COVID-19 serology: use and interpretation in New Zealand

Serology is now a well-established diagnostic tool for the diagnosis of COVID-19 infections in New Zealand. Using local and international experience, we provide an overview of serological response to infection and vaccination as well as the use and interpretation of antibody tests in our setting. We also discuss the potential future role of post-vaccination serology testing as a correlate of immunity. We conclude that, given the pitfalls of testing, clinical microbiologist advice is necessary for interpretation of high-consequence cases.

COVID-19 serology: use and interpretation in New Zealand

Serology is now a well-established diagnostic tool for the diagnosis of COVID-19 infections in New Zealand. Using local and international experience, we provide an overview of serological response to infection and vaccination as well as the use and interpretation of antibody tests in our setting. We also discuss the potential future role of post-vaccination serology testing as a correlate of immunity. We conclude that, given the pitfalls of testing, clinical microbiologist advice is necessary for interpretation of high-consequence cases.

Demographic and behavioural factors associated with antimicrobial susceptibility to azithromycin and ceftriaxone in Neisseria gonorrhoeae

Antimicrobial resistance of Neisseria gonorrhoeae (NG) is of global public health concern. The aim of this study was to explore demographic and behavioural factors associated with antimicrobial susceptibility of NG to ceftriaxone and azithromycin. Gonococcal isolates (n = 391) from clients attending the Auckland Sexual Health Service, New Zealand, from July 2014 - June 2015 (n = 206), and July 2017 - June 2018 (n = 185), were tested for susceptibility to ceftriaxone and azithromycin. Laboratory data were linked with behavioural and demographic data. Geometric mean azithromycin MICs increased across the two time periods (0.239 mg/L in 2014/15 to 0.347 mg/L in 2017/18, p < 0.001), and ceftriaxone MICs decreased (0.007 mg/L in 2014/15 to 0.005 mg/L in 2017/18, p < 0.001). Demographic and behavioural factors were not associated with differences in ceftriaxone MICs; however azithromycin MICs were higher in men who have sex with men (0.356 mg/L) compared with the heterosexual study population (0.192 mg/L, p < 0.001) and were lower in Pacific peoples (0.201 mg/L, p < 0.001) and Māori (0.244 mg/L, p = 0.05) compared with those of European ethnicity (0.321 mg/L). Our findings show that azithromycin MICs increased in our region between 2014 and 2018; associations were seen with sexual orientation and ethnicity.

Appropriateness of trimethoprim as empiric treatment for cystitis in 15-55 year-old women: an audit

AIM

To assess whether trimethoprim remains an appropriate empiric treatment for uncomplicated cystitis in women 15-55 years old.

METHODS

General practitioners in Auckland, Nelson-Marlborough, Otago and Southland were invited to participate in this audit of current practice. Participating general practitioners were asked to submit urine to the laboratory for microscopy and culture from any woman aged 15-55 years presenting with uncomplicated cystitis. Urine samples submitted as part of the audit were identified by a "copy to" code. Data on laboratory results were extracted from the laboratory information system.

RESULTS

Data were collected from June 2016 to August 2018. Four hundred and eighty-one samples were submitted, of which 340 (70.7%) met the inclusion criteria of the audit. A urinary pathogen was identified in 181 (53.2%) specimens, of which 148 (81.8%) were E. coli, 13 (7.2%) other coliforms and 20 (11.0%) Staphylococcus saprophyticus. Of the E. coli isolates, 109 of 148 (73.6%, 95% CI 66.6-80.7) were susceptible to trimethoprim, 144 of 144 (100%, 95% CI 100-100) to nitrofurantoin and 143 of 148 (96.6%, 95% CI 93.7-99.5) to cefalexin. Of the urinary pathogens, 139 of 185 (75.1%, 95% CI 68.9-81.4) were susceptible to trimethoprim, 164 of 177 tested (92.7%, 95% CI 88.8-96.5) to nitrofurantoin and 166 of 178 tested (93.3%, 95% CI 89.6-96.9) to cefalexin. Overall, a uropathogen resistant to trimethoprim was detected in 13.5%, to nitrofurantoin in 3.8%, and to cefalexin in 3.5% of samples tested.

