Antimicrobial Susceptibility Testing Data Research Articles

Selection and Evaluation of Suitable Quality Control Strains for Meropenem Antimicrobial Susceptibility Testing through Preliminary External Quality Assessment

BackgroundQuality control (QC) of carbapenem susceptibility testing for Gram-negative bacteria faces challenges due to limited measuring ranges and the lack of suitable QC strains. This study aimed to select and evaluate QC strains for meropenem antimicrobial susceptibility testing (AST) through a pilot external quality assessment (EQA). MethodsCandidate QC strains for meropenem AST were selected based on primary AST data and genomic information from the Japan Antimicrobial Resistant Bacterial Bank. Phenotype stability was verified through serial passaging and MIC comparison with original strains. The validated broth microdilution method was used to determine the target MIC value in a pilot EQA involving 47 clinical laboratories in Japan using ten different AST methods. ResultsTwo strains, Citrobacter freundii JBBDAJB-19-0032 (Strain-A) and Enterobacter hormaechei subsp. steigerwaltii JBEBAAB-19-0102 (Strain-B), both carrying blaIMP-1, were selected as candidate QC strains. The meropenem MICs for Strain-A and Strain-B were 4 mg/L and 2 mg/L, respectively. In the pilot EQA, 43 laboratories reported appropriate results for Strain-A and 40 laboratories reported appropriate results for Strain-B. The MIC range was 2-8 mg/L for Strain-A and 1-4 mg/L for Strain-B. However, 19 and 12 laboratories, respectively, reported out-of-range MICs using AST plates on the MicroScan WalkAway (Beckman Coulter). Inappropriate results were reported by four and seven laboratories, respectively, using common methods for Strain-A and Strain-B, respectively. ConclusionsThe candidate QC strains selected for this study are suitable for meropenem AST EQA, except when the measuring range of certain methods does not match their QC range.

Integrating whole genome sequencing and machine learning for predicting antimicrobial resistance in critical pathogens: a systematic review of antimicrobial susceptibility tests.

Infections caused by antibiotic-resistant bacteria pose a major challenge to modern healthcare. This systematic review evaluates the efficacy of machine learning (ML) approaches in predicting antimicrobial resistance (AMR) in critical pathogens (CP), considering Whole Genome Sequencing (WGS) and antimicrobial susceptibility testing (AST). The search covered databases including PubMed/MEDLINE, EMBASE, Web of Science, SCOPUS, and SCIELO, from their inception until June 2024. The review protocol was officially registered on PROSPERO (CRD42024543099). The review included 26 papers, analyzing data from 104,141 microbial samples. Random Forest (RF), XGBoost, and logistic regression (LR) emerged as the top-performing models, with mean Area Under the Receiver Operating Characteristic (AUC) values of 0.89, 0.87, and 0.87, respectively. RF showed superior performance with AUC values ranging from 0.66 to 0.97, while XGBoost and LR showed similar performance with AUC values ranging from 0.83 to 0.91 and 0.76 to 0.96, respectively. Most studies indicate that integrating WGS and AST data into ML models enhances predictive performance, improves antibiotic stewardship, and provides valuable clinical decision support. ML shows significant promise for predicting AMR by integrating WGS and AST data in CP. Standardized guidelines are needed to ensure consistency in future research.

Prevalence and distribution of carbapenem-resistant Enterobacterales in companion animals: A nationwide study in the United States using commercial laboratory data.

Carbapenem-resistant Enterobacterales (CRE) are a concern in both human and animal medicine globally. Despite extensive research in humans, limited data exist on CRE in companion animals, with a lack of nationwide prevalence estimates. To assess the occurrence and trends of CRE in cats and dogs across the United States by analyzing 4 years of commercial antimicrobial susceptibility testing (AST) data. Between 2019 and 2022, 477 426 ASTs were conducted on Enterobacterales isolates against imipenem. Isolates were derived from 379 598 dogs and 97 828 cats. Animal origin was not disclosed. In this retrospective study, antimicrobial susceptibility test data from IDEXX Laboratories were analyzed. Analysis included resistance estimations to imipenem stratified by sampling site, an assessment of resistance patterns over time and location, and the application of space-time cluster analysis to identify potential outbreaks. Antibiograms were produced for carbapenem-resistant isolates. Susceptibility to imipenem was high, at 98.86%. Temporal analysis indicated stability in susceptibility, with an unexplained reduction in susceptible isolates in June 2019. Spatial analysis identified 2 high-risk clusters along the Western Coast (relative risk [RR]: 23.26; P < .001) and in Texas (RR: 10.72; P < .001) in that month. Three other clusters were found, in Missouri (RR: 39.55; P = .038), Florida (RR: 4.53; P < .001), and New York (RR: 9.20; P < .001). CRE are present at a low prevalence in dogs and cats across the United States. Variations in prevalence across patient-level and environmental factors highlight the need for tailored stewardship programs.

