John Turnidge

The Burkholderia cepacia complex (BCC) is comprised of 24 species of gram-negative bacteria that cause opportunistic infections. While antimicrobial susceptibility testing (AST) has historically been used to guide treatment for BCC infections, recent work highlighting problems with AST for these organisms led the Clinical and Laboratory Standards Institute (CLSI) to remove disk diffusion and minimal inhibitory concentration (MIC) breakpoints for BCC from its M100 standards document. Epidemiological cut-off values (ECVs) may be helpful to clinicians in the absence of breakpoints, as they may be used to determine whether an isolate has a wild-type or non-wild-type phenotype. Here, we present an analysis of BCC ECVs for ceftazidime (CAZ), levofloxacin (LVX), meropenem (MEM), minocycline (MIN), and trimethoprim-sulfamethoxazole (TMP-SMX). ECVs were calculated using MIC data from 3 previous studies and 3 independent laboratories for 1,896 BCC isolates. ECVs were 16 μg/mL for CAZ, 8 μg/mL for LVX, 16 μg/mL for MEM, and 8 μg/mL for MIN. The ECV for TMP-SMX varied depending on the analysis from 2, 8, and 16 μg/mL and therefore could not be reliably established. Challenges with establishing ECVs for BCC include limitations with the pooled MIC data set, broad MIC distributions, and high ECVs that are above the obsolete susceptible MIC breakpoints. These challenges limit the clinical utility of ECVs for these organisms and support the removal of ECVs from the CLSI M100 standards document. IMPORTANCE: The Burkholderia cepacia complex is a group of bacterial species that cause difficult-to-treat opportunistic infections. Recently, clinical breakpoints, which are used to determine whether organisms are susceptible to certain antimicrobials, were removed from Clinical and Laboratory Standards Institute (CLSI) standards for these organisms due to problems with antimicrobial susceptibility testing performance. Clinicians are now faced with the challenge of how to treat these complex infections without clinical breakpoints. Here, we determine epidemiological cut-off values (ECVs) for relevant antimicrobials for the B. cepacia complex. While we established ECVs for ceftazidime, levofloxacin, meropenem, and minocycline, we were unable to determine a reliable ECV for trimethoprim-sulfamethoxazole. Additionally, we encountered significant challenges in our analyses, including data limitations for these organisms and high ECVs that are not clinically useful. These challenges limit the practical use of these ECVs in helping guide treatment and support the removal of ECVs from the CLSI M100 standards document.

The Burkholderia cepacia complex (BCC) is comprised of 24 species of Gram-negative bacteria that cause opportunistic infections. While antimicrobial susceptibility testing (AST) has historically been used to guide treatment for BCC infections, recent work highlighting problems with AST for these organisms led the Clinical and Laboratory Sciences Institute (CLSI) to remove disk diffusion (DD) and minimal inhibitory concentration (MIC) breakpoints for BCC from its M100 standards document. Epidemiological cut-off values (ECVs) may be helpful to clinicians in the absence of breakpoints, as they may be used to determine whether an isolate has a wild-type or non-wild- type phenotype. Here we present an analysis of BCC ECVs for ceftazidime (CAZ), levofloxacin (LVX), meropenem (MEM), minocycline (MIN), and trimethoprim-sulfamethoxazole (TMP-SMX). ECVs were calculated using MIC data from 3 previous studies and 3 independent laboratories for 1,896 BCC isolates. ECVs were 16 μg/ml for CAZ, 8 μg/ml for LVX, 16 μg/ml for MEM, and 8 μg/ml for MIN. The ECV for TMP-SMX varied depending on the analysis from 2 μg/ml, 8 μg/ml, and 16 μg/ml and therefore could not be reliably established. Challenges with establishing ECVs for BCC include limitations with the pooled MIC dataset, broad MIC distributions, and high ECVs that are above the obsolete susceptible MIC breakpoints. These challenges limit the clinical utility of ECVs for these organisms and supported removal of ECVs from the CLSI M100 standards document.

