Antimicrobial Susceptibility Testing Results Research Articles

Characterization of antimicrobial susceptibility, extended-spectrum \u03b2-lactamase genes and phylogenetic groups of Shigatoxin producing Escherichia coli isolated from patients with diarrhea in Iran

BackgroundShiga toxin‐producing Escherichia coli (STEC) are among common foodborne bacterial pathogens and healthy livestock are the main source of this bacterium. Severe diseases attribute to two types of cytotoxin Stx1 and Stx2, which are also called Shiga toxin (Stx). Infection of humans with STEC may result in Acute diarrhea with or without bleeding, hemorrhagic colitis (HC) and the hemolytic uremic syndrome (HUS). As antibiotic resistance is increasingly being reported among STEC isolates obtained from livestock and patients worldwide, in this study the pattern of antibiotic resistance in clinical isolates was determined.MethodsStool samples were collected from patients with diarrhea. All samples were cultured and identified by biochemical and molecular tests. Antimicrobial susceptibility test and assessment of extended-spectrum β-lactamase (ESBL)-related genes were conducted. Moreover, phylogenetic groups were analyzed using quadruplex PCR, and DNA analysis assessed multi-locus sequence types (MLST).ResultsOut of 340 E. coli samples, 174 were identified as STEC by PCR. Antimicrobial susceptibility test results showed that, 99.4%, 96% and 93.1% of isolates were susceptible to imipenem/ertapenem, piperacillin–tazobactam and amikacin, respectively. The highest resistance was towards ampicillin (68.4%), followed by trimethoprim–sulfamethoxazole (59.8%), and tetracycline (57.5%). A total of 106 (60.9%) isolates were multidrug resistance (MDR) and 40.8% of isolates were determined to be extended spectrum β-lactamase producers. In 94.4% of isolates, genes responsible for ESBL production could be detected, and blaTEM was the most prevalent, followed by blaCTX-M9. Furthermore, phylogenetic grouping revealed that majority of STEC strains belonged to Group C, followed by Groups E, B2 and A. MLST unveiled diverse ST types.ConclusionA periodical surveillance studies and thorough understanding of antibiotic resistant profiles in STEC isolates could help select effective antibiotic treatment for patients and develop strategies to effectively manage food contamination and human infections.

Arthrobacter woluwensis Bacteremia: A Clinical and Genomic Report.

Arthrobacter woluwensis is a Gram-positive, aerobic Actinobacteria that is widely distributed in the environment worldwide. Little is known about A. woluwensis infection and it is commonly mis-identified by culturing with commercial kits. To date, only six cases of bacteremia caused by A. woluwensis have been reported in the literature. Herein, we report a case of Arthrobacter woluwensis bacteremia in an immunocompromised host. In this case report, the results of antimicrobial susceptibility testing showed that this clinical isolate of A. woluwensis is sensitive to vancomycin, teicoplanin, but resistant to penicillin, cephalosporin and ciprofloxacin. Additionally, whole genome sequencing analysis identified common subunits of the urease system.

On the Consequences of Poorly Defined Breakpoints for Rifampin Susceptibility Testing of Mycobacterium tuberculosis Complex.

In a recent report of a systematic review of critical concentrations (CCs), the World Health Organization (WHO) lowered the rifampin (RIF) CC for antimicrobial susceptibility testing (AST) of the Mycobacterium tuberculosis complex using Middlebrook 7H10 medium and the Bactec Mycobacterial Growth Indicator Tube (MGIT) 960 system from 1 to 0.5 μg/ml. The previous RIF CC for 7H10 had been in use for over half a century. Because it had served as the de facto reference standard, it contributed to the endorsement of inappropriately high CCs for other AST methods, including the U.S. Food and Drug Administration (FDA)-approved MGIT system. Moreover, this resulted in confusion about the interpretation of seven borderline resistance mutations in rpoB (i.e., L430P, D435Y, H445L, H445N, H445S, L452P, and I491F). In this issue of the Journal of Clinical Microbiology, Shea et al. (J Clin Microbiol 59:e01885-20, 2021, https://doi.org/10.1128/JCM.01885-20) provide evidence that the CC endorsed by the Clinical and Laboratory Standards Institute for the Sensititre MYCOTB system, which is not FDA approved but is CE-IVD marked in the European Union, is likely also too high. These findings underscore the importance of calibrating AST methods against a rigorously defined reference standard, as recently proposed by the European Committee on Antimicrobial Susceptibility Testing, as well as the value of routine next-generation sequencing for investigating discordant AST results.

