Multiplex real-time PCR assays for the prediction of cephalosporin, ciprofloxacin and azithromycin antimicrobial susceptibility of positive Neisseria gonorrhoeae nucleic acid amplification test samples

BACKGROUND

The incidence of antimicrobial-resistant Neisseria gonorrhoeae (GC) is rising in Canada; however, antimicrobial resistance (AMR) surveillance data are unavailable for infections diagnosed directly from clinical specimens by nucleic acid amplification tests (NAATs), representing over 80% of diagnoses. We developed a set of 10 improved molecular assays for surveillance of GC-AMR and prediction of susceptibilities in NAAT specimens.

METHODS

Multiplex real-time PCR (RT-PCR) assays were developed to detect SNPs associated with cephalosporin (ponA, porB, mtrR -35delA, penA A311V, penA A501, N513Y, G545S), ciprofloxacin (gyrA S91, parC D86/S87/S88) and azithromycin [23S (A2059G, C2611T), mtrR meningitidis-like promoter] resistance. The assays were validated on 127 gonococcal isolates, 51 non-gonococcal isolates and 50 NAATs with matched culture isolates. SNPs determined from the assay were compared with SNPs determined from in silico analysis of WGS data. MICs were determined for culture isolates using the agar dilution method.

RESULTS

SNP analysis of the 50 NAAT specimens had 96% agreement with the matched culture RT-PCR analysis. When compared with MICs, presence of penA A311V or penA A501 and two or more other SNPs correlated with decreased susceptibility and presence of three or more other SNPs correlated with intermediate susceptibility to cephalosporins; presence of any associated SNP correlated with ciprofloxacin or azithromycin resistance. NAAT-AMR predictions correlated with matched-culture cephalosporin, ciprofloxacin and azithromycin MICs at 94%, 100% and 98%, respectively.

CONCLUSIONS

We expanded molecular tests for N. gonorrhoeae AMR prediction by adding new loci and multiplexing reactions to improve surveillance where culture isolates are unavailable.

The Impact of Prior Season Vaccination on Subsequent Influenza Vaccine Effectiveness to Prevent Influenza-related Hospitalizations Over 4 Influenza Seasons in Canada

BACKGROUND

Recent studies have demonstrated the possibility of negative associations between prior influenza vaccines and subsequent influenza vaccine effectiveness (VE), depending on season and strain. We investigated this association over 4 consecutive influenza seasons (2011-2012 through 2014-2015) in Canada.

METHODS

Using a matched test-negative design, laboratory-confirmed influenza cases and matched test-negative controls admitted to hospitals were enrolled. Patients were stratified into 4 groups according to influenza vaccine history (not vaccinated current and prior season [referent], vaccinated prior season only, vaccinated current season only, and vaccinated both current and prior season). Conditional logistic regression was used to estimate VE; prior vaccine impact was assessed each season for overall effect and effect stratified by age (<65 years, ≥65 years) and type/subtype (A/H1N1, A/H3N2, influenza B).

RESULTS

Overall, mainly nonsignificant associations were observed. Trends of nonsignificant decreased VE among patients repeatedly vaccinated in both prior and current season relative to the current season only were observed in the A/H3N2-dominant seasons of 2012-2013 and 2014-2015. Conversely, in 2011-2012, during which B viruses circulated, and in 2013-2014, when A/H1N1 circulated, being vaccinated in both seasons tended to result in a high VE in the current season against the dominant circulating subtype.

CONCLUSIONS

Prior vaccine impact on subsequent VE among Canadian inpatients was mainly nonsignificant. Even in circumstances where we observed a trend of negative impact, being repeatedly vaccinated was still more effective than not receiving the current season's vaccine. These findings favor continuation of annual influenza vaccination recommendations, particularly in older adults.

CLINICAL TRIALS REGISTRATION

NCT01517191.

Validation of the Seegene RV15 multiplex PCR for the detection of influenza A subtypes and influenza B lineages during national influenza surveillance in hospitalized adults

Background. The Serious Outcomes Surveillance Network of the Canadian Immunization Research Network (CIRN SOS) has been performing active influenza surveillance since 2009 (ClinicalTrials.gov identifier: NCT01517191). Influenza A and B viruses are identified and characterized using real-time reverse-transcriptase polymerase chain reaction (RT-PCR), and multiplex testing has been performed on a subset of patients to identify other respiratory virus aetiologies. Since both methods can identify influenza A and B, a direct comparison was performed.Methods. Validated real-time RT-PCRs from the World Health Organization (WHO) to identify influenza A and B viruses, characterize influenza A viruses into the H1N1 or H3N2 subtypes and describe influenza B viruses belonging to the Yamagata or Victoria lineages. In a subset of patients, the Seeplex RV15 One-Step ACE Detection assay (RV15) kit was also used for the detection of other respiratory viruses.Results. In total, 1111 nasopharyngeal swabs were tested by RV15 and real-time RT-PCRs for influenza A and B identification and characterization. For influenza A, RV15 showed 98.0 % sensitivity, 100 % specificity and 99.7 % accuracy. The performance characteristics of RV15 were similar for influenza A subtypes H1N1 and H3N2. For influenza B, RV15 had 99.2 % sensitivity, 100 % specificity and 99.8 % accuracy, with similar assay performance being shown for both the Yamagata and Victoria lineages.Conclusions. Overall, the detection of circulating subtypes of influenza A and lineages of influenza B by RV15 was similar to detection by real-time RT-PCR. Multiplex testing with RV15 allows for a more comprehensive respiratory virus surveillance in hospitalized adults, without significantly compromising the reliability of influenza A or B virus detection.

