Susceptibility Testing Data Research Articles

Routinely available antimicrobial susceptibility information can be used to increase the efficiency of screening for carbapenemase-producing Enterobacteriaceae.

Introduction. Increased carbapenem resistance is often caused by carbapenemase production.Aim. The objective of our study was to assess which antibiotic susceptibility patterns, as tested by automated systems, are highly associated with the absence of carbapenemase production in Enterobacteriaceae isolates, and could therefore be used as a screening tool.Methodology. Routine antibiotic susceptibility testing data from 42 medical microbiology laboratories in the Netherlands in the period between January 2011 and June 2017 were obtained from the national antimicrobial resistance surveillance programme. Data on Enterobacteriaceae isolates that had an elevated minimum inhibitory concentration (MIC) for carbapenems (meropenem >0.25 mg l-1 or imipenem >1.0 mg l-1) were selected and subjected to phenotypic or genotypic carbapenemase production testing. Routinely available amoxicillin/clavulanic acid, piperacillin/tazobactam, cefuroxime and ceftriaxone/cefotaxime susceptibilities were studied in relation to carbapenemase production by calculating the negative predictive value.Results. No evidence for carbapenemase-producing Enterobacteriaceae (CPE) was found in 767 of 1007 (76 %) isolates. The negative predictive value was highest for amoxicillin/clavulanic acid (99.6 %) and piperacillin/tazobactam (98.8 %).Conclusion. Enterobacteriaceae isolates with elevated carbapenem MICs that are susceptible to amoxicillin/clavulanic acid or piperacillin/tazobactam are unlikely to be carbapenemase producers. Preselection based on this susceptibility pattern may lead to increased laboratory efficiency and reduction of costs. Whether this is also true for countries with a different distribution of CPE species and types or a higher prevalence of CPE needs to be studied.

Isolates, antimicrobial susceptibility profiles and multidrug resistance of bacteria cultured from samples collected from sheep in New Zealand (2003–2016)

ABSTRACT Aim: To describe the common species, antimicrobial susceptibility and multidrug resistance (MDR) of bacteria cultured from samples submitted to veterinary diagnostic laboratories from sheep in New Zealand between 2003 and 2016. Methods: Bacterial culture and antimicrobial susceptibility test data from June 2003 to March 2016 for animals identified as sheep were obtained from two commercial veterinary diagnostic laboratories in New Zealand. Submission information included animal signalment, geographic origin, specimen description, the organisms cultured, and where available, antimicrobial susceptibilities of the isolates. MDR was defined as any isolate with resistance to ≥3 antimicrobial classes. Results: There were 1,971 unique laboratory submissions, yielding 2,188 isolates. Of the 1,971 submissions, the most commonly represented breeds were Romney (933; 47.3%), Romney cross (264; 13.4%), and Coopworth (197; 10.0%), and there were more submissions from females (1,006; 51.0%) than males (184; 9.3%). Most submissions were from Canterbury (549; 27.9%), Southland (471; 23.9%), and Manawatu-Wanganui (272; 13.8%) regions. Other signalment data were inconsistently described. Submitted samples most commonly originated from the gastrointestinal tract (852; 43.2%), faeces (378; 12.1%), or liver (146; 7.4%). Of the 2,188 isolates, 1,771 (80.9%) were identified by species and 247 (11.4%) by genus, with the most common isolates being Salmonella spp. (880; 40.2%), Campylobacter spp. (408; 18.6%), Listeria spp. (140; 6.4%) and Yersinia spp. (113; 5.2%). Susceptibility results were available for 117/2,188 (5.3%) isolates from 51/1,971 (2.6%) submissions. No antimicrobial susceptibility data were available for Salmonella spp., Campylobacter spp., Listeria spp. or Yersinia spp. Overall for the isolates tested, susceptibility to the fluoroquinolones and tetracyclines was greatest, and MDR was found in 24/117 (20.5%) isolates. MDR was a more frequent finding for Enterococcus spp., Bacillus spp., and Proteus mirabilis, but was infrequent in isolates of Staphylococcus aureus, alpha-haemolytic streptococci, Escherichia coli or Enterobacter spp. Conclusions and clinical relevance: This is the first report on antimicrobial susceptibility and MDR for isolates from laboratory submissions from sheep in New Zealand. The low numbers of isolates submitted for antimicrobial susceptibility testing during the period studied mean that these findings provide limited insights into antimicrobial resistance in this population, and highlight the need to address significant gaps in our understanding of why veterinarians do not more frequently submit samples from sheep for bacterial culture and susceptibility testing. Abbreviation: AMR: Antimicrobial resistance; MDR: Multidrug resistance

Evaluation of standardized automated rapid antimicrobial susceptibility testing of Enterobacterales-containing blood cultures: a proof-of-principle study.