CONCLUSION

Similar rates of resistance to trimethoprim were seen in women 15-55 years old presenting with cystitis compared with unselected samples submitted from the general community. Given the high rates of resistance, trimethoprim is no longer appropriate as an empiric treatment option for cystitis in this group. Nitrofurantoin or cefalexin are appropriate alternative empiric treatment options. Given the current recommendation that a urine sample should not be submitted to the laboratory from women with uncomplicated cystitis, ongoing audits will be required to ensure that empiric treatment recommendations remain appropriate.

Isolate independent molecular typing improves the yield of O typing of infections due to Shiga toxin producing Escherichia coli

Molecular screening has increased detection of Shiga-toxin producing Escherichia coli (STEC). However, it is difficult to isolate the organism for epidemiological typing. We applied a molecular method for direct detection of nine O types from 110 stx positive faeces samples and compared the results with conventional isolate based methods. Using conventional methods 55/110 (50%) samples were O typed. Using the molecular method, 72/110 (65%) were O typed, including 23/38 (61%) culture negative samples. Combining both techniques typed 88/110 (80%) of samples. Molecular typing increased detection of O128 (2-25%, p<0.001), O26 (11-16%) O45 (0-6%) and O103 (1-6%) infections. Molecular typing of STEC direct from faecal samples improved O type yield; risk of bias in epidemiological and surveillance activities may be reduced by inclusion of culture independent typing methods.

Suboptimal performance of rotavirus testing in a vaccinated community population should prompt laboratories to review their rotavirus testing algorithms in response to changes in disease prevalence

Rotavirus vaccine has reduced disease prevalence in many countries. Consequently, we aimed to assess the reliability of a rotavirus immunoassay in the community population of Auckland and Northland, New Zealand. Between 22 October 2015 and 31 December 2016, 2873 fecal samples were tested by enzyme immunoassay (EIA, Rotascreen II, Microgen, UK) from 2748 patients (median age 8 years, range 0-101 years). Eighty-nine (3.1%) samples were reactive; 86 samples were tested by a second method. Rotavirus was confirmed in 49/86 (57%). Positive rotavirus EIAs were more likely to be confirmed in samples from cases ≥1 year of age (positive predictive value [PPV] 61%, 95% confidence interval [CI] 50-72%, P = 0.049) and in spring/summer (PPV 67%, 95% CI 55-78%, P = 0.003). Reactive rotavirus tests required confirmatory testing regardless of demographic, vaccine, or seasonal factors; a review of rotavirus testing algorithms may be necessary in other vaccinated community populations.

International normalised ratio monitoring in the community populations of the Auckland and Northland regions of New Zealand: time in therapeutic range and frequency of testing

BACKGROUND

Warfarin remains a commonly used anticoagulant for the treatment and prevention of thrombosis. To balance the risks and benefits of therapy, monitoring of the international normalised ratio (INR) is necessary. Patients derive most benefit from warfarin when they spend ≥65% of time in the therapeutic range (INR 2-3). We performed an analysis of INR monitoring for the Auckland and Northland regions of New Zealand in order to estimate anticoagulation control and appropriateness of testing at the population level.

METHODS

INR test results and patient demographics (age and sex) were extracted from the laboratory information system of Labtests and Northland Pathology Laboratories for the period of 1 January 2016 to 27 July 2016.

RESULTS

We included 126 184 INR results from 10 922 patients. The median age of patients represented was 74 years and 57% were male. The overall mean time in therapeutic range was 63%, with a mean interval between INR tests of 14 days.

CONCLUSION

Our results indicate that anticoagulant control in our communities could be improved, and that inappropriately frequent INR testing should be redressed. Appropriate interventions could lead to net clinical benefits and reduce resource misallocation.

Dwarf tapeworm (Hymenolepis nana): Characteristics in the Northern Territory 2002-2013

AIM

Review of dwarf tapeworm (Hymenolepis nana) presentations to Northern Territory (NT) Government health-care facilities over 12 years. We postulated H. nana infections would remain unchanged despite the introduction of deworming programmes as H. nana is not eradicated with albendazole treatment.