Evaluation of minimum inhibitory concentration data in National Healthcare Safety Network’s Antimicrobial Resistance Option

Background: Clinical laboratories perform antimicrobial susceptibility testing (AST) primarily by determining the minimum inhibitory concentration (MIC) for an organism–antimicrobial combination and comparing it with established breakpoints to generate interpretations. The Antimicrobial Resistance (AR) Option of CDC’s National Healthcare Safety Network (NHSN) permits hospitals to submit clinical isolate AST data, including test values and interpretations (Figure 1). The Clinical and Laboratory Standards Institute (CLSI) periodically revises breakpoints, but their adoption by clinical laboratories can be delayed, potentially affecting national AR surveillance data accuracy. Using MIC values, instead of clinical laboratory interpretations, can improve surveillance data accuracy and overcome misclassification due to delayed uptake of revised breakpoints. We evaluated the completeness and consistency of MIC data submitted to the AR Option for fluoroquinolone-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus (MRSA). Methods: We included data on (1) E. coli isolates tested for ciprofloxacin or levofloxacin susceptibility and (2) S. aureus isolates tested for oxacillin or cefoxitin susceptibility in 2022 and reported by October 1, 2023. We evaluated completeness among isolates reporting a final AST interpretation as the proportion of isolates reporting both an MIC value and interpretation. We evaluated consistency using percent agreement comparing the laboratory’s MIC interpretation (classified as resistant or not resistant) with the interpretation derived by applying 2021 CLSI M100 breakpoints to the MIC values reported for the same isolate. Results: Across 974 hospitals, fluoroquinolone MICs and interpretations were reported for 172,012/393,359 E. coli isolates (43.7%), and oxacillin or cefoxitin MICs and interpretations were reported for 38,519/79,372 S. aureus isolates (48.5%). Of isolates with both MIC values and interpretations, 157,902 (91.8%) E. coli and 7,808(79.7%) S. aureus isolates had MICs that could be classified as resistant or non-resistant (i.e., intermediate or susceptible) per CLSI breakpoints (Figure 2). The remaining MICs were unclassifiable (reported as intervals spanning CLSI breakpoints, e.g., ≤1 μg/ml ciprofloxacin for E. coli). Among isolates with classifiable MICs, the agreement between the clinical laboratory and CLSI-based interpretation was 99.5% for E. coli and 99.7% for S. aureus. Conclusion: MIC values and interpretations were available for

Uptake of Revised CLSI Breakpoints and Potential Impact among Hospitals Reporting to The NHSN AR Option, 2022

Background: Antimicrobial susceptibility testing (AST) is critical for detecting antimicrobial resistance (AR) and guiding antimicrobial treatment. The Clinical and Laboratory Standards Institute (CLSI) regularly publishes and revises breakpoints to guide the interpretation of AST results. In 2010–2019, CLSI has lowered many breakpoints for Enterobacterales and Pseudomonas aeruginosa. Timely implementation of updated breakpoints can vary across hospital laboratories, leading to shifts in the interpretation of AST results. This issue is a potential threat to the estimation of national prevalence estimates for AR and limits the comparability of AR data across hospitals. Hospitals submit AST data with clinical laboratory interpretations to the AR Option of CDC’s National Healthcare Safety Network (NHSN). NHSN tracks whether a hospital adopted the revised CLSI breakpoints for six organism-antimicrobial combinations involving AR phenotypes commonly associated with healthcare associated infections through hospital self-reporting status into a structured survey — 2022 NHSN Annual Hospital Survey (Table). For this analysis, we describe the uptake of revised CLSI breakpoints and compare cumulative antibiograms among hospitals that used various breakpoints. Methods: We included hospitals that completed the 2022 NHSN annual survey and submitted data to the NHSN AR Option for at least 9 months in 2022 by November 1, 2023. The percentage of hospitals that implemented CLSI breakpoints, published during 2010–2019, were determined for combinations of antibiotic class, organism, and CLSI revision year (Table). We calculated percent resistance (%R) as the number of isolates meeting AR phenotype definitions divided by the total number of Isolates tested for the following phenotypes: carbapenem-resistant Enterobacterales (CRE) which included E. coli, Klebsiella, and Enterobacter species; extended-spectrum cephalosporin-resistant Enterobacterales (ESC); carbapenem-non-susceptible P. aeruginosa; fluoroquinolone-resistant P. aeruginosa; and fluoroquinolone-resistant Enterobacterales. Results: Among the 741 hospitals included, 75%–93% implemented any of the six revised CLSI breakpoints (Table). The %R was higher among isolates from hospitals that adopted revised breakpoints compared to those that did not (p &lt; 0 .0001). The largest difference was observed for carbapenem-non-susceptible P. aeruginosa (14.91% vs 10.11%). Conclusions: The uptake of revised CLSI breakpoints varied across hospitals, organism-antimicrobial combinations, and CLSI versions. This analysis indicates that the prevalence of AR for corresponding phenotypes could be underestimated if data from hospitals using higher, outdated breakpoints are included. It is important for NHSN to continue tracking breakpoints used in individual hospitals and encourage hospitals to report complete data on the original AST results, such as MIC, to optimize the accuracy of national AR surveillance.