Rapid antimicrobial susceptibility testing (RAST) of bacteria causing bloodstream infections is critical for implementation of appropriate antibiotic regimens. We have established a procedure to prepare standardized bacterial inocula for Enterobacterales-containing clinical blood cultures and assessed antimicrobial susceptibility testing (AST) data generated with the WASPLabTM automated reading system. A total of 258 blood cultures containing Enterobacterales were examined. Bacteria were enumerated by flow cytometry using the UF-4000 system and adjusted to an inoculum of 106 cfu/mL. Disc diffusion plates were automatically streaked, incubated for 6, 8 and 18 h and imaged using the fully automated WASPLabTM system. Growth inhibition zones were compared with those obtained with inocula prepared from primary subcultures following the EUCAST standard method. Due to time-dependent variations of the inhibition zone diameters, early AST readings were interpreted using time-adjusted tentative breakpoints and areas of technical uncertainty. Inhibition zones obtained after 18 h incubation using an inoculum of 106 cfu/mL prepared directly from blood cultures were highly concordant with those of the EUCAST standard method based on primary subcultures, with categorical agreement (CA) of 95.8%. After 6 and 8 h incubation, 89.5% and 93.0% of the isolates produced interpretable results, respectively, with CA of >98.5% and very low numbers of clinical categorization errors for both the 6 h and 8 h readings. Overall, with the standardized and automated RAST method, consistent AST data from blood cultures containing Enterobacterales can be generated after 6-8 h of incubation and subsequently confirmed by standard reading of the same plate after 18 h.

Prevalence and temporal trends in antimicrobial resistance of bovine respiratory disease pathogen isolates submitted to the Wisconsin Veterinary Diagnostic Laboratory: 2008–2017

The objective of this study was to describe the prevalence and trends in antimicrobial resistance for bacterial pathogens associated with bovine respiratory disease (BRD) isolated from samples submitted to the Wisconsin Veterinary Diagnostic Laboratory (WVDL). Data were retrospectively collected from bovine respiratory isolates including Pasteurella multocida, Mannheimia haemolytica, Histophilus somni, and Bibersteinia trehalosi identified at the WVDL between January 2008 and December 2017. Antimicrobial susceptibility testing data were queried from antimicrobial resistance databases at the WVDL. A total of 4,261 isolates were identified. Pasteurella multocida was most frequently identified, accounting for 2,094 isolates (49% of total) over the study period. Mannheimia haemolytica was the second most frequently isolated bacterial respiratory pathogen (n = 1,267, 30%) followed by H. somni (n = 749, 18%) and B. trehalosi (n = 151, 4%). Over the 10-yr period, B. trehalosi had the highest median percentage of isolates that were resistant to at least one antibiotic at 33% (interquartile range: 24, 47) followed by M. haemolytica (13%; 8, 23). For P. multocida, 10% (4, 26) of isolates were classified as resistant to at least one antibiotic, whereas H. somni had the fewest resistant isolates (9%; 3, 15). When comparing 2013-2017 to 2008-2012, the overall percentage of resistant isolates for P. multocida and B. trehalosi decreased, whereas the percentage of resistant isolates for M. haemolytica and H. somni increased. Increased resistance against florfenicol, fluoroquinolones, gentamicin, tilmicosin, and tulathromycin was observed for M. haemolytica. These data show that antimicrobial susceptibility for BRD bacterial pathogens has changed in the population served by the WVDL over this 10-yr period. For P. multocida, resistance is relatively low and has either improved or at least remained constant for the majority of drugs labeled for treatment of respiratory disease in dairy cattle. Veterinarians and producers should be aware of the bacterial pathogens most commonly associated with BRD and work toward early disease detection, proper antibiotic administration, and monitoring lung lesions to ensure that their treatment protocols improve lung health.

Hospital surveillance predicts community pneumococcal antibiotic resistance in Vietnam.

