to return a questionnaire collecting details of household members with or without similar symptoms. We used logistic and Poisson regression to assess the key characteristics of household transmission.

Results

258 participants from multi-occupancy households experienced 279 ILI episodes and returned a questionnaire. Of these, 183 were the primary case in the household allowing assessment of factors associated with transmission. Transmission was significantly associated in univariate analyses with female sex (27% vs. 13%, risk ratio (RR) = 2.13 (1.08, 4.21)) and the presence of a child in the house (33% vs. 17%, RR = 1.90 (1.11, 3.26)). The secondary household attack proportion (SHAP) was 0.14, higher if influenza was isolated (RR = 2.1 (1.0, 4.5)). Vaccinated participants who nonetheless became infected with influenza had a higher SHAP (Incidence RR = 5.24 (2.17, 12.6)).

Conclusions

The increased SHAP in households of vaccinated participants who nonetheless had confirmed influenza infection supports the hypothesis that in years of vaccine mismatch, not only is influenza vaccine less protective for the vaccine recipient, but that the population’s immunity is also lower.

Virus detection and its association with symptoms during influenza-like illness in a sample of healthy adults enrolled in a randomised controlled vaccine trial

BACKGROUND

Viral respiratory infections are associated with significant morbidity and mortality. Many new aetiological agents have been described recently.

OBJECTIVES

We looked for respiratory viruses in a population-based sample of healthy adults with influenza-like illness (ILI). We investigated host and spatio-temporal associations with virus isolation and host, spatio-temporal and virus associations with self-reported symptoms.

PATIENTS/METHODS

We recruited 586 participants experiencing 651 illness episodes from a population of healthy adults enrolled in an influenza vaccine effectiveness trial. At ILI assessment visits, a respiratory swab was collected and tested for viruses using a combination of polymerase chain reaction (PCR) assays. Participants also completed a questionnaire detailing their clinical course in 336 episodes.

RESULTS

Of 643 samples analysed, a virus was identified in 44%. Half were picornaviruses, with influenza and coronaviruses the next most common. Individuals with influenza were significantly less likely to have been immunised than the reference (virus negative) population (OR = 0·52 (0·31, 0·87) P = 0·01). The mean symptom score (95% CI) reported by individuals with influenza was significantly higher than in all other episodes [Influenza: 10·2 (9·4, 10·9); Other: 7·4 (7·2, 7·7); Difference (95% CI): 2·5 (1·5, 3·5); P < 0·001]. In an analysis restricted to influenza-positive cases, the symptom score was not attenuated by vaccination.

CONCLUSIONS

Our findings indicate that a greater number of symptoms are displayed by individuals presenting with influenza confirmed ILI compared with other agents that cause ILI. While influenza vaccination reduced the probability of influenza virus detection, symptom score for influenza-positive ILI was not attenuated.

PrimRglo: a multiplexable quantitative real-time polymerase chain reaction system for nucleic acid detection

We report the development of a new real-time polymerase chain reaction (PCR) detection system that uses oligonucleotide "tagged" PCR primers, a fluorophore-labeled "universal" detection oligonucleotides, and a complementary quenching oligonucleotide. The fluorescence signal decreases as PCR product accumulates due to the increase in detection/quencher hybrid formation as the tagged primer is consumed. We use plasmids containing the influenza A matrix gene and the porA and ctrA genes of Neisseria meningitidis as targets for developing the system. Cycle threshold (Ct) values were generated, and the sensitivity of the new system (dubbed "PrimRglo") compared favorably with the commonly used SYBR green and Taqman detection systems and, unlike the latter system, does not require the design of a new dual-labeled detection oligonucleotide for each new target sequence.

Viral-bacterial co-infection in Australian Indigenous children with acute otitis media

Background

Acute otitis media with perforation (AOMwiP) affects 40% of remote Indigenous children during the first 18 months of life. Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis are the primary bacterial pathogens of otitis media and their loads predict clinical ear state. Our hypothesis is that antecedent respiratory viral infection increases bacterial density and progression to perforation.

Methods

A total of 366 nasopharyngeal swabs from 114 Indigenous children were retrospectively examined. A panel of 17 respiratory viruses was screened by PCR, and densities of S. pneumoniae, H. influenzae and M. catarrhalis were estimated by quantitative real time PCR. Data are reported by clinical ear state.

Results

M. catarrhalis (96%), H. influenzae (91%), S. pneumoniae (89%) and respiratory viruses (59%) were common; including rhinovirus (HRV) (38%), polyomavirus (HPyV) (14%), adenovirus (HAdV) (13%), bocavirus (HBoV) (8%) and coronavirus (HCoV) (4%). Geometric mean bacterial loads were significantly higher in children with acute otitis media (AOM) compared to children without evidence of otitis media. Children infected with HAdV were 3 times more likely (p < 0.001) to have AOM with or without perforation.