A five-year retrospective antibiogram review in the paediatric burns unit at a tertiary South African Hospital

BackgroundThere is a global concern regarding increasing colonization and/or infection of paediatric burns patients with multi-drug-resistant organisms, especially in Africa. Surveillance of antimicrobial resistant patterns enables clinicians to opt for the most appropriate empiric antimicrobial agent according to the unit’s susceptibility profile. ObjectiveThis study sought to compile unit-specific antibiograms comparing the organism prevalence and their antimicrobial resistance trends in the paediatric burns unit, Chris Hani Baragwanath Academic Hospital (CHBAH) from January 2015 to December 2019. MethodsA retrospective, laboratory-based review was conducted of bacterial and fungal isolates including antimicrobial susceptibility testing (AST) data from blood cultures and tissue samples. Enterobacterales, non-fermenters, gram-positive organisms, and yeasts were analysed as a percentage of total positive blood cultures comparing 2015–2017 to 2018–2019 data. Analysis of antimicrobial resistance trends was performed for extended-spectrum beta-lactamases (ESBLs), carbapenem-resistant Enterobacterales (CRE), extensively-drug-resistant (XDR) Acinetobacter baumannii, and meticillin-resistant Staphylococcus aureus (MRSA) for the years 2015, 2017, and 2019. ResultsA total of 1243 blood culture isolates were studied with A.baumannii (208/1243;17 %), coagulase negative staphylococci (141/1243; 11 %) and Candida auris (53/1243; 4 %) representing the predominant gram-negative bacteria, gram-positive bacteria, and yeast, respectively. A significant decrease in ESBLs (p = 0.00) was noted with a rise in CREs (p = 0.00) during the study period. Majority of the A. baumannii were XDR (≥77 %) despite an appreciable decrease. A notable decrease in MRSA (p = 0.00) isolates was observed. Pseudomonas aeruginosa (72/275; 26 %) was the leading organism recovered from a total of 275 tissue isolates. ConclusionThe results of this study encourage review of the current antimicrobial choices in the unit for empiric antibacterial cover. Due to the low numbers of yeasts, we cannot comment on the institution of early antifungal strategies. We support reinforced infection prevention and control practices as well as antimicrobial stewardship initiatives.

Practice of standardization of CLSI M45 A3 antimicrobial susceptibility testing of Infrequently Isolated or Fastidious Bacteria strains isolated from blood specimens in Guangdong Province 2017-2021.