In Vietnam, Streptococcus pneumoniae is a leading cause of disease, including meningitis. Antibiotics are available without physician prescription at community pharmacies and rates of antibiotic non-susceptibility are high. Appropriate treatment and antibiotic stewardship need to be informed by surveillance data. To report community-based pneumococcal antibiotic susceptibility testing data from children enrolled in a pneumococcal conjugate vaccine trial in Ho Chi Minh City [the Vietnam Pneumococcal Project (ViPP)] and compare these with published hospital-based data from the nationwide Survey of Antibiotic Resistance (SOAR) to determine whether hospital surveillance data provide an informative estimate of circulating pneumococcal resistance. Pneumococcal isolates from 234 nasopharyngeal swabs collected from ViPP participants at 12 months of age underwent antibiotic susceptibility testing using CLSI methods and the data were compared with SOAR data. Antibiotic susceptibility testing identified penicillin-non-susceptible pneumococci in 93.6% of pneumococcus-positive ViPP swabs (oral, non-meningitis breakpoints). Non-susceptibility to erythromycin, trimethoprim/sulfamethoxazole, clindamycin and tetracycline also exceeded 79%. MDR, defined as non-susceptibility to three or more classes of antibiotic, was common (94.4% of swabs). Low or no resistance was detected for ceftriaxone (non-meningitis breakpoints), ofloxacin and vancomycin. Antibiotic non-susceptibility rates in ViPP and SOAR were similar for several antibiotics tested. A very high proportion of pneumococci carried in the community are MDR. Despite wide disparities in population demographics between ViPP and SOAR, the non-susceptibility rates for several antibiotics were comparable. Thus, with some qualification, hospital antibiotic susceptibility testing data in Vietnam can inform circulating pneumococcal antibiotic non-susceptibility in young children, the group at highest risk of pneumococcal disease, to guide antibiotic prescribing and support surveillance strategies.

Prevalence and Antifungal Susceptibility of Pathogenic Yeasts in China: A 10-Year Retrospective Study in a Teaching Hospital.

To determine the dynamic changes of pathogenic yeast prevalence and antifungal susceptibility patterns in tertiary hospitals in China, we analyzed 527 yeast isolates preserved in the Research Center for Medical Mycology at Peking University, Beijing, China, between Jan 2010 and Dec 2019 and correctly identified 19 yeast species by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and ribosomal DNA sequencing. Antifungal susceptibility testing was performed following a Sensititre YeastOne colorimetric microdilution panel with nine clinically available antifungals. The Clinical and Laboratory Standards Institute (CLSI)-approved standard M27-A3 (S4) and newly revised clinical breakpoints or species-specific and method-specific epidemiological cutoff values were used for the interpretation of susceptibility test data. In this study, although Candida albicans was the predominant single species, non-C. albicans species constituted >50% of isolates in 6 out of 10 years, and more rare species were present in the recent 5 years. The non-C. albicans species identified most frequently were Candida parapsilosis sensu stricto, Candida tropicalis, and Candida glabrata. The prevalence of fluconazole and voriconazole resistance in the C. parapsilosis sensu stricto population was <3%, but C. tropicalis exhibited decreased susceptibility to fluconazole (42, 57.5%) and voriconazole (31, 42.5%), and 22 (30.1%) C. tropicalis isolates exhibited wild-type minimum inhibitory concentrations (MICs) to posaconazole. Furthermore, fluconazole and voriconazole cross-resistance prevalence in C. tropicalis was 19 (26.1%). The overall prevalence of fluconazole resistance in the C. glabrata population was 14 (26.9%), and prevalence of isolates exhibiting voriconazole non-wild-type MICs was 33 (63.5%). High-level echinocandin resistance was mainly observed in C. glabrata, and the prevalence rates of isolate resistance to anidulafungin, micafungin, and caspofungin were 5 (9.6%), 5 (9.6%), and 4 (7.7%), respectively. Moreover, one C. glabrata isolate showed multidrug resistant to azoles, echinocandins, and flucytosine. Overall, the 10-year surveillance study showed the increasing prevalence of non-C. albicans species over time; the emergence of azole resistance in C. tropicalis and multidrug resistance in C. glabrata over the years reinforced the need for epidemiological surveillance and monitoring.

Influence of analysis conditions for antimicrobial susceptibility test data on susceptibility rates.