Background: Residential aged care facilities (RACFs) are potential reservoirs for methicillin‐resistant Staphylococcus aureus (MRSA), with residents at increased risk due to compromised immunity, comorbidities, frequent hospital visits, and close living quarters. Objectives: This study is aimed at assessing MRSA prevalence in RACFs and analyzing antimicrobial resistance mechanisms both phenotypically and genotypically. Methods: A total of 106 participants were recruited: 84 from three RACFs and 22 from retirement villages (as control samples). MRSA was isolated from nasal, wound, and urine samples using selective media. Identification was confirmed via MALDI‐TOF MS. Antimicrobial susceptibility testing and MRSA screening were conducted using ISO broth microdilution and EUCAST disc diffusion. Whole‐genome sequencing and bioinformatics were used to explore resistance mechanisms and clonal transmission. Results: Nasal carriage of MRSA was 8.2% ( n = 7/85) among RACF residents; none were found in retirement village participants. All isolates formed strong biofilms, and 66.6% (10/15) showed multidrug resistance. Genotypic analysis revealed ST22 as the predominant clone. Genotypic resistance largely matched phenotypic profiles, except for unexplained tetracycline resistance. No isolates carried Panton–Valentine leukocidin (PVL), consistent with previously reported data on MRSA in long‐term care facilities. SNP‐based phylogenetic analysis indicated persistent colonization and circulation of multidrug‐resistant clones within the facilities. Nasal carriage of MRSA was associated with UTIs and/or wound infections in some cases, whereas a UTI caused by the same clone in a resident within the same facility without nasal carriage indicates possible intrafacility clonal dissemination. Conclusion: This study highlights persistent colonization with hospital‐associated MRSA and potential clonal transmission among residents of aged care facilities despite several courses of antibiotics. The predominance of the epidemic ST22 clone and high rates of multidrug resistance underscore the urgent need for targeted infection control, routine genomic surveillance, and antimicrobial stewardship in long‐term care settings to prevent MRSA dissemination.

Antimicrobial resistance (AMR) poses a global threat to public health. The excessive use of antibiotics significantly contributed to the rise of resistance. Recent evidence suggests that non-antibiotic medications (NAMs) also play a role in antimicrobial resistance development, although this aspect remains less explored and understood. This issue is particularly relevant in residential aged care facilities (RACFs) where both NAMs and antibiotics are frequently used, and AMR is prevalent. We investigated the propensity of NAMs that are commonly used in RACFs and contribute to polypharmacy including non-steroidal anti-inflammatory drugs (NSAIDs) such as ibuprofen and diclofenac, acetaminophen (antipyretic), metformin (glucose-lowering medication), atorvastatin (lipid-lowering agent), tramadol (opioid analgesic), temazepam (hypnotic), and pseudoephedrine (sympathomimetic) to promote bacterial antibiotic resistance by increasing the acquisition of mutations. Escherichia coli was exposed to different NAMs at their gut concentration, combined with ciprofloxacin and the mutation frequency was determined. Additionally, we explored the simultaneous effect of two NAMs as a starting point for studying polypharmacy. Ibuprofen and acetaminophen significantly increased mutation frequency, and conferred high levels of ciprofloxacin resistance, especially when E. coli was exposed to two NAMs. Whole genome sequencing revealed that these changes correlated with mutations in DNA gyrase GyrA, the multiple antibiotic resistance regulator, MarR, and the drug efflux pump expression suppressor, AcrR. Consequently, an increase in transcription of the acrA gene from the AcrAB-TolC drug efflux pump was observed. The combination of two NAMs increased the mutation rate. These multiple mutations caused the higher levels of ciprofloxacin resistance that were observed. Given the risk of polypharmacy to induce AMR, and the results observed in this study, the assessment NAMs in their ability to promote bacterial resistance warrants special attention in future studies into prescribing practices.

The COVID-19 pandemic coincided with a significant reduction in systemic antibacterial use in the community; however, antimicrobial use in residents of aged-care homes remains at a high level. What do these trends tells us, and what further work is required to reduce inappropriate antimicrobial use long term?

SUMMARY: The characterization of wild-type minimum inhibitory concentration (MIC) and zone diameter distributions with the setting of epidemiological cut-off values (ECOFFs or ECVs) provides a reference for the otherwise relative MIC values in the international system for antimicrobial susceptibility testing. Distributions of MIC values for a species and an agent follow a log-normal distribution, which in the absence of resistance mechanisms is monomodal and designated wild type (WT). The upper end of the WT distribution, the ECOFF, can be identified with statistical methods. In the presence of phenotypically detectable resistance, the distribution has at least one more mode (the non-WT), but despite this, the WT is most often identifiable using the same methods. The ECOFF provides the most sensitive measure of resistance development in a species against an agent. The WT and non-WT modes are independent of the organism´s response to treatment, but when the European Committee on Antimicrobial Susceptibility Testing (EUCAST) determines the clinical breakpoints, the committee avoids breakpoints that split WT distributions of target species. This is to avoid the poorer reproducibility of susceptibility categorization when breakpoints split major populations but also because the EUCAST has failed to identify different clinical outcomes for isolates with different MIC values inside the wild-type distribution. In laboratory practice, the ECOFF is used to screen for and exclude resistance and allows the comparison of resistance between systems with different breakpoints from different breakpoint organizations, breakpoints evolving over time, and different breakpoints between human and animal medicine. The EUCAST actively encourages colleagues to question MIC distributions as presented on the website ( https://www.eucast.org/mic_and_zone_distributions_and_ecoffs ) and to contribute MIC and inhibition zone diameter data.