The concentration of antimicrobial agents in environments like water and food has increased rapidly, which led to a rapid increase in antimicrobial resistance levels in the environment. Monitoring of bacterial resistance levels is considered as a necessary means to control the bacterial resistance. Reference standards are critical for antimicrobial susceptibility testing. CLSI M45 A3 standard defines pathogenic microorganisms that cause infections less frequently than those covered by CLSI M02, M07, and M100 as Infrequently Isolated or Fastidious Bacteria and specifies antimicrobial susceptibility testing methods. Our study investigated the epidemiology and antimicrobial susceptibility testing data of Infrequently Isolated or Fastidious Bacteria strains isolated from blood specimens in 70 hospitals in Guangdong Province between 2017 and 2021. We defined testing methods other than those specified in CLSI M45 A3 as "Non-Standardized." The proportion of standardized antimicrobial susceptibility testing for penicillin increased significantly (Corynebacterium spp. 17.4% vs. 50.0% p < 0.05; Micrococcus spp. 50.0% vs. 77.8% p < 0.05; Abiotrophia spp. and Granulicatella spp. 21.4% vs. 90.9% p < 0.001), while for cefotaxime (Corynebacterium spp. 0.0% vs. 45.2% p < 0.05; Abiotrophia spp. and Granulicatella spp. 0.0% vs. 14.3% p = 0.515) and vancomycin increased finitely. Non-standardized methods were used for all other antimicrobials. Due to limitations in the economic and medical environment, some clinical laboratories are unable to fully comply with CLSI M45 A3 standard. We recommend that CLSI should add breakpoints for disk diffusion method to improve the standardization of antimicrobial susceptibility testing.

The modern alchemy of clinical pathology: turning the output of microbiology laboratory operations into gold.

The clinical microbiology laboratory generates a huge amount of high-quality data that play a vital role in clinical care. With proper extraction, cleaning, analysis, and validation pipelines, these data can serve multiple other purposes that include supporting laboratory operations, understanding local epidemiology, informing hospital-specific policies, and public health surveillance. In this review, I use one of the core activities of the microbiology laboratory, antimicrobial susceptibility testing (AST), to illustrate several potential applications of next-generation data analytics. The first involves continuous monitoring of commercial AST systems using comparisons of minimum inhibitory concentration (MIC) distributions over time to trigger re-verification when statistically significant differences are detected. An extension of this is temporal analysis of joint MIC distributions to understand performance for multidrug-resistant organisms. More sophisticated analyses involve linking microbiologic data to clinical metadata to gain insight into the clinical validity of AST data and to inform treatment policies. The elements of a robust, validated analysis engine using routine data streams already exist, but numerous challenges must be overcome to make it a reality. Most importantly, it will require the sustained collaboration and advocacy of hospital leadership, microbiologists, clinicians, antimicrobial stewardship, data scientists, and regulatory agencies. Though no small feat, achieving this vision would provide an important resource for microbiology laboratories facing a rapidly evolving practice landscape and further cement its role as an integral part of a learning health system.

Antimicrobial susceptibility testing data analysis over 3 years at the Yaoundé General Hospital, Cameroon.

Antimicrobial resistance (AMR) is a major health concern with high rates in low-income countries. Bacteriology laboratories sustain the fight against AMR by providing antibiotic susceptibility testing (AST) results to ensure appropriate therapies. These laboratories generate a lot of data, which are usually used for prospective interventions. Our study conducted in a lower-middle-income hospital setting aimed to describe the profile of bacteria isolated from the specimens received over 3 years, assess their susceptibility profile and identify potential gaps or area of improvement from the analysis of our data. Monthly data were retrieved from registers for all specimens received between January 2020 until December 2022. Data were compiled and analysed using the R and WHONET software. Out of 3582 specimens received, 797 were culture positive (22.3%). Escherichia coli and Klebsiella pneumoniae were frequently isolated (30.5% and 24.2%, respectively). AST results analysis showed high resistance of Gram-negative bacteria to penams and cephems, whereas low resistance was observed to carbapenems. Susceptibility to antibiotics based on the AWaRe antibiotic classification was variable. The bacteriological profile in the various types of specimen was established and rational information to design a therapeutic protocol adapted to our hospital setting was obtained. AST results may not only be used for prospective guidance for treatment, but rather cumulative data analysis can contribute to design effective antibiotic prescriptions and improve general practices at the laboratory. This is, however, dependent on a good record-keeping, standardization of practices and collaboration between clinicians and laboratory scientists.

Assessing stakeholders' opinions on sharing antimicrobial susceptibility testing data from animals is key to developing a centralized database and dashboard tool.