To support effective antibiotic selection in empirical treatments, infection control interventions, and antimicrobial resistance containment strategies, many medical institutions collect antimicrobial susceptibility test data conducted at their facilities to prepare cumulative antibiograms. To evaluate how the setpoints of duplicate isolate removal period and data collection period affect the calculated susceptibility rates in antibiograms. The Sakai City Medical Center is a regional core hospital for tertiary emergency medical care with 480 beds for general clinical care. In this study, all the Pseudomonas aeruginosa, Escherichia coli, and Klebsiella pneumoniae isolates collected at the Sakai City Medical Center Clinical Laboratory between July 2013 and December 2018 were subjected to antimicrobial susceptibility tests and the resulting data was analyzed. The longer the duplicate isolate removal period, the fewer the isolates are available for every bacterial species. Differences in the length of the duplicate isolate removal period affected P. aeruginosa susceptibility rates to β-lactam antibiotics by up to 10.8%. The setpoint of the data collection period affected the antimicrobial susceptibility rates by up to 7.3%. We found that a significant change in susceptibility could be missed depending on the setting of the data collection period, in preparing antibiogram of β-lactam antibiotics for P. aeruginosa. When referring to antibiograms, medical professionals involved in infectious disease treatment should be aware that the parameter values, such as the duplicate isolate removal period and the data collection period, affect P. aeruginosa susceptibility rates especially to β-lactam antibiotics. And antibiogram should be updated within the shortest time period that is practically possible, taking into account restrictions such as numbers of specimen.

Assessment of Antimicrobial Susceptibility of Virulent Strains of Rhodococcus equi Isolated From Foals and Soil of Horse Breeding Farms With and Without Endemic Infections

Rhodococcus equi is an opportunistic, intracellular saprophyte that causes severe pyogranulomatous pneumonia in foals. The bacterium displays in vitro susceptibility to many antibiotics. The highest efficacy against R. equi in vitro and in vivo is achieved by using a combination of rifampicin and macrolide antibiotics. Recent years have seen an upward trend in the minimum inhibitory concentration (MIC) of rifampicin and erythromycin, suggesting increasing resistance of R. equi to these antibiotics. The aim of the study was to determine the antimicrobial activity of 24 selected antibiotics against R. equi strains isolated from dead foals and from the environment of horse breeding farms with and without endemic R. equi infections. Minimum inhibitory concentration gradient strips were used to determine the lowest concentration of the antibiotic that inhibited the growth of R. equi. Based on normal MIC distribution, an epidemiologic cutoff values (ECOFF) were assessed for particular antibiotics and R. equi strains. The results were compared with ECOFFs for S. aureus, according to the European Committee on Antimicrobial Susceptibility Testing data. The data indicate that the lowest MIC values were obtained for clarithromycin, rifampicin, imipenem, and vancomycin. The majority of R. equi strains can be classified as wild type in relation to the majority of antibiotics. A small percentage of strains presented non-WT (NWT) with the exception of SXT, for which 35% of strains were classified as NWT. The lack of interpretative criteria for R. equi creates a real problem in the assessment of antibiotic sensitivity both for clinical and scientific purposes.

Validation of an antimicrobial susceptibility testing protocol for Brachyspira hyodysenteriae and Brachyspira pilosicoli in an international ring trial

Brachyspira hyodysenteriae and Brachyspira pilosicoli cause economically important enteric disease in pigs. Treatment of these infections often includes antimicrobial administration, which can be most effective when therapeutic options are informed by antimicrobial susceptibility testing data. Here we describe a method for broth dilution antimicrobial susceptibility testing of these bacteria, both of which are difficult to culture in vitro. The protocol was evaluated for its fitness for use in an inter-laboratory ring trial involving eight laboratories from seven countries, and employing eleven test strains (5 Brachyspira hyodysenteriae including the type strain B78T and 6 Brachyspira pilosicoli) and six antibiotics. Overall intra- and inter-laboratory reproducibility of this method was very good (>90 % MICs at mode +/- 1 log2). Whole genome sequencing revealed good correspondence between reduced susceptibility and the presence of previously defined antimicrobial resistance determinants. Interestingly, lnu(C) was identified in B. pilosicoli isolates with elevated MICs of lincomycin, whilst tva(B) was associated with elevated MICs of pleuromutilins in this species. We designated two new control strains with MICs lying within currently tested ranges, including for the pleuromutilins, in contrast to the control strain B. hyodysenteriae B78T. These were deposited at the DSMZ-German Collection of Microorganisms and Cell Cultures GmbH. The validation of a standard protocol and identification of new control strains facilitates comparisons between studies, establishment of robust interpretative criteria, and ultimately contributes to rational antimicrobial use when treating infected livestock.