High and often inappropriate antibiotic use has been documented for residential aged care facilities (RACFs). As a result, RACFs represent selective environments favoring the development of antimicrobial resistance (AMR). However, surveillance of the prevalence and scope of AMR in RACFs is limited. Here, wastewater-based epidemiology encompassing culture-based methods in combination with whole genome sequencing and metagenomics allowed for the in-depth analysis of the prevalence of antimicrobial-resistant Escherichia coli in two RACFs and one retirement facility. Wastewater was collected at five different time points over 18 months. From these, E. coli were isolated and assessed for phenotypic and genotypic resistance. The antimicrobial resistome of each wastewater sample was also determined. A comparison of facilities revealed a higher prevalence of AMR and multidrug-resistant E. coli observed in one RACF. The international high-risk E. coli clone, ST131, carrying CTX-M-like extended-spectrum beta-lactamases was exclusively isolated from this facility. A high proportion of these isolates were classified as belonging to phylogroups B2 and D, associated with virulent extra-intestinal E. coli infections. The resistome of this facility also revealed a higher prevalence of mobile resistance genes such as sul1 and sul2 , conferring sulfamethoxazole resistance, the plasmid-mediated quinolone-resistance gene qnrS , and qacEdelta1 that confers biocide resistance. High fluoroquinolone resistance rates were observed in all three sample sites despite measures in place limiting the use of this class of antibiotics. The findings of this study illustrate that RACFs are highly selective environments that require measures to limit AMR development, potentially through antimicrobial stewardship. IMPORTANCE: Antimicrobial resistance (AMR) is a global threat that imposes a heavy burden on our health and economy. Residential aged care facilities (RACFs), where frequent inappropriate antibiotic use creates a selective environment that promotes the development of bacterial resistance, significantly contribute to this problem. We used wastewater-based epidemiology to provide a holistic whole-facility assessment and comparison of antimicrobial resistance in two RACFs and a retirement village. Resistant Escherichia coli , a common and oftentimes problematic pathogen within RACFs, was isolated from the wastewater, and the phenotypic and genotypic AMR was determined for all isolates. We observed a high prevalence of an international high-risk clone, carrying an extended-spectrum beta-lactamase in one facility. Analysis of the entire resistome also revealed a greater number of mobile resistance genes in this facility. Finally, both facilities displayed high fluoroquinolone resistance rates—a worrying trend seen globally despite measures in place aimed at limiting their use.

Objectives: In 2016, The Royal College of Pathologists of Australasia (RCPA) initiated the formation of a working group comprising medical microbiologists to establish guidelines to assist Australian laboratories to implement selective and cascade reporting of antimicrobials—the first guidelines of this type in the world. Methods: A 2017 audit of antimicrobial reporting in Australian and New Zealand laboratories identified significant opportunities for improvement and standardization of selective reporting. Results: The first draft of the RCPA Selective Reporting Guidelines was circulated to all RCPA Microbiology fellows for feedback in August 2018 and the first version was published in February 2019. Subsequently, version two of the guidelines has recently been published in Australia, and New Zealand adapted these guidelines for formulation of their own national guidelines to accommodate local needs. Conclusions: Here we describe the processes, acceptance and challenges associated with the establishment of these guidelines and measurement of their impact.

The European Committee on Antimicrobial Susceptibility Testing (EUCAST) is an international susceptibility testing committee, organized by the European Society for Clinical Microbiology and Infectious Diseases (ESCMID) and functioning as the breakpoint advisory committee of the European Medicines Agency (EMA). The original remit of EUCAST was to harmonize European clinical breakpoints, but very soon, the activities expanded beyond the borders of Europe and included newly licensed agents in Europe.