METHODS

A retrospective observational analysis of consecutive microbiologically confirmed cases of H. nana identified by NT Government health-care facilities between 2002 and 2013.

RESULTS

Four hundred sixty-one episodes of H. nana infection were identified over the 12-year period from 68 387 faecal samples. Infections were overwhelmingly in young children with a median age of patients being 3.0 years (interquartile range 2.25-4.67). Patients were predominantly Indigenous (98.9%, P = 0.001) and infections occurred across the entire NT. Infections were associated with anaemia (18.2%) and eosinophilia (39.6%). The annual prevalence of NT Government health-care facility diagnosed H. nana infection remains relatively constant from 6.9 {4.8-9.0 (confidence interval (CI))} cases per 10 000 Indigenous population in 2002, compared with 6.6 (4.7-8.4 CI) cases per 10 000 Indigenous population in 2013. Infection rates in Indigenous children <5 years of age were: 46.1 (16.4-75.8 CI) cases/10 000 in 2002, compared with 44.3 (15.3-73.3 CI) cases/10 000 Indigenous population in 2013.

CONCLUSION

H. nana is the most frequently identified cestode (tapeworm) in NT Government health-care facilities. H. nana remains endemic throughout the NT, predominantly infecting Indigenous children less than 5 years of age.

Relative frequency, characteristics, and antimicrobial susceptibility patterns of Vibrio spp., Aeromonas spp., Chromobacterium violaceum, and Shewanella spp. in the northern territory of Australia, 2000-2013

Vibrio, Aeromonas, Chromobacterium violaceum, and Shewanella (VACS) are water-associated Gram-negative organisms that can cause a variety of infections. The frequency, patient characteristics, and antimicrobial susceptibilities for 468 isolates from 442 patients from the Northern Territory were reviewed. Aeromonas spp. (312 of 468; 67%) were most commonly isolated followed by Vibrio spp. (71 of 468; 15%), Shewanella spp. (61 of 468; 13%), and C. violaceum (24 of 468; 5%). A strong male predominance was found (male to female ratio of 2.3:1). Skin and soft tissue isolations (373 of 468; 80%) from lower limb infections (222 of 371; 60%) were the most common clinical manifestation. The episodes were usually polymicrobial (281 of 468; 60%). Coisolates included Staphylococcus aureus (137 of 468; 29%), β-hemolytic streptococci (74 of 468; 16%), enterobacteriaceae (111 of 468; 24%), non-fermentative Gram-negative bacilli (35 of 468; 7%), and other VACS organisms (37 of 468; 8%). Antimicrobial resistance of VACS organisms to ciprofloxacin (0-4%), cefepime (0-3%), and gentamicin (0-0.8%) and Vibrio spp., Aeromonas spp., and Shewanella to cotrimoxazole (0-3%) was rarely shown. For water-associated lower limb skin and soft tissue infections in the tropics, clinicians should consider empirical antimicrobial therapy with agents active against S. aureus and VACS organisms.

Differences in risk-factor profiles between patients with ESBL-producing Escherichia coli and Klebsiella pneumoniae: a multicentre case-case comparison study

Background

Generic epidemiological differences between extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) and Klebsiella pneumoniae (ESBL-KP), are poorly defined. Nonetheless, defining such differences and understanding their basis could have strategic implications for infection control policy and practice.

Methods

Between 2009 and 2011 patients with bacteraemia due to ESBL-EC or ESBL-KP across all three acute hospitals in the city of Auckland, New Zealand, were eligible for inclusion. Recognised risk factors for ESBL bacteraemia were compared between species in a retrospective case-case study design using multivariate logistic regression. Representative isolates underwent ESBL gene characterisation and molecular typing.