Taxonomy and nomenclature of bacteria with clinical and scientific importance: current concepts for pharmacists and pharmaceutical scientists

Taxonomy is the science of the classification of various living organisms consisting of three independent, but interrelated disciplines, namely classification, nomenclature and identification. With the advent of molecular biological methods and sequencing, a revolution is currently occurring with regards to the reporting of novel taxa and changes in the taxonomy of already described bacterial species. The applications of taxonomic changes can be broad ranging: they may impact the clinical care of patients, through variations in choosing the appropriate antimicrobial susceptibility testing standards or data interpretation, or even their clinical relevance and epidemiology. The aim of this paper was to aid healthcare professionals and pharmaceutical scientists to navigate through the ‘maze’ of bacterial taxonomy, and to aid in finding authentic information regarding the description of taxonomic changes and to present some examples of changes in bacterial taxonomy which have proven to be clinically significant.

Antimicrobial Sensitivity Testing of Mycoplasma bovis Isolates Derived from Western Canadian Feedlot Cattle.

Mycoplasma bovis is particularly adept at evading the immune system, resulting in chronic infections of the lungs and joints of feedlot cattle. The chronicity of the lesions results in prolonged antimicrobial therapy, possibly exacerbating antimicrobial resistance. This cross-sectional study generated in vitro antimicrobial susceptibility testing (AST) data on 211 M. bovis isolates recovered from 159 healthy, diseased, and dead cattle, spanning the period of 2006–2018. Nine antimicrobials commonly administered to western Canadian feedlot cattle were assessed. The data were analyzed with non-parametric statistical tests with a level of significance of p < 0.05 (two-tailed). Minimum inhibitory concentration (MIC) values tended to increase between the isolates from healthy versus dead cattle and over time (2006–2018). Isolates from dead versus healthy cattle were more likely to be resistant to tulathromycin, gamithromycin, tylosin and enrofloxacin. There was no difference in the distributions of the MICs generated from the isolates recovered from the lungs and joints (p ≥ 0.124) and the lungs and deep nasal passages (p ≥ 0.157) of the same animals.

PIN79 ECONOMIC EVALUATION OF ANTIMICROBIAL STEWARDSHIP PROGRAMS IN CHINESE HOSPITALS

As part of the nationwide initiative to optimize antibiotic use and control antimicrobial resistance, many Chinese hospitals have started antimicrobial stewardship (AMS) programs. We conducted a study to understand the impact of AMS in China. A previously developed China-specific conceptual economic evaluation framework based on the U.S. Centers for Disease Control and Prevention guidelines and Chinese experts’ feedback was used for this study. Data were collected from three tertiary teaching hospitals (bed size: 1159 to 2300) in Beijing (n=2) and Hunan (n=1). Hospital AMS coordinators responded to the evaluation questionnaire and follow-up calls/emails for data clarification. Data were analyzed in an Excel economic model developed based on the conceptual economic evaluation framework. Among the three participating hospitals, core elements of the AMS programs included pre-authorization, “no indication, no treatment,” post-operative antibiotic use monitoring, nosocomial infection reporting, and training programs. After implementing AMS (vs. pre-AMS), the average length of stay decreased in all three hospitals by 3.5% to 5.7%. Occupancy rates increased in two hospitals (2.5%, 6.1%) and decreased in the other (3.6%). Mortality rates decreased by approximately 14% in two hospitals and remained the same in the other hospital. The proportion of hospitalized patients receiving antimicrobial treatment decreased by 1.4% to 7.3%. The defined daily dose of antimicrobial drugs decreased by approximately 10% in two hospitals. Two hospitals reported the costs of implementing the AMS programs, including labor and equipment for susceptibility testing or laboratory data collection. All three hospitals experienced an increase in revenue (1.8% to 11.9%) and net benefit (23 to 139 million RMB). These findings indicate a positive impact of AMS on economic and clinical outcomes in these hospitals and provide insights into the costs and benefits that can be considered when implementing AMS in other Chinese hospitals.