Variability of antibiograms: how often do changes in the antimicrobial susceptibility pattern occur in isolates from one patient?

ObjectivesMany laboratories do not perform antimicrobial susceptibility testing (AST) for all consecutive isolates of the same species from one patient. The objective of this study was to assess how often changes in antimicrobial susceptibility patterns (cASP) occur in such isolates. MethodsAST was performed for all isolates of defined species obtained from clinical routine (2015–2018) without restrictions for consecutive or sequential isolates of one patient. Occurrence of cASP and time between the first sampling date and first cASP were determined by combining antibiograms from all specimens and after stratification into species and specimens. ResultsA total of 35 473 AST results were included (range 2–71 per case). Combining pathogens and specimens, 1991 cASP occurred in 1269/8502 (14.9%) of all cases after a median time until cASP of 5 days (range 0–364). Of these, 628/1991 (31.5%) occurred on the day of first sampling (predominantly due to phenotypic variants in the same specimen). Excluding isolates with differing AST pattern on the first day of sampling, the median time until cASP was 12 days (range 1–364). Stratification into species and specimen revealed a large variance of the median time until cASP (e.g. in Escherichia coli: 5 days; range 1–48 for blood cultures or 16 days; 1–364 for urine). DiscussionUsing routine microbiological data in a large tertiary hospital, cASP occurs occasionally. The time to perform subsequent AST to detect cASP depends on the species and type of specimen. Other studies are needed to evaluate whether ideal time intervals applicable beyond local settings can be defined.

Molecular characterization of Clostridioides difficile ribotype 027 in a major Chinese hospital

The rapid spread of C. difficile 027 has become one of the leading threats of healthcare-associated infections wordwild. However, C. difficile 027 infections have rarely been reported in China. The objective of this study was to strengthen the understanding of the molecular characterizations of C. difficile 027 in China. In this study, stool specimens from 176 suspected CDI cases were collected from 1 Jan 2018 to 30 Jun 2019. These specimens were measured by GeneXpert test and C.difficile colonies were identified and analyzed. There were five samples positive for tcdA, tcdB, binary toxin genes and had deletions in tcdC gene. These five Clostridioides difficile isolates belonged to ST1 and confirmed as Clostridioides difficile 027 strains by PCR ribotyping. Through using whole genome sequencing, , we found that these five strains were closely clustered into the same predominant evolutionary branch and were highly similar to C. difficile 027 strain R20291. Antimicrobial susceptibility testing result showed they were highly resistant to fluoroquinolones. In Our study, five C. difficile 027 isolates were identified and characterized using MLST, PCR ribotyping and whole genome sequencing. We proposed that C. difficile 027 infections are probably neglected in China. Further epidemiological studies across the country together with the introduction of routine diagnostic testing and multi-center or national level surveillance are needed to ascertain the size of this potentially significant problem.

Performance of the VITEK®2 advanced expert system™ for the validation of antimicrobial susceptibility testing results.

Time to reporting antimicrobial susceptibility testing (AST) results to physicians plays an essential role in antibiotic stewardship programs. Expert software has been developed for facilitating the microbiologists' AST review process. The reliability of the VITEK®2 Advanced Expert™ software to effectively alert the microbiologist in detection of atypical and inconsistent AST results was assessed at the Labor Berlin-Charité Vivantes services. The results demonstrated a confidence rate of 99.3% in reporting fully consistent AST results to physicians.