To present, analyze, and discuss stakeholders' opinions regarding sharing antimicrobial susceptibility testing (AST) data from animals into a centralized database and dashboard tool that would collect, aggregate, store, and analyze this type of data from veterinary diagnostic laboratories (VDLs) across the country. 1 in-person focus group (9 participants), 9 virtual focus groups (49 participants), and online pre- and postmeeting surveys (76 and 35 participants, respectively). Focus groups and surveys were conducted to assess the opinions of veterinarians, producers, researchers, diagnosticians, and government officials. A strong majority of stakeholders recognize AMR as a serious concern for both human and animal health and see several benefits in establishing a centralized AMR database; however, several concerns were raised associated with data confidentiality, security, curation, and harmonization. In the interest of alleviating those concerns, among other items, stakeholders suggested education and training of data users, providers, and the public in addition to assuring strong data confidentiality protections. Stakeholder engagement is a critical component of all stages of development, implementation, and utilization of an AMR database and dashboard tool that could be used to inform antimicrobial stewardship in veterinary medicine. This assessment of stakeholders' needs and concerns can be used to help guide future recommendations for data legal protections as well as a data confidentiality and security framework. Maintaining open communication on data usage, storage, and security as well as involvement and education of data providers, users, and the public will remain key to enabling development of an AMR database and dashboard tool for domesticated animals.

Predicting Antibiotic Tolerance in hvKP and cKP Respiratory Infections Through Biofilm Formation Analysis and Its Resistance Implications.

Respiratory infections are a major global health concern, with Klebsiella pneumoniae standing out due to its evolving antibiotic resistance. This study compares the resistance profiles of hypervirulent Klebsiella pneumoniae (hvKP) and classical Klebsiella pneumoniae (cKP), aiming to shed light on their clinical implications. We analyzed 86 cases, comprising 42 hvKP and 44 cKP strains, using comprehensive antimicrobial susceptibility testing and clinical data evaluation to assess antibiotic tolerance and resistance mechanisms. Our findings reveal distinct resistance patterns between hvKP and cKP, highlighting the role of chromosomal mutations and plasmid-mediated gene transfer in conferring antibiotic resistance. Notably, hvKP strains exhibited unique resistance trends, including the production of extended-spectrum β-lactamases (ESBLs) and carbapenemases, differing from those of cKP. This research underscores the importance of continuous surveillance and the development of targeted therapies against antibiotic-resistant Klebsiella pneumoniae. It emphasizes the critical need for judicious antibiotic use and novel therapeutic approaches to combat respiratory infections caused by these increasingly resistant pathogens.

Effective Stakeholder Engagement for Collation, Analysis and Expansion of Antimicrobial Resistance (AMR) Data: A CAPTURA Experience.

An effective implementation of antimicrobial resistance (AMR) surveillance projects requires sustainable and multidisciplinary engagement with stakeholders from various backgrounds, interests and aims. The "Capturing Data on Antimicrobial resistance Patterns and Trends in Use in Regions of Asia" (CAPTURA) project, funded by the Fleming Fund, initially targeted 12 countries in South Asia (SA) and Southeast Asia (SEA) to "expand the volume of historical and current data on AMR and antimicrobial usage" and support local agencies through capacity building activities. In this article, we focus on early stakeholder engagement activities and present overall statistics on AMR data collated from 72 laboratories across seven countries. This included 2.3 million records of antimicrobial susceptibility testing (AST) data, which were curated, analyzed, and shared back to the facilities for informed decision making. Approximately 98% of the data collated by CAPTURA originated from laboratories based in SA countries. Furthermore, country-wide data were analyzed to identify commonly reported pathogens in each country, followed by descriptions of AST practices and multidrug-resistant (MDR) pathogens. Overall, we found meager adherence to standard guidelines to perform and record AST results, and a significant number of MDR pathogens were reported. We conclude that close collaboration with the existing national mechanisms for identifying AMR data sources was crucial for the project's success. Although we show a vast retrospective dataset on AMR is available for data sharing in Asia, there remain critical gaps in data generation/management practice and analysis capacity for AMR data at most facilities.

Antimicrobial Susceptibility Patterns Among a Large, Nationwide Cohort of Chryseobacterium Species Clinical Isolates