Conclusion

This study confirms a positive association between nasopharyngeal bacterial load and clinical ear state, exacerbated by respiratory viruses, in Indigenous children. HAdV was independently associated with acute ear states.

Two cases of failed ceftriaxone treatment in pharyngeal gonorrhoea verified by molecular microbiological methods

Diagnostic, genotypic and antibiotic-resistance determinants of Neisseria gonorrhoeae were analysed by molecular methods to verify the failure of ceftriaxone treatment in two cases of pharyngeal gonorrhoea. Monoplex assays were needed to define competitive inhibition of a positive Chlamydia PCR in a duplex assay. Different penA changes were detected in the N. gonorrhoeae isolated from the two cases. These were associated with raised ceftriaxone MICs of 0.03 and 0.016 mg l−1, which may have contributed to the treatment failures in these cases.

Respiratory infections in the newborn

It is well recognised that acute respiratory tract infection (ARTI) occurs commonly in children younger than 5 years of age, with pneumonia being the most serious complication. The greatest risk of death from pneumonia in childhood is in the neonatal period; it is estimated that pneumonia contributes to between 0.75-1.2 million neonatal deaths annually, accounting for approximately 10% of global child mortality. Of all neonatal deaths due to pneumonia, 96% occur in the developing world.

Applications of molecular testing in clinical laboratories for the diagnosis and control of gonorrhea

The potential for enhanced diagnosis and control of gonococcal infection through the application of advances in molecular medicine is now being realized. However, the introduction of diagnostic nucleic acid amplification assays (NAATs) revealed some significant limitations of these applications. Resolution of some, but not all, of these problems has led to recommendations for refined testing algorithms and a better recognition and acceptance of the limitations of NAATs. Resource restriction has limited the use of diagnostic NAATs, especially in less-developed countries where disease rates are highest. However, NAATs have also proved useful in public health approaches to gonorrhea control in all settings. Additional applications including molecular typing of gonococci to identify and interrupt gonococcal transmission chains and definition of antimicrobial resistance patterns in the gonococcus have been proposed. These approaches, especially those for antimicrobial resistance determination, have been less successful for a number of reasons, including their cost and other unresolved issues.

Perspective on the host response to human metapneumovirus infection: what can we learn from respiratory syncytial virus infections?

Human metapneumovirus (HMPV) is a recently discovered pathogen first identified in respiratory specimens from young children suffering from clinical respiratory syndromes ranging from mild to severe lower respiratory tract illness. HMPV has worldwide prevalence, and is a leading cause of respiratory tract infection in the first years of life, with a spectrum of disease similar to respiratory syncytial virus (RSV). The disease burden associated with HMPV infection has not been fully elucidated; however, studies indicate that HMPV may cause upper or lower respiratory tract illness in patients between ages 2 months and 87 years, may co-circulate with RSV, and HMPV infection may be associated with asthma exacerbation. The mechanisms and effector pathways contributing to immunity or disease pathogenesis following infection are not fully understood; however, given the clinical significance of HMPV, there is a need for a fundamental understanding of the immune and pathophysiological processes that occur following infection to provide the foundation necessary for the development of effective vaccine or therapeutic intervention strategies. This review provides a current perspective on the processes associated with HMPV infection, immunity, and disease pathogenesis.

Validation of assembled nucleic acid-based tests in diagnostic microbiology laboratories

Medical microbiology and virology laboratories use nucleic acid tests (NAT) to detect genomic material of infectious organisms in clinical samples. Laboratories choose to perform assembled (or in-house) NAT if commercial assays are not available or if assembled NAT are more economical or accurate. One reason commercial assays are more expensive is because extensive validation is necessary before the kit is marketed, as manufacturers must accept liability for the performance of their assays, assuming their instructions are followed. On the other hand, it is a particular laboratory's responsibility to validate an assembled NAT prior to using it for testing and reporting results on human samples. There are few published guidelines for the validation of assembled NAT. One procedure that laboratories can use to establish a validation process for an assay is detailed in this document. Before validating a method, laboratories must optimise it and then document the protocol. All instruments must be calibrated and maintained throughout the testing process. The validation process involves a series of steps including: (i) testing of dilution series of positive samples to determine the limits of detection of the assay and their linearity over concentrations to be measured in quantitative NAT; (ii) establishing the day-to-day variation of the assay's performance; (iii) evaluating the sensitivity and specificity of the assay as far as practicable, along with the extent of cross-reactivity with other genomic material; and (iv) assuring the quality of assembled assays using quality control procedures that monitor the performance of reagent batches before introducing new lots of reagent for testing.

Comparison of seroprevalences of human herpesvirus-6 and -7 in healthy blood donors from nine countries

BACKGROUND AND OBJECTIVES

The purpose of the study was to register antibody prevalences of HHV-7 in various locations of the world in comparison to the closely related HHV-6.