1831. Machine Learning Approaches to Predicting Resistance in Pseudomonas aeruginosa

BackgroundMulti-drug-resistant (MDR) P. aeruginosa (PA) infections continue to cause significant morbidity and mortality in various patient groups including those with malignancies. Predicting antimicrobial resistance (AMR) from whole-genome sequencing data if done rapidly, could aid in providing optimal care to patients.MethodsTo better understand the connections between DNA variation and phenotypic AMR in PA, we developed a new algorithm, variant mapping and prediction of antibiotic resistance (VAMPr), to build association and machine learning prediction models of AMR based on publicly available whole-genome sequencing and antibiotic susceptibility testing (AST) data. A validation cohort of contemporary PA bloodstream isolates was sequenced and AST was performed. Accuracy of predicting AMR for various PA–drug combinations was calculated.ResultsVAMPr was built from 3,393 bacterial isolates (83 PA isolates included) from 9 species that contained AST data for 29 antibiotics. 14,615 variant genotypes were identified within the dataset and 93 association and prediction models were built. 120 PA bloodstream isolates from cancer patients were included for analysis in the validation cohort. ~15% of isolates were carbapenem resistant and ~20% were quinolone resistant. For drug-isolate combinations where >100 isolates were available, machine-learning prediction accuracies ranged from 75.6% (PA and ceftazidime; 90/119 correctly predicted) to 98.1% (PA and amikacin; 105/107 correctly predicted). Machine learning accurately identified known variants that strongly predicted resistance to various antibiotic classes. Examples included specific gyrA mutations (T83I; P < 0.00001) and quinolone resistance.ConclusionMachine learning predicted AMR in P. aeruginosa across a number of antibiotics with high accuracy. Given the genomic heterogeneity of PA, increased genomic data for this pathogen will aid in further improving prediction accuracy across all antibiotic classes.DisclosuresSamuel L. Aitken, PharmD, Melinta Therapeutoics: Grant/Research Support, Research Grant; Merck, Sharpe, and Dohme: Advisory Board; Shionogi: Advisory Board

2467. Inferring Strain Type Attribution from Antibiotic Resistance Profiles among E. coli Causing Healthcare-Associated Infections in the United States, 2013–2017

BackgroundE. coli is a leading cause of healthcare-associated infections; clonal group ST131, which has expanded worldwide with notable increased severity of infections, is commonly resistant to extended-spectrum cephalosporins (ESC) and fluoroquinolones (FQ). Herein, we relate ESC and FQ resistance profiles from CDC’s National Healthcare Safety Network (NHSN) with specific strain types from CDC laboratory surveillance collections.MethodsNHSN isolate and antibiotic susceptibility testing data were collected from all E. coli associated with central line-associated bloodstream infections, catheter-associated urinary tract infections, ventilator-associated events, or surgical site infections from 2013–2017. Resistance was scored as non-susceptibility to at least one drug per class [susceptible (S); resistant (R)]. ESC and FQ susceptibilities and multilocus sequence types (ST) using the Achtman 7 loci scheme were determined for a contemporaneous set of E. coli isolates collected through CDC laboratory surveillance.ResultsOf 96,672 E. coli infections reported to NHSN, 13% were ESC-R/FQ-R, 23% ESC-S/FQ-R, 4% ESC-R/FQ-S, and 60% were ESC-S/FQ-S. Among 105 ESC-R/FQ-R and 21 ESC-S/FQ-R laboratory isolates, the majority (67.6% and 52.4%, respectively) were ST131, whereas of 38 ESC-R/FQ-S and 53 ESC-S/FQ-S isolates, ST131 was a minority (18.4% and 7.5%, respectively). The odds of an isolate being ST131 were 10.5 if FQ-R (P < 0.001), 3.4 if ESC-R (P < 0.001), and 6.0 if ESC-R/FQ-R (P < 0.001). Using the national distribution of resistance combinations from NHSN, and assuming static ST-resistance distribution, we can infer that ST131 was responsible for 25.8% (95% CI, 23.9%-27.6%) of all E.coli healthcare-associated infections in the United States in 2013–2017.ConclusionMolecular inferences generated by applying laboratory data to resistance signature data in reportable datasets may make national E. coli ST burden estimates possible. Further characterization of resistance combinations with strain type, infection rates, and clinical outcomes may inform targeted prevention strategies at the local/regional level.Disclosures All authors: No reported disclosures.

Performance of Three Commercial Assays for Colistin Susceptibility in Clinical Isolates and Mcr-1 Carrying Reference Strain

AbstractObjective: Commercially available antibiotic susceptibility tests (cAST) for colistin are reported to shows variable performance. The current controversy on the colistin susceptibility testing and scarce data from India has left the clinical laboratories in a dilemma on the appropriate and practical approach to tackle the colistin antimicrobial susceptibility testing (AST) issue. This study was aimed to evaluate the performance of commonly used cAST for colistin against broth microdilution (BMD) as the reference method in the clinical isolates. Materials and Methods: Colistin AST was performed on 225 nonduplicate isolates of Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii by BMD as the reference method and compared with Vitek-2, Micronaut-S and E-test. The accuracy of the various cASTs was analysed by assessing categorical and essential agreement (EA). Results: We observed an overall categorical agreement of 98.2%, 99.6% and 96.4% and EA of 92%, 92.4% and 72% for Vitek-2, Micronaut-S and E-test, respectively. Unacceptable rates of major error (10.5%) and very major error (21%) were observed for P. aeruginosa with Vitek-2 and E-test, respectively. All the categorical errors (CEs) (7.7%) with Vitek-2 were seen for minimum inhibitory concentrations ranging within two-fold dilution breakpoint of 2 mg/L. Conclusion: Micronaut-S was found to be an acceptable method for colistin AST. In contrast, E-test was unreliable in terms of EA. Vitek-2 was found to be reliable for colistin AST, although it was more prone to CE near the colistin breakpoints.