Biotyping and Antimicrobial Susceptibility of Enterococcus faecalis and E. faecium Isolated from Urine and Stool Samples

Background: Enterococci are one of the opportunistic pathogenic microorganisms that can cause significant problems for human and animal health. Enterococcus faecium seems to be more resistant to antibiotics than E. faecalis. It is thought that pathogenic E. faecium can develop antibiotic resistance very quickly, and the ability to transfer this feature is considered to be an important health risk. Objectives: This study aimed to determine the prevalence, biotypes, and in vitro antimicrobial susceptibility of E. faecalis and E. faecium strains isolated from 267 routine urine and stool samples that were brought to the microbiology laboratory of Regional Training and Research Hospital of Van, with permission of the patients. Methods: In the present study, enterococci using species-specific primers to examine E. faecalis and E. faecium multiplex PCR technique was applied. Biotyping of the isolates was used to identify them as E. faecalis and E. faecium by molecular techniques, and antibiotic susceptibility of all samples was examined, as well. Results: The isolates were identified by multiplex PCR using species-specific primers for E. faecalis and E. faecium. Biotyping based on 13 biochemical tests showed that 72.5%, 12.5%, and 15% of E. faecalis strains were of biotypes I, II, and III, respectively, whereas E. faecium strains could be divided into biotype I (10%), biotype II (12.5%), biotype III (27.5%), and biotype IV (50%). Additionally, all E. faecalis strains were found to be susceptible to penicillin G and imipenem. On the other hand, 95% of the E. faecalis strains were found to be resistant to clindamycin, 77.5% to tetracycline and trimethoprim/sulfamethoxazole, 42.5% to erythromycin, 32.5% to gentamicin, and 17.5% to ciprofloxacin. Of E. faecium strains, 37.5% were found to be resistant to clindamycin, 32.5% to penicillin G, 27.5% to erythromycin and imipenem, 20% to ciprofloxacin, 17.5% to tetracycline and trimethoprim/sulfamethoxazole, 15% to gentamicin, and 5% to vancomycin. Conclusions: In conclusion, the identification of E. faecalis and E. faecium strains by PCR is reliable and faster than biochemical tests. Additionally, the results of antimicrobial susceptibility tests may provide important contributions to the clinical approach.

Assessment of version 2.5 of QMAC-dRAST for rapid antimicrobial susceptibility testing with reduced sample-to-answer turnaround time and an integrated expert system

ObjectiveTo assess the performance of the new rapid antimicrobial susceptibility testing (AST) QMAC-dRAST V2.5 system. MethodsASTs were performed using QMAC-dRAST-V2.5 and a disk diffusion method, directly from positive blood bottles with Gram-negative bacteria. Discrepancies between the results obtained using the two methods were categorized into very major errors (VME, S with dRAST vs. R with disk diffusion), major errors (ME, R vs. S, respectively), minor errors (mE, S vs. I or I vs. R, respectively), and very minor errors (Vme, I vs. S or R vs. I, respectively). For each AST, results were recorded after 4, 5, and 6h of incubation. ResultsFrom 106 bacteremia, 1416 individual AST results were obtained. Overall agreement between results using the two methods was 91%, ranging from 76.9% to 99.1% depending upon the antibiotic, with 128 errors, i.e. 14/1416 (1%) VME, 59/1416 (4.2%) ME, 25/1416 (1.8%) mE and 30/1416 (2.1%) Vme. VMEs were encountered for Klebsiellasp and Serratia marcescens isolates with low-level piperacillin and amikacin resistance, respectively. Using the integrated QMAC-dRAST-V2.5 expert system, all 14 VMEs and 3 mEs were eliminated, leading to 92.2% categorical agreement. After 45min of pre-incubation in the QMAC-dRAST-V2.5 device, 22.2% of the 1416 AST results were obtained after 4h, an additional 31.4% after 5h and a further 46.3% after 6h. ConclusionQMAC-dRAST-V2.5 is an optimized version of QMAC-dRAST V2.0, particularly with respect to utilization of an expert system and reduced TAT according to the antibiotic tested.