MATERIALS AND METHODS

Sera of healthy blood donors from nine countries in five continents were titered by indirect immunofluorescent assays using HHV-6 infected HSB2 and HHV-7 infected SupT1 cells.

RESULTS

Antibody prevalence for HHV-7 is high (75-98%) in practically all countries except for Northern Japan (44%), with no simple correlation to elevated HHV-6 antibody titers. There were regions of low, intermediate and high mean antibody titers against HHV-7 such as 78.5-91.3 for Belgium, Israel, Japan, USA and Australia, 175.4-182.6 for Mexico and Cologne/Germany, and 389.2 for South Africa for which geographic characteristics may be responsible.

CONCLUSION

HHV-7, similar to HHV-6, is a widespread human herpesvirus with elevated antibody titers in the healthy human population essentially everywhere. The data warrant further studies to evaluate its possible pathologic potential, preferentially in persons with defective immune responses.

Human herpesvirus type 8 in salivary gland tumors

BACKGROUND

The new human herpesvirus type 8 (HHV-8) has been detected in all types of Kaposi's sarcomas, as well as in body-cavity lymphomas and Castleman's disease, furthermore molecular biologic studies have identified a number of potential viral oncogenes. There is evidence for sexual transmission of HHV-8 in HIV-seropositive patients, but the route of infection among the HIV-seronegative population is uncertain. Findings of HHV-8 DNA in saliva in some cases are suggestive of nonsexual transmission associated with latent infection of the salivary gland (as it is known for EBV, CMV, HHV-6 and HHV-7).

OBJECTIVE

As little is known about the etiological factors of salivary gland tumors and to give more insights into HHV-8 cell tropism normal salivary gland tissue (n=12) and different salivary glands neoplasm (n=58) were tested for HHV-8 sequences and antigens in HIV-seronegative patients.

STUDY DESIGN

Biopsies of both normal salivary gland and tumors were investigated for HHV-8 sequences. A nested-PCR method was used for amplification of HHV-8 DNA fragments and the nature of the amplification products was confirmed by Southern blot hybridization. In addition, we used an in situ hybridization technique and immunohistochemical staining for detection of HHV-8 infected cells. The sera of the respective patients were tested for anti-HHV-8 antibodies using commercial IFA and an ELISA-assay.

RESULTS

HHV-8 DNA sequences could be detected in one bilateral MALT-lymphoma of the parotid gland of a HHV-8 seropositive female patient suffering from Sjögren's syndrome (SS). The remaining parotid samples did neither show HHV-8 sequences nor HHV-8 antigens. Using above assays only one additional patient was seropositive for HHV-8.

CONCLUSION

Our data suggest that HHV-8 does not usually infect the salivary gland in HIV-seronegative patients and does not seem to play a pathogenic role in vascular and epithelial salivary gland neoplasm. Pathogenic role of HHV-8 in Sjögren's syndrome associated MALT-lymphoma remains unclear and should be subject of further studies.

Ultrastructural study of human herpesvirus-7 replication in tissue culture

Human herpesvirus 7 (HHV-7) was grown in a CD4+ lymphoblastic cell line (SupT1) and in cord blood mononuclear cells (CBMC). Virus infection was demonstrated by immunohistology with positive control sera, with monoclonal antibodies and by in situ hybridization for viral DNA. Cytopathic effects following HHV-7 infection generally resemble those after HHV-6 infection but are less pronounced. The ultrastructural appearance of HHV-7 and the replicative stages were similar to those described by Kramarsky and Sander for HHV-6. There were some minor discrepancies, including quite an extensive and space-filling tegument, a slightly different structure of the nucleoid, the frequent finding of nucleocapsids without any visible core and apparently scarce or delicate spikes on the envelope. These differences may suggest HHV-7 rather than HHV-6, but this finding needs confirmation. Mature HHV-7 particles measured 170 nm in diameter, with nucleocapsids of 90-95 nm and a tegument of about 30 nm.

Evaluation of four commercial enzyme immunoassays for detection of immunoglobulin M antibodies to human parvovirus B19

Four commercial enzyme immunoassays (EIAs) for the detection of parvovirus B19-specific immunoglobulin M (IgM) antibodies [Biotrin Parvovirus B19 IgM (Biotrin International, Ireland); Parvoscan B19 IgM (Euro-Diagnostica, Sweden); Parvovirus IgM (Immunobiological Laboratories [IBL], Germany); and human parvovirus B19 IgM (Hillcrest Biologicals, USA)] were compared to indirect immunofluorescence assay (IFA) and polymerase chain reaction (PCR). Using IFA as the reference test, high sensitivities (> or = 97%) were observed with all four EIAs, though the specificities of the Biotrin and IBL EIAs (99% and 96% respectively) were significantly higher than those of the Hillcrest and Euro-Diagnostica EIAs (81% and 79% respectively).