42936 pathogens from Canadian hospitals: 10 years of results (2007-16) from the CANWARD surveillance study.

The CANWARD surveillance study was established in 2007 to annually assess the in vitro susceptibilities of a variety of antimicrobial agents against bacterial pathogens isolated from patients receiving care in Canadian hospitals. 42 936 pathogens were received and CLSI broth microdilution testing was performed on 37 355 bacterial isolates. Limited patient demographic data submitted with each isolate were collated and analysed. Of the isolates tested, 43.5%, 33.1%, 13.2% and 10.2% were from blood, respiratory, urine and wound specimens, respectively; 29.9%, 24.8%, 19.0%, 18.1% and 8.2% of isolates were from patients in medical wards, emergency rooms, ICUs, hospital clinics and surgical wards. Patient demographics associated with the isolates were: 54.6% male/45.4% female; 13.1% patients aged ≤17 years, 44.3% 18-64 years and 42.7% ≥65 years. The three most common pathogens were Staphylococcus aureus (21.2%, both methicillin-susceptible and MRSA), Escherichia coli (19.6%) and Pseudomonas aeruginosa (9.0%). E. coli were most susceptible to meropenem and tigecycline (99.9%), ertapenem and colistin (99.8%), amikacin (99.7%) and ceftolozane/tazobactam and plazomicin (99.6%). Twenty-three percent of S. aureus were MRSA. MRSA were most susceptible to ceftobiprole, linezolid and telavancin (100%), daptomycin (99.9%), vancomycin (99.8%) and tigecycline (99.2%). P. aeruginosa were most susceptible to ceftolozane/tazobactam (98.3%) and colistin (95.0%). The CANWARD surveillance study has provided 10 years of reference antimicrobial susceptibility testing data on pathogens commonly causing infections in patients attending Canadian hospitals.

Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs

BackgroundMycobacterium tuberculosis resistance to anti-tuberculosis drugs is a major threat to global public health. Whole genome sequencing (WGS) is rapidly gaining traction as a diagnostic tool for clinical tuberculosis settings. To support this informatically, previous work led to the development of the widely used TBProfiler webtool, which predicts resistance to 14 drugs from WGS data. However, for accurate and rapid high throughput of samples in clinical or epidemiological settings, there is a need for a stand-alone tool and the ability to analyse data across multiple WGS platforms, including Oxford Nanopore MinION.ResultsWe present a new command line version of the TBProfiler webserver, which includes hetero-resistance calling and will facilitate the batch processing of samples. The TBProfiler database has been expanded to incorporate 178 new markers across 16 anti-tuberculosis drugs. The predictive performance of the mutation library has been assessed using > 17,000 clinical isolates with WGS and laboratory-based drug susceptibility testing (DST) data. An integrated MinION analysis pipeline was assessed by performing WGS on 34 replicates across 3 multi-drug resistant isolates with known resistance mutations. TBProfiler accuracy varied by individual drug. Assuming DST as the gold standard, sensitivities for detecting multi-drug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB) were 94% (95%CI 93–95%) and 83% (95%CI 79–87%) with specificities of 98% (95%CI 98–99%) and 96% (95%CI 95–97%) respectively. Using MinION data, only one resistance mutation was missed by TBProfiler, involving an insertion in the tlyA gene coding for capreomycin resistance. When compared to alternative platforms (e.g. Mykrobe predictor TB, the CRyPTIC library), TBProfiler demonstrated superior predictive performance across first- and second-line drugs.ConclusionsThe new version of TBProfiler can rapidly and accurately predict anti-TB drug resistance profiles across large numbers of samples with WGS data. The computing architecture allows for the ability to modify the core bioinformatic pipelines and outputs, including the analysis of WGS data sourced from portable technologies. TBProfiler has the potential to be integrated into the point of care and WGS diagnostic environments, including in resource-poor settings.