Bir Üniversite Hastanesinde Kan Kültürlerinden İzole Edilen Enterobacterales Takımı Üyelerinin Dağılımının ve Antimikrobiyal Duyarlılıklarının İncelenmesi

Objective: Members of Enterobacterales can cause various diseases in humans. The objective of this study was to determine the genus/species distribution and antimicrobial susceptibilities of Enterobacterales isolated from blood cultures in Central Laboratory of Hacettepe University Hospital. Method: Enterobacterales isolated from blood between July-2014 and April-2018 were included in the study. MALDI-TOF MS was used for the identification of isolates. Antimicrobial susceptibilities were determined with automated system (VITEK 2 Compact for the isolates between 2014 and 2018; BD Phoenix for the isolates in 2018) and disk diffusion method. Results of antimicrobial susceptibility testing were interpreted according to EUCAST breakpoints. Results: In total, 1765 isolates belonging to the order Enterobacterales were isolated from blood cultures. The most common microorganisms were Escherichia coli (47.6%), Klebsiella (34.1%), Enterobacter (6%), Proteus (4.4%) and Serratia spp. (3.5%), respectively. The remaining isolates included Salmonella, Citrobacter, M. morganii, Pantoea, Raoultella and Providencia spp. The lowest resistance rates among E. coli, Klebsiella and Enterobacter spp. isolates were observed against meropenem and amikacin. However, 21.1% of Klebsiella isolates were resistant to meropenem. The most active antimicrobials against Proteus isolates were piperacillintazobactam and meropenem. Resistance was not observed against piperacillin-tazobactam and meropenem among Proteus isolates. The most active antimicrobial against Serratia isolates was trimethoprim/ sulfamethoxazole with a resistance rate of 0%. Resistance was not noted against ampicillin and trimethoprim/ sulfamethoxazole among Salmonella isolates, whereas 26.1% of isolates were resistant to ciprofloxacin. All Citrobacter isolates were susceptible to meropenem, amikacin and cefepime. Conclusion: Findings of our study may guide the selection of proper antimicrobials for the treatment of bacteremia caused by Enterobacterales. Furthermore, this study provides important epidemiological information regarding the distribution of members of Enterobacterales causing bacteremia.

Occurrence, Molecular Characterization and Antimicrobial Assay of Escherichia coli Isolates from Milk and Milk Products

The present study was conducted to examine the occurrence of E. coli in milk and milk products and their characterization. A total of 300 samples of milk and milk products were screened from different areas in Jabalpur. The bacteria were isolated and characterized biochemically, genotypically and on the basis of antimicrobial profile. Out of 300 samples of milk and milk products, 24.0% (n=72) were found positive for E. coli. The incidence of E. coli in milk and ice cream was 30.0% and 27.0%, respectively while none of the shrikhand samples showed E. coli presence. Molecular study revealed 70.8%, 11.1% and 20.8% uspA, stx1 and stx2 gene, respectively in the E. coli isolates. Results of antimicrobial susceptibility test of E. coli showed that isolates were sensitive to ofloxacin (100.0%), netilin (88.8%), ciprofloxacin (85.1%), norfloxacin (81.4%), ceftazidime (66.6%), streptomycin, chloramphenicol and tetracycline (62.5%), cefotaxime and nalidixic acid (55.5%), gentamicin (52.5%) and kanamycin (50.0%) but resistant to nitrofurantoin (66.6%), ampicillin (52.5%), amikacin (40.0%) and co-trimoxazole (37.5%). The presence of zoonotic E. coli along with multidrug strains in the milk and milk products may lead to food borne and systemic infections therefore; the sanitary quality should be maintained while handling food products

97. Assessment of the accuracy of direct antimicrobial susceptibility testing from positive blood cultures in pediatric patients and its utility as an antimicrobial stewardship tool

