Antibiotic resistance in uropathogens across northern Australia 2007-20 and impact on treatment guidelines

Antibiogram development for Australian residential aged care facilities

OBJECTIVE

Knowledge of local antibiotic resistance data, provided by antibiograms (a cumulative summary of in vitro-antimicrobial-susceptibility-test results), can aid prescribing of appropriate empirical antibiotics. This study aimed to explore the feasibility of antibiogram development for residential aged care facilities (RACFs).

DESIGN

Retrospective observational study of culture and sensitivity data.

SETTING

Nine RACFs in Queensland, Australia.

METHOD

Available antimicrobial susceptibility results were collected retrospectively for all residents of recruited RACFs from January 1, 2020, to December 31, 2022. Data were managed and analyzed with WHONET software®, and antibiograms were developed in accordance with the CLSI-M39 guidelines. Antibiogram data beyond the standard 12-months and pooling of data from geographically similar RACFs were explored as options to improve feasibility and validity of the antibiograms.

RESULTS

The most prevalent bacteria in the RACFs were Escherichia coli and Staphylococcus aureus. Due to the low number of positive cultures (less than 30) for individual RACFs, an annual antibiogram was not feasible. Extending the time-period to three years improved feasibility of antibiograms for E.coli in seven RACFs and S.aureus in five RACFs. Combining the data from closely located RACFs allowed for sufficient urinary and skin swab isolates to produce annual pooled antibiograms for all three years.

CONCLUSION

Use of extended time period antibiograms can provide RACF specific urinary and skin/soft tissue resistance data without the necessity of private pathology provider input. However, pooled syndromic antibiograms can be made available on an annual basis, which may be the preferred option.

Resistance to first-line antibiotic therapy among patients with uncomplicated acute cystitis in Melbourne, Australia: prevalence, predictors and clinical impact

Background

Australian guidelines recommend trimethoprim or nitrofurantoin as first-line agents for uncomplicated urinary tract infections (UTIs). Laboratory surveillance indicates high rates of trimethoprim resistance among urinary bacterial isolates, but there are scant local clinical data about risk factors and impact of trimethoprim resistance.

Objectives

To determine the prevalence, risk factors, mechanism and impact of resistance to first-line antibiotic therapy for uncomplicated UTIs in the community setting.

Methods

A prospective observational study from October 2019 to November 2021 in four general practices in Melbourne, Australia. Female adult patients prescribed an antibiotic for suspected or confirmed uncomplicated acute cystitis were eligible. Primary outcome was urine isolates with resistance to trimethoprim and/or nitrofurantoin.

Results

We recruited 87 participants across 102 UTI episodes with median (IQR) age of 63 (47-76) years. Escherichia coli was the most common uropathogen cultured (48/62; 77%); 27% (13/48) were resistant to trimethoprim (mediated by a dfrA gene) and none were resistant to nitrofurantoin. Isolates with resistance to a first-line therapy were more common among patients reporting a history of recurrent UTIs [risk ratio (RR): 2.08 (95% CI: 1.24-3.51)] and antibiotic use in the previous 6 months [RR: 1.89 (95% CI: 1.36-2.62)]. Uropathogen resistance to empirical therapy was not associated with worse clinical outcomes.

Conclusions

Resistance to trimethoprim is common in uncomplicated UTIs in Australia but may not impact clinical outcomes. Further research is warranted on the appropriateness of trimethoprim as empirical therapy, particularly for patients with antimicrobial resistance risk factors.

Clinical Setting Comparative Analysis of Uropathogens and Antibiotic Resistance: A Retrospective Study Spanning the Coronavirus Disease 2019 Pandemic

Background

Antimicrobial resistance (AMR) in uropathogens has been increasing in Australia. Many nations observed heightened AMR during the coronavirus disease 2019 (COVID-19) pandemic, but it is not known how this may vary across clinical settings and in nations with lower infection rates.

Methods

We investigated the uropathogen composition and corresponding antibiotic resistance of 775 559 Australian isolates from the community, hospitals, and aged care facilities before (2016-2019) and during (2020-2022) the COVID-19 pandemic. A mathematical model was developed to predict the likelihood of resistance to currently recommended antibiotics for treating urinary tract infections (UTIs).