Abstract Background Chryseobacterium species are ubiquitous in nature that can be found in soil, water, sinks, and medical devices. They have been implicated in various infections including ventilator-associated pneumonia, catheter-related bloodstream infections (CRBSI), skin and soft tissue infections, and meningitis. C. indologenes has been shown to possess an extended-spectrum beta-lactamase (ESBL) and metallo-β-lactamase (MBL) that render it resistant to most antibiotics. Antimicrobial susceptibility testing (AST) data are required to help clinicians choose effective empiric antibiotics and to investigate potential resistance mechanisms. Methods Chryseobacterium spp. identification was determined prior to submission by client laboratories or performed in our laboratory by MALDI-TOF (Bruker Biotyper) or 16S rRNA gene sequencing. AST was performed on Chryseobacterium species isolates received from across the United States between April 2004 and December 2018. AST was performed using custom-made broth microdilution panels, and minimal inhibitory concentrations (MICs) were interpreted using CLSI M100 MIC breakpoints for non-Enterobacterales organisms. Isolates from a range of clinical specimens including blood, respiratory, wound, tissue, bone, and body fluids were included. Quality control was performed using Escherichia coli ATCC 25922 and Pseudomonas aeruginosa ATCC 27853. Results were included only if the QC values were within range. The MIC50, MIC90, and MIC ranges for antimicrobials for frequently tested Chryseobacterium species were determined. Results AST was completed for 245 Chryseobacterium species clinical isolates, and the most frequently tested species were C. gleum/ indologenes (n = 78), C. hominis (n = 25), C. taklimakanense (n = 14), C. anthropi/ haifense (n = 12), C. arthrospharae (n = 12), C. bernardetii/jejuense (n = 3), C. pallidum (n = 3), and C. solincola/treverense (n = 3). 84 isolates were unable to be identified to species level, and were grouped as “Chryseobacterium spp.” Regarding susceptibility, across all Chryseobacterium species, the antibiotics with the most activity included minocycline (97.8%), trimethoprim-sulfamethoxazole (TMP-SMX; 95.5%), levofloxacin (92.3%), and ciprofloxacin (82.8%). Comparing the β-lactams, piperacillin-tazobactam had the most activity (59.7%), whereas ceftazidime (42.2%), cefepime (44.3%), meropenem (41.2%), and imipenem (46.3%) had similar low activity. The highest resistance rates were found for tobramycin (96%), aztreonam (94.6%), and gentamicin (62.7%). Among the Chryseobacterium isolates, certain species were found to be largely pan-susceptible, including C. anthropic/haifense, C. hominis, and C. taklimakanense. Conclusions Chryseobacterium species display significant resistance against β-lactam antibiotics, which are often used for empiric therapy. Minocycline, TMP-SMX, and fluoroquinolones have the most activity against Chryseobacterium species clinical isolates.

Comparison of carbapenem-susceptible and carbapenem-resistant Enterobacterales at nine sites in the USA, 2013-2016: a resource for antimicrobial resistance investigators.

Carbapenem-resistant Enterobacterales (CRE) are an urgent public health threat. Genomic sequencing is an important tool for investigating CRE. Through the Division of Healthcare Quality Promotion Sentinel Surveillance system, we collected CRE and carbapenem-susceptible Enterobacterales (CSE) from nine clinical laboratories in the USA from 2013 to 2016 and analysed both phenotypic and genomic sequencing data for 680 isolates. We describe the molecular epidemiology and antimicrobial susceptibility testing (AST) data of this collection of isolates. We also performed a phenotype-genotype correlation for the carbapenems and evaluated the presence of virulence genes in Klebsiella pneumoniae complex isolates. These AST and genomic sequencing data can be used to compare and contrast CRE and CSE at these sites and serve as a resource for the antimicrobial resistance research community.

Nocardia species distribution and antimicrobial susceptibility within Australia.

Nocardia is a ubiquitous saprophyte capable of causing human disease. Disease is primarily respiratory or cutaneous, usually acquired via inhalation or inoculation. Under the influence of environmental and host factors, Nocardia incidence and species distribution demonstrate geographical variation. To examine for differences in Nocardia incidence within Western Australia (WA) and analyse species distribution in the context of prior published studies. To analyse antibiogram data from a nationwide passive antimicrobial resistance surveillance program. Retrospective extraction of laboratory data for Western Australian Nocardia isolates over a 21-year period. Analysis of Nocardia antimicrobial susceptibility testing data submitted to the Australian Passive Antimicrobial Resistance Surveillance (APAS) program between 2005 and 2022. Nine hundred sixty WA isolates were identified, giving an annual incidence of 3.03 per 100 000 population with apparent latitudinal variation. The four most common species identified within WA and amongst APAS isolates were N. nova, N. cyriacigeorgica, N. brasiliensis and N. farcinica. APAS data demonstrated that all species exhibited high rates of susceptibility to linezolid (100%) and trimethoprim-sulfamethoxazole (98%). Amikacin (>90% susceptibility for all species except N. transvalensis) was the next most active parenteral agent, superior to both carbapenems and third-generation cephalosporins. Susceptibility to oral antimicrobials (other than linezolid) demonstrated significant interspecies variation. We demonstrate geographical variation in the distribution of Nocardia incidence. Four species predominate in the Australian setting, and nationwide data confirm a high in vitro susceptibility to trimethoprim-sulphamethoxazole and linezolid, justifying their ongoing role as part of first-line empiric therapy.