Results

170 patients and 176 isolates were included in the study (92 patients with ESBL-EC, 78 with ESBL-KP). 92.6% had CTX-Ms. 39% of EC were ST131 while 51% of KP belonged to 3 different STs (i.e. ST20, ST48 & ST1087). Specific sequence types were associated with specific hospitals for ESBL-KP but not ESBL-EC. Variables positively associated with ESBL-EC on multivariate analysis were: community acquired infection (odds ratio [OR] 7.9; 95% CI: 2.6-23.9); chronic pulmonary disease (OR 5.5; 95% CI: 1.5-20.1); and high prevalence country of origin (OR 4.3; 95% CI: 1.6-11.6). Variables negatively associated with ESBL-EC were previous transplant (OR 0.06; 95% CI: 0.007-0.6); Hospital 2 (OR 0.3; 95% CI: 0.1-0.7) and recent ICU admission (OR 0.3; 95% CI: 0.07-0.9).

Conclusions

Differences in risk profiles between patients with ESBL-EC and ESBL-KP suggest fundamental differences in transmission dynamics. Understanding the biological basis for these differences could have implications for infection control practice. Tailoring of infection control measures according to ESBL species may be indicated in some instances.

Clostridium difficile as a cause of healthcare-associated diarrhoea among children in Auckland, New Zealand: clinical and molecular epidemiology

We aimed to determine the incidence of Clostridium difficile infection (CDI), the molecular epidemiology of circulating C. difficile strains and risk factors for CDI among hospitalised children in the Auckland region. A cross-sectional study was undertaken of hospitalised children <15 years of age in two hospitals investigated for healthcare-associated diarrhoea between November 2011 and June 2012. Stool specimens were analysed for the presence of C. difficile using a two-step testing algorithm including polymerase chain reaction (PCR). C. difficile was cultured and PCR ribotyping performed. Demographic data, illness characteristics and risk factors were compared between children with and without CDI. Non-duplicate stool specimens were collected from 320 children with a median age of 1.2 years (range 3 days to 15 years). Forty-six patients (14 %) tested met the definition for CDI. The overall incidence of CDI was 2.0 per 10,000 bed days. The percentage of positive tests among neonates was only 2.6 %. PCR ribotyping showed a range of strains, with ribotype 014 being the most common. Significant risk factors for CDI were treatment with proton pump inhibitors [risk ratio (RR) 1.74, 95 % confidence interval (CI) 1.09-5.59; p = 0.002], presence of underlying malignancy (RR 2.71, 95 % CI 1.65-4.62; p = 0.001), receiving chemotherapy (RR 2.70, 95 % CI 1.41-4.83; p = 0.003) and exposure to antibiotics (RR 1.17, 95 % CI 0.99-1.17; p = 0.03). C. difficile is an important cause of healthcare-associated diarrhoea in this paediatric population. The notion that neonatal populations will always have high rates of colonisation with C. difficile may not be correct. Several risk factors associated with CDI among adults were also found to be significant.

Systematic application of multiplex PCR enhances the detection of bacteria, parasites, and viruses in stool samples

OBJECTIVES

To determine whether systematic testing of faecal samples with a broad range multiplex PCR increases the diagnostic yield in patients with diarrhoea compared with conventional methods and a clinician initiated testing strategy.

METHODS

1758 faecal samples from 1516 patients with diarrhoea submitted to two diagnostic laboratories were tested for viral, bacterial, and parasitic pathogens by Fast-Track Diagnostics multiplex real-time PCR kits and conventional diagnostic tests.

RESULTS

Multiplex PCR detected pathogens in 530 samples (30%): adenovirus (51, 3%), astrovirus (95, 5%), norovirus (172, 10%), rotavirus (3, 0.2%), Campylobacter jejuni/coli (85, 5%), Salmonella spp. (22, 1%), Clostridium difficile (72, 4%), entero-haemorrhagic Escherichia coli (21, 1%), Cryptosporidium spp. (3, 0.2%), Entamoeba histolytica (1, 0.1%), and Giardia lamblia (59, 3%). In contrast, conventional testing detected a pathogen in 324 (18%) samples.

CONCLUSIONS

Using a systematic approach to the diagnosis of gastroenteritis improved diagnostic yield. This enhanced detection with PCR was achieved by a combination of improved detection of individual pathogens and detection of pathogens not requested or unable to be tested by conventional tests. This approach also allowed earlier identification for most pathogens and created a workflow which is likely to adapt well for many diagnostic laboratories.