Results

Among uropathogens originating from the community, hospitals, and aged care facilities, Escherichia coli accounted for 71.4%, 57.6%, and 65.2%, respectively. During the COVID-19 pandemic period, there was an increase in UTIs caused by E coli across all settings. Uropathogens from aged care and hospitals frequently showed higher resistance to antibiotics compared to those isolated from the community. Interestingly, AMR among uropathogens showed a declining trend during the COVID-19 pandemic. Based on the resistance patterns of the past 3 years, our modeling predicted that 30%, 42.6%, and 38.8% of UTIs in the community, hospitals, and aged care facilities, respectively, would exhibit resistance to trimethoprim treatment as empirical therapy. In contrast, resistance to nitrofurantoin was predicted to be 14.6%, 26%, and 24.1% from these 3 respective settings.

Conclusions

Empirical therapy of UTIs in Australia with trimethoprim requires evaluation due to high rates of resistance observed across clinical settings.

Repurposing antibiotic resistance surveillance data to support treatment of recurrent infections in a remote setting

In northern Australia, a region with limited access to healthcare and a substantial population living remotely, antibiotic resistance adds to the complexity of treating infections. Focussing on Escherichia coli urinary tract infections (UTIs) and Staphylococcus aureus skin & soft tissue infections (SSTIs) captured by a northern Australian antibiotic resistance surveillance system, we used logistic regression to investigate predictors of a subsequent resistant isolate during the same infection episode. We also investigated predictors of recurrent infection. Our analysis included 98,651 E. coli isolates and 121,755 S. aureus isolates from 70,851 patients between January 2007 and June 2020. Following an initially susceptible E. coli UTI, subsequent recovery of a cefazolin (8%) or ampicillin (13%) -resistant isolate during the same infection episode was more common than a ceftriaxone-resistant isolate (2%). For an initially susceptible S. aureus SSTI, subsequent recovery of a methicillin-resistant isolate (8%) was more common than a trimethoprim-sulfamethoxazole-resistant isolate (2%). For UTIs and SSTIs, prior infection with a resistant pathogen was a strong predictor of both recurrent infection and resistance in future infection episodes. This multi-centre study demonstrates an association between antibiotic resistance and an increased likelihood of recurrent infection. Particularly in remote areas, a patient's past antibiograms should guide current treatment choices since recurrent infection will most likely be at least as resistant as previous infection episodes. Using population-level surveillance data in this way can also help clinicians decide if they should switch antibiotics for patients with ongoing symptoms, while waiting for diagnostic results.

Nitrofuran Derivatives Cross-Resistance Evidence-Uropathogenic Escherichia coli Nitrofurantoin and Furazidin In Vitro Susceptibility Testing

The treatment of urinary tract infections is usually empirical. For example, nitrofuran derivatives, mainly nitrofurantoin (but also furazidin), are used in Eastern Europe. A significant problem is the assessment of the usefulness of furazidin, as there are no standards for susceptibility testing. Additionally, a high percentage of strains resistant to nitrofurantoin should prompt caution when choosing furazidin in therapy. This study aimed to answer the question of whether it is possible to use nitrofurantoin susceptibility for furazidin drug susceptibility analyses and if there is any cross-resistance in the nitrofuran derivatives group. One hundred E. coli clinical isolates, obtained from the Central Teaching Hospital of the Medical University of Lodz, were cultured from positive urine samples. For susceptibility testing, microdilution and disk diffusion methods, following EUCAST guidelines, were used. The results showed that the MICs of furazidin were equal to or lower than those of nitrofurantoin in 89% of the tested strains. The MIC50/90 values for furazidin were two times lower than those for nitrofurantoin. Positive correlations were found between MICs and growth inhibition zones for both antibiotics. Based on the obtained data and previous studies, it was assumed that the transfer of susceptibility testing results from nitrofurantoin to furazidin is acceptable due to cross-resistance in nitrofuran derivatives.

Disease burden, associated mortality and economic impact of antimicrobial resistant infections in Australia

BACKGROUND

The growing spread of antimicrobial resistance (AMR) is accepted as a threat to humans, animals and the environment. This threat is considered to be both country specific and global, with bacteria resistant to antibiotic treatment geographically dispersed. Despite this, we have very few Australian estimates available that use national surveillance data supplemented with measures of risk, to generate reliable and actionable measures of AMR impact. These data are essential to direct policies and programs and support equitable healthcare resource utilisation. Importantly, such data can lead to implementation of programs to improved morbidity and mortality of patients with a resistant infection.

METHODS

Using data from a previous case-cohort study, we estimated the AMR-associated health and economic impact caused by five hospital-associated AMR pathogens (Enterococcus spp., E. coli, K. pneumoniae, P. aeruginosa and S. aureus) in patients with a bloodstream, urinary tract, or respiratory tract infection in Australia in 2020. We estimated disease burden based on the counterfactual scenario in which all AMR infections were replaced by no infection.We used a population-level simulation model to compute AMR-associated mortality, loss of quality-adjusted life years and costs.