Benefits and challenges of creating veterinary antibiograms for empiric antimicrobial selection in support of antimicrobial stewardship and advancement of one-health goals.

Antibiograms are important tools for antimicrobial stewardship that are often underutilized in veterinary medicine. Antibiograms summarize cumulative antimicrobial susceptibility testing (AST) data for specific pathogens over a defined time period; in veterinary medicine, they are often stratified by host species and site of infection. They can aid practitioners with empiric therapy choices and assessment of antimicrobial resistance trends within a population in support of one-health goals for antimicrobial stewardship. For optimal application, consideration must be given to the number of isolates used, the timeframe of sample collection, laboratory analytical methodology, and the patient population contributing to the data (eg, treatment history, geographic region, and production type). There are several limitations to veterinary antibiograms, including a lack of breakpoint availability for bacterial species, a lack of standardization of laboratory methodology and technology for culture and AST, and a lack of funding to staff veterinary diagnostic laboratories at a level that supports antibiogram development and education. It is vital that veterinarians who use antibiograms understand how to apply them in practice and receive relevant information pertaining to the data to utilize the most appropriate antibiogram for their patients. This paper explores the benefits and challenges of developing and using veterinary antibiograms and proposes strategies to enhance their applicability and accuracy. Further detail regarding the application of veterinary antibiograms by privately practicing clinicians is addressed in the companion Currents in One Health article by Lorenz et al (JAVMA, September 2023).

Analysis of cumulative antibiogram reports in intensive care units at an Egyptian University Hospital

BackgroundInstitutions must have access to antibiograms to monitor changes in antimicrobial resistance and direct empirical antibiotic therapy. The first facility-specific cumulative antibiogram was launched in the ICU in 2019. Consequently, many antibiogram-operation-related actions have been adopted in the institution based on reported data. This study aimed to analyze the cumulative antibiogram reports for multiple intensive care units (ICUs) for 2020, and compare the antimicrobial susceptibility testing (AST) patterns between the 2019 and 2020 years in an academic medical center. MethodsThis cross-sectional study was performed of routine bacterial culture and AST data extracted from a laboratory information system in a 2252-bed capacity hospital. Only the first diagnostic isolate of a given species per patient per year was included in the study. Interpretation and reporting were done in accordance with the applicable Clinical and Laboratory Standards Institute and European Committee on Antimicrobial Susceptibility Testing guidelines. ResultsOf the 46,791 clinical isolates, the Gram-negative bacilli isolation rate witnessed a significant increase: 35,670 isolates in 2020 versus. 33,652 isolates in 2019. Klebsiella pneumoniae showed a statistically significant increase, mainly in pediatric, emergency, and cardiothoracic ICUs (p < 0.001). Neonatal and pediatric ICUs showed statistically significant increases in Pseudomonas aeruginosa and Proteus mirabilis isolates (p < 0.001). A statistically significant decrease was noted in the prevalence of Acinetobacter, Escherichia coli, Burkholderia cepacia, and Enterobacter cloacae. The sensitivities of K. pneumoniae and E. coli to imipenem and tigecycline significantly improved (p < 0.001). The sensitivity to colistin was significantly decreased (p < 0.001). The sensitivity of P. aeruginosa isolates to colistin and carbapenems was improved (p < 0.001). We reported a statistically significant decrease in all Gram-positive cocci (11,121 in 2020 versus. 11,528 in 2019). Staphylococcus aureus showed a statistically significant increase (p < 0.001), particularly in the medical ICU. ConclusionThe high susceptibility rates of Enterobacteriaceae toward colistin and tigecycline, should be cautiously considered in empiric therapy while looking for alternatives. The majority of isolates of Gram-positive cocci were coagulase negative staphylococci (CONS), we still need to confirm whether they are true pathogens or commensals before considering anti-staphylococcal agents in the empirical therapy. We underscored some corrective actions that might have improved the susceptibility rates, such as antibiotic cycling

Clinical and Genomic Characteristics of Carbapenem-Resistant Klebsiella pneumoniae Isolates from Acute Pancreatitis with Infection in China.