BackgroundHospitalized pediatric patients with bacteremia receive broad-spectrum antibiotics while organism identification and antibiotic susceptibilities are pending. Direct susceptibility testing (DST) using unstandardized Kirby-Bauer disk diffusion provides early results before standardized (final) antimicrobial susceptibility testing (AST) is available. The accuracy of DST in comparison with AST has been poorly studied. If DST is highly accurate, it could facilitate earlier de-escalation of antibiotics.MethodsRetrospective cohort study of all positive blood cultures at Boston Children’s Hospital between January 1, 2017 and October 20, 2019. Isolates were eligible for inclusion if a DST result was available. Isolates were excluded if more than one organism grew from a blood culture or if a patient had repeat blood cultures positive for the same organism within 14 days. Patient characteristics and antibiotic orders were identified via a local data warehouse. Positive and negative predictive value (PPV: accuracy of susceptibility on DST in identifying susceptibility on AST result; NPV: accuracy of DST in identifying non-susceptibility on AST result) and 95% confidence interval were calculated for each bug-drug combination. Antibiotic Spectrum Index was evaluated at 3 time points to assess change in antibiotic prescribing after availability of DST and AST results.Results496 patients (median age: 51 months, IQR: 7–165 months) with 603 positive blood cultures were included in the final analysis. PPV of DST was ≥96%for most organism-antibiotic pairs (Table). NPV of DST varied substantially across organism-antibiotic pairs and was frequently lower than PPV. The proportion of patients with more narrow spectrum antibiotic orders increased after the DST result and again after the AST result (Figure).TableTest performance of direct susceptibility testing (DST) of clinical isolates from patients with bacteremia to identify organism susceptibility to the noted antibiotic. Positive predictive value measures the ability of a susceptible DST result to predict a susceptible AST result. Negative predict value measures the ability of an intermediate or resistant DST result to predict an intermediate or resistant AST result. *Includes Staphylococcus capitis, Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus pettenkoferi, and Staphylococcus warneri. ‡Includes Citrobacter freundii complex, Citrobacter koseri, Enterobacter aerogenes, Enterobacter cloacae complex, Escherichia coli, Escherichia vulneris, Klebsiella oxytoca, Klebseilla pneumoniae, Klebsiella variicola, Pantoea species, Proteus mirabilis, Salmonella species, Salmonella typhi, Serratia liquefaciens, and Serratia marcescens. FigureDistribution of spectrum of antibiotics ordered to treat bacteremia in pediatric patients. Antibiotic spectrum, as measured by the antibiotic spectrum index, is represented in this Sankey diagram on the Y-axis. The height of each group indicates the proportion of patients with an aggregate antibiotic spectrum falling in that category at three time points. The ASI of empiric antibiotics was measured just before the DST result to provide time for a treating physician to settle on an empiric regimen. The ASI with the DST result was measured just before the ASI result. The ASI with the AST result was measured 24 hours after the AST result was available. Green bars indicate the proportion of patients within a group whose ASI remained unchanged between time points. Blue bars indicate the proportion of patients within a group whose ASI decreased, and red bars indicate the proportion of patients whose ASI increased between time points. ConclusionDST is highly accurate at identifying susceptibility to antibiotics for many bug-drug combinations in pediatric blood culture isolates, but its ability to identify non-susceptibility is less robust. The observed spectrum of prescribed antibiotics was narrower after DST results, suggesting some clinicians may be using the result to de-escalate therapy. DST may be a useful low-cost tool for antimicrobial stewardship.Disclosures All Authors: No reported disclosures

1673. Epidemiology of Complicated Urinary Tract Infections (cUTIs) Presenting in Emergency Departments Across the United States (US)

BackgroundComplicated urinary tract infection (cUTI) is a common emergency department (ED) diagnosis. Results of urine culture and antimicrobial susceptibility testing are usually not available for up to 48 hours after an ED visit; therefore, diagnosis and treatment decisions are empiric and based on symptoms, physical findings, and underlying risk of resistance. We sought to understand the epidemiology and incidence of resistance to commonly used oral antibiotics among patients presenting to US EDs with cUTI.MethodsA retrospective multi-center study using data from the Premier Healthcare Database (2013-18) was performed. Inclusion criteria: (1) age ≥ 18 years, (2) primary cUTI ED/inpatient discharge diagnosis, (3) positive blood or urine culture between index ED service days -5 to +2. Transfers from acute care facilities were excluded. We examined rates of resistance to the following drugs/classes: 3rd generation cephalosporins, fluoroquinolones, trimethoprim-sulfamethoxazole, fosfomycin, and nitrofurantoin in patients presenting to the ED, stratified by those who were ultimately admitted as inpatients vs. not. Regional variation by US Census Division was examined.Results187,789 patients met inclusion criteria; 119,668 (63.7%) were admitted to the hospital. 4.6% had positive cultures only with gram-positive bacteria; the remainder had at least one gram-negative pathogen. E