FINDINGS

In 2020, there were 1,031 AMR-associated deaths (95% uncertainty interval [UI] 294, 2,615) from the five resistant hospital-associated infections in Australia. The greatest odds of dying were from respiratory infections (ceftazidime-resistant P. aeruginosa) and bloodstream infections, both resulting in high hospital and premature death costs. MRSA bacteraemia contributed the most to hospital costs (measured as bed-days) as patients with this infection resulted in additional 12,818 (95% UI 7246, 19966) hospital bed-days and cost the hospitals an extra $24,366,741 (95%UI $13,774,548, $37,954,686) per year. However, the cost of premature death from five resistant pathogens was $438,543,052, which was by far greater than the total hospital cost ($71,988,858). We estimate a loss of 27,705 quality-adjusted life years due to the five AMR pathogens.

INTERPRETATION

These are the first Australian estimates of AMR-associated health and economic impact. Country-level estimates of AMR impact are needed to provide local evidence to better inform programs and health policies to reduce morbidity and mortality associated with infection. The burden in hospital is likely an underestimate of the impact of AMR due to community-associated infections where data are limited, and the AMR burden is high. This should now be the focus of future study in this area.

FUNDING

TMW was supported by the Australian Partnership for Preparedness Research on Infectious Disease Emergencies (APPRISE) (grant number GNT1116530) Fellowship.

Antimicrobial Resistance, Virulence Factor-Encoding Genes, and Biofilm-Forming Ability of Community-Associated Uropathogenic Escherichia coli in Western Saudi Arabia

To explore the prevalence of multidrug-resistant community-associated uropathogenic Escherichia coli (UPEC) and their virulence factors in Western Saudi Arabia. A total of 1,000 urine samples were examined for the presence of E. coli by selective plating on MacConkey, CLED, and sheep blood agar. Antimicrobial susceptibility patterns were determined using Vitek^® 2 Compact (MIC) and the disc diffusion method with Mueller-Hinton agar. Genes encoding virulence factors (kpsMTII, traT, sat, csgA, vat, and iutA) were detected by PCR. The overall prevalence of UTI-associated E. coli was low, and a higher prevalence was detected in samples of female origin. Many of the isolates exhibited resistance to norfloxacin, and 60% of the isolates showed resistance to ampicillin. No resistance to imipenem, meropenem, or ertapenem was detected. In general, half of the isolates showed multiple resistance patterns. UPEC exhibited a weak ability to form biofilms, where no correlation was observed between multidrug resistance and biofilm-forming ability. All uropathogenic E. coli isolates carried the kpsMTII, iutA, traT, and csgA genes, whereas the low number of the isolates harbored the sat and vat genes. The diversity of virulence factors harbored by community-associated UPEC may render them more virulent and further explain the recurrence/relapse cases among community-associated UITs. To the best of our knowledge, this study constitutes the first exploration of virulence, biofilm-forming ability, and its association with multidrug resistance among UPEC isolates in Saudi Arabia. Further investigations are needed to elucidate the epidemiology of community-associated UPEC in Saudi Arabia.

The increased length of hospital stay and mortality associated with community-associated infections in Australia

Background

An increasing proportion of antibiotic-resistant infections are community acquired. However, the burden of community-associated infections (CAIs) and the resulting impact due to resistance have not been well described.

Methods

We conducted a multisite, retrospective case–cohort study of all acute care hospital admissions across 134 hospitals in Australia. Patients admitted with a positive culture of 1 of 5 organisms of interest, namely Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, and Enterococcus faecium, from January 1, 2012, through December 30, 2016, were included. Data linkage was used to link hospital admissions and pathology data. Patients with a bloodstream infection (BSI), urinary tract infection (UTI), or respiratory tract infection (RTI) were included in the analysis. We compared patients with a resistant and drug-sensitive infection and used regression analyses to derive the difference in length of hospital stay (LOS) and mortality estimates associated with resistance.

Results

No statistically significant impact on hospital LOS for patients with resistant CAIs compared with drug-sensitive CAIs was identified. CAI patients with drug-resistant Enterobacteriaceae (E. coli, K. pneumoniae) BSIs were more likely to die in the hospital than those with drug-sensitive Enterobacteriaceae BSIs (odds ratio [OR], 3.28; 95% CI, 1.40–6.92). CAI patients with drug-resistant P. aeruginosa UTIs were more likely to die in the hospital than those with the drug-sensitive counterpart (OR, 2.43; 95% CI, 1.12–4.85).

Conclusions

The burden of CAI in the hospital is significant, and antibiotic resistance is adding to associated mortality.