Whole-Genome Sequencing for Drug Resistance Profile Prediction in Mycobacterium tuberculosis

Whole-genome sequencing allows rapid detection of drug-resistant Mycobacterium tuberculosis isolates. However, the availability of high-quality data linking quantitative phenotypic drug susceptibility testing (DST) and genomic data have thus far been limited. We determined drug resistance profiles of 176 genetically diverse clinical M. tuberculosis isolates from the Democratic Republic of the Congo, Ivory Coast, Peru, Thailand, and Switzerland by quantitative phenotypic DST for 11 antituberculous drugs using the BD Bactec MGIT 960 system and 7H10 agar dilution to generate a cross-validated phenotypic DST readout. We compared DST results with predicted drug resistance profiles inferred by whole-genome sequencing. Classification of strains by the two phenotypic DST methods into resistotype/wild-type populations was concordant in 73 to 99% of cases, depending on the drug. Our data suggest that the established critical concentration (5 mg/liter) for ethambutol resistance (MGIT 960 system) is too high and misclassifies strains as susceptible, unlike 7H10 agar dilution. Increased minimal inhibitory concentrations were explained by mutations identified by whole-genome sequencing. Using whole-genome sequences, we were able to predict quantitative drug resistance levels for the majority of drug resistance mutations. Predicting quantitative levels of drug resistance by whole-genome sequencing was partially limited due to incompletely understood drug resistance mechanisms. The overall sensitivity and specificity of whole-genome-based DST were 86.8% and 94.5%, respectively. Despite some limitations, whole-genome sequencing has the potential to infer resistance profiles without the need for time-consuming phenotypic methods.

Ten years of external quality assessment (EQA) of Neisseria gonorrhoeae antimicrobial susceptibility testing in Europe elucidate high reliability of data

BackgroundConfidence in any diagnostic and antimicrobial susceptibility testing data is provided by appropriate and regular quality assurance (QA) procedures. In Europe, the European Gonococcal Antimicrobial Susceptibility Programme (Euro-GASP) has been monitoring the antimicrobial susceptibility in Neisseria gonorrhoeae since 2004. Euro-GASP includes an external quality assessment (EQA) scheme as an essential component for a quality-assured laboratory-based surveillance programme. Participation in the EQA scheme enables any problems with the performed antimicrobial susceptibility testing to be identified and addressed, feeds into the curricula of laboratory training organised by the Euro-GASP network, and assesses the capacity of individual laboratories to detect emerging new, rare and increasing antimicrobial resistance phenotypes. Participant performance in the Euro-GASP EQA scheme over a 10 year period (2007 to 2016, no EQA in 2013) was evaluated.MethodsAntimicrobial susceptibility category and MIC results from the first 5 years (2007–2011) of the Euro-GASP EQA were compared with the latter 5 years (2012–2016). These time periods were selected to assess the impact of the 2012 European Union case definitions for the reporting of antimicrobial susceptibility.ResultsAntimicrobial susceptibility category agreement in each year was ≥91%. Discrepancies in susceptibility categories were generally because the MICs for EQA panel isolates were on or very close to the susceptibility or resistance breakpoints. A high proportion of isolates tested over the 10 years were within one (≥90%) or two (≥97%) MIC log2 dilutions of the modal MIC, respectively. The most common method used was Etest on GC agar base. There was a shift to using breakpoints published by the European Committee on Antimicrobial Susceptibility Testing (EUCAST) in the latter 5 years, however overall impact on the validity of results was limited, as the percentage categorical agreement and MIC concordance changed very little between the two five-year periods.ConclusionsThe high level of comparability of results in this EQA scheme indicates that high quality data are produced by the Euro-GASP participants and gives confidence in susceptibility and resistance data generated by laboratories performing decentralised testing.

Developing a hybrid antimicrobial resistance surveillance system in India: Needs & challenges.

Growing resistance to antimicrobials has become one of the most important problems of the 21st century. The development of new antibiotics is a time-consuming process involving huge financial resources. An alternate approach is proper utilization of the existing antibiotics through the surveillance of resistance. An important component of surveillance is the informatics tool for collection, management and analysis of antimicrobial resistance susceptibility testing data. Based on the scope, antimicrobial resistance surveillance resistance tools can be broadly classified as collectors and integrators. Individually, both the integrators and collectors have limitations which restrict their use in India. There is a strong requirement to develop a hybrid AMR surveillance tool that captures standardized data from small laboratories and integrates data from multiple sources to present a complete picture of the country. Here we describe a tool i-AMRSS developed by the Indian Council of Medical Research for collection, storage and management of AMR data from collaborating institutes/laboratories and to generate real-time analytics and reports.