What is the real number of Lyme disease cases in Canada?

BACKGROUND

Lyme disease is emerging in Canada due to expansion of the range of the tick vector Ixodes scapularis from the United States. National surveillance for human Lyme disease cases began in Canada in 2009. Reported numbers of cases increased from 144 cases in 2009 to 2025 in 2017. It has been claimed that few (< 10%) Lyme disease cases are reported associated with i) supposed under-diagnosis resulting from perceived inadequacies of serological testing for Lyme disease, ii) expectation that incidence in Canadian provinces and neighbouring US states should be similar, and iii) analysis of serological responses of dogs to the agent of Lyme disease, Borrelia burgdorferi. We argue that performance of serological testing for Lyme disease is well studied, and variations in test performance at different disease stages are accounted for in clinical diagnosis of Lyme disease, and in surveillance case definitions. Extensive surveillance for tick vectors has taken place in Canada providing a clear picture of the emergence of risk in the Canadian environment. This surveillance shows that the geographic scope of I. scapularis populations and Lyme disease risk is limited but increasing in Canada. The reported incidence of Lyme disease in Canada is consistent with this pattern of environmental risk, and the differences in Lyme disease incidence between US states and neighbouring Canadian provinces are consistent with geographic differences in environmental risk. Data on serological responses in dogs from Canada and the US are consistent with known differences in environmental risk, and in numbers of reported Lyme disease cases, between the US and Canada.

CONCLUSION

The high level of consistency in data from human case and tick surveillance, and data on serological responses in dogs, suggests that a high degree of under-reporting in Canada is unlikely. We speculate that approximately one third of cases are reported in regions of emergence of Lyme disease, although prospective studies are needed to fully quantify under-reporting. In the meantime, surveillance continues to identify and track the ongoing emergence of Lyme disease, and the risk to the public, in Canada.

Interim estimates of 2014/15 influenza vaccine effectiveness in preventing laboratory-confirmed influenza-related hospitalisation from the Serious Outcomes Surveillance Network of the Canadian Immunization Research Network, January 2015

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Interim estimates of 2013/14 influenza clinical severity and vaccine effectiveness in the prevention of laboratory-confirmed influenza-related hospitalisation, Canada, February 2014

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Oseltamivir pharmacokinetics in morbid obesity (OPTIMO trial)

BACKGROUND

Detailed pharmacokinetics to guide oseltamivir (Tamiflu®) dosing in morbidly obese patients is lacking.

METHODS

The OPTIMO trial was a single-centre, non-randomized, open-label pharmacokinetic study of single-dose and steady-state oral oseltamivir phosphate and its carboxylate metabolite in healthy, morbidly obese [body mass index (BMI) >  40)] and healthy, non-obese (BMI  <  30) subjects.

RESULTS

In the morbidly obese versus control subjects, respectively, the single-dose median oseltamivir oral clearance (CL/F) [840 (range 720-1640) L/h versus 580 (470-1800) L/h] was higher, the area under the curve from time zero to infinity (AUC(0-∞)) [89 (46-104) ng·h/mL versus 132 (42-160) ng·h/mL] was lower and the volume of distribution (V/F) [2320 (900-8210) L versus 1670 (700-7290) L] was unchanged. In the morbidly obese versus control subjects, respectively, the single-dose median oseltamivir carboxylate CL/F [22 (17-40) L/h versus 23 (12-33) L/h], AUC(0-∞) [3100 (1700-4100) ng·h/mL versus 3000 (2100-5900) ng·h/mL] and V/F [200 (130-370) L versus 260 (150-430) L] were similar. Similar results for oseltamivir and oseltamivir carboxylate CL/F, AUC₀₋₁₂ and V/F values were observed in the multiple-dose study.

CONCLUSIONS

With single and multiple dosing, the systemic exposure to oseltamivir is decreased but that of oseltamivir carboxylate is largely unchanged. Based on these pharmacokinetic data, an oseltamivir dose adjustment for body weight would not be needed in morbidly obese individuals.

Laboratory diagnosis of mumps in a partially immunized population: The Nova Scotia experience

BACKGROUND

In 2007, Atlantic Canada experienced a large outbreak of mumps predominately in university students who had received a single dose of measles, mumps and rubella vaccine. The present study describes the performance characteristics of reverse transcriptase polymerase chain reaction (RT-PCR) on buccal and urine specimens and immunoglobulin M (IgM) serology in this partially immune population.