The aim of the study was to provide a clinical treatment reference for acute pancreatitis (AP) with infection, we analyzed the clinical and genomic characteristic of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates from AP with infection in China. Our clinical database was retrospectively analyzed with focus on the carbapenem-resistant characteristics among AP with infection in our Intensive Care Unit (ICU). Whole-genome sequencing (WGS) was used to analyze the antibiotic resistance gene, and antimicrobial susceptibility testing (AST) was performed to study the relevant phenotype in vitro. The CRISPR-Cas9 system was used to verify the relevant phenotype. Based on 2,211 AST data of 627 AP patients with infection, CRKP had the highest proportion among carbapenem-resistant Enterobacteriaceae (CRE), at 37.8% for imipenem and 45.3% for meropenem. WGS revealed key β-lactamase genes, specifically blaCTX-M-15, blaCTX-M-65, blaKPC-2, blaLAP-2, blaNDM-5, blaTEM-181, blaOXA-1, and blaSHV. A total of 31.3% of CRKP were NDM-5-KPC-2-producing strains, and NDM-5-producing CRKP was resistant to imipenem/meropenem combined with avibactam, with an MIC of 512 mg/L. In addition, after knocking out blaKPC-2 and blaNDM-5, NDM-5-producing and KPC-2-producing CRKP had the same resistance level to imipenem/ meropenem. We first provided key insights into the clinical and genomic characteristic of CRKP in AP with infection and then made it clear that NDM-5 and KPC-2 had the same resistance level to carbapenems.

Risk Factors and Molecular Mechanism of Polymyxin B Resistance in Carbapenem-Resistant Klebsiella pneumoniae Isolates from a Tertiary Hospital in Fujian, China.

The emergence of polymyxin B resistance among carbapenem-resistant Klebsiella pneumoniae (CRKP) causes clinical treatment to be more difficult. We aimed to investigate the risk factors and resistance mechanisms in the polymyxin resistant CRKP (PR-CRKP) strains. From January 2021 to January 2022, 239 CRKP strains were selected, all of which were analyzed using antimicrobial susceptibility testing and clinical data. Polymerase chain reaction (PCR) was performed for the detection of resistance genes. RT-qPCR was used to quantify transcriptional levels of polymyxin resistance genes. Risk factors for polymyxin B resistant isolates were identified by logistic regression analysis. The resistance rate of polymyxin B was 5.02%. In all CRKP strains, 41.84% came from the ICU. The percentage of carbapenemase producing strains was 93.72%. The main carbapenem resistance gene was blaKPC (90.79%). In the 12 strains of PR-CRKP screened, pmrB and pmrK were overexpressed in all samples which were linked with polymyxin B resistance. Multivariate analysis showed that coronary heart disease may be an independent risk factor predisposing patients to polymyxin B resistance. We determine the multifaceted mechanism and risk factors of polymyxin B resistance in CRKP. Polymyxin resistance is a complex and changing problem, and more research is required.

Towards a Harmonized Terminology: A Glossary for Biocide Susceptibility Testing.

Disinfection is a key strategy to reduce the burden of infections. The contact of bacteria to biocides-the active substances of disinfectants-has been linked to bacterial adaptation and the development of antimicrobial resistance. Currently, there is no scientific consensus on whether the excessive use of biocides contributes to the emergence and spread of multidrug resistant bacteria. The comprehensive analysis of available data remains a challenge because neither uniform test procedures nor standardized interpretive criteria nor harmonized terms are available to describe altered bacterial susceptibility to biocides. In our review, we investigated the variety of criteria and the diversity of terms applied to interpret findings in original studies performing biocide susceptibility testing (BST) of field isolates. An additional analysis of reviews summarizing the knowledge of individual studies on altered biocide susceptibility provided insights into currently available broader concepts for data interpretation. Both approaches pointed out the urgent need for standardization. We, therefore, propose that the well-established and approved concepts for interpretation of antimicrobial susceptibility testing data should serve as a role model to evaluate biocide resistance mechanisms on a single cell level. Furthermore, we emphasize the adaptations necessary to acknowledge the specific needs for the evaluation of BST data. Our approach might help to increase scientific awareness and acceptance.