METHODS

Patients presenting with symptoms suspicious for mumps had a serum, urine and a buccal swab collected for diagnostic testing. Persons were classified as a 'confirmed' case according to the Public Health Agency of Canada's definition. Sera were tested using an enzyme-linked immunoassay. Detection of mumps virus in buccal swabs and urine samples was performed by RT-PCR.

RESULTS

A subset of 155 cases and 376 non-cases that had all three specimens submitted was used for calculating the performance characteristics. The sensitivity of RT-PCR on buccal swabs, urine specimens and IgM serology were 79%, 43% and 25%, respectively. The specificity of RT-PCR on buccal swabs, urine specimens and IgM serology was 99.5%, 100% and 99.7%, respectively. Only 12 of 134 (9%) patients had positive urine specimens in the presence of negative oral swabs.

CONCLUSION

RT-PCR on buccal swabs is the ideal specimen for diagnosis. Testing an additional urine sample in an outbreak setting did not increase the diagnostic yield significantly, but doubled testing volume and cost. In addition, the data suggest that, in this partially immune group, IgM serology has little value in the diagnosis of acute infection.

BK virus nephropathy in a heart transplant recipient: case report and review of the literature

The human polyomavirus BK virus (BKV) remains latent in the urinary tract and may be reactivated in immunocompromised states. BKV is noted to be the etiologic agent of polyomavirus-associated nephropathy (PVAN), which is a significant cause of allograft failure in renal transplant patients. Renal dysfunction following non-renal solid organ transplantation is common and is typically attributed to drug toxicity or patient comorbidities. In this article we describe a case of PVAN in the native kidneys of a heart transplant recipient and review the literature. Although this is only the fourth case reported, BKV nephropathy should be considered in the differential diagnosis of new renal failure following non-kidney solid organ transplantation, as early diagnosis of PVAN is necessary to prevent irreversible renal damage.

The effect of C. burnetii infection on the quality of life of patients following an outbreak of Q fever

Sixty-six cases of Q fever were diagnosed in people affiliated with a goat-farming co-operative in rural Newfoundland in the spring of 1999. Follow-up studies which included administration of the Short Form 36 Health Survey (SF-36) were conducted 3 and 27 months after the initial outbreak to prospectively follow the effects of acute Q fever on the quality of life of the participants. Twenty-seven months after the outbreak 51% of those who had Q fever reported persistent symptoms including seven participants whose symptoms had initially resolved 3 months after the outbreak. Individuals with Q fever had significantly lower scores on five of the eight scales in the SF-36 and lower scores in the mental and physical summary scales compared to uninfected controls. Although this supports the hypothesis of a 'post Q fever fatigue syndrome' (QFFS), further study is warranted.

Atypical manifestations of chronic Q fever

Chronic Q fever is uncommon, with the majority of cases manifesting as culture-negative endocarditis. In this report, we describe 3 patients who present with atypical manifestations of chronic Q fever. These were a 43-year-old man whose site of chronic Q fever was the central nervous system, a 53-year-old woman who underwent coronary angioplasty 6 days before the onset of symptoms of acute Q fever and within 4 months had serologic evidence consistent with chronic Q fever, and a 66-year-old man with fever of unknown origin, a pancreatic mass, and aorto-bifemoral grafts.

Goat-associated Q fever: a new disease in Newfoundland

In the spring of 1999 in rural Newfoundland, abortions in goats were associated with illness in goat workers. An epidemiologic investigation and a serologic survey were conducted in April 1999 to determine the number of infections, nature of illness, and risk factors for infection. Thirty-seven percent of the outbreak cohort had antibody titers to phase II Coxiella burnetii antigen >1:64, suggesting recent infection. The predominant clinical manifestation of Q fever was an acute febrile illness. Independent risk factors for infection included contact with goat placenta, smoking tobacco, and eating cheese made from pasteurized goat milk. This outbreak raises questions about management of such outbreaks, interprovincial sale and movement of domestic ungulates, and the need for discussion between public health practitioners and the dairy industry on control of this highly infectious organism.

Pseudomonas aeruginosa community-acquired pneumonia in previously healthy adults: case report and review of the literature

We report a case of rapidly fatal Pseudomonas aeruginosa community-acquired pneumonia (CAP) in a previously healthy 67-year-old woman. Eleven published case reports of P. aeruginosa CAP in previously healthy adults are reviewed. According to our review, the mean age of affected patients is 45.3 years. Five patients described in the literature were smokers with a mean smoking history of 40 pack-years. The clinical presentation is nonspecific, and although the pneumonia can be rapidly fatal, only 33% of the patients who were reported died. However, mortality may be independent of treatment within the first 36 hours of presentation. Exposure to aerosols of contaminated water is a risk factor for P. aeruginosa CAP in this population. Pseudomonas CAP should be considered in the differential diagnosis for anyone with a smoking history who presents with rapidly progressive pneumonia. We discuss treatment recommendations that are based on evidence in the currently available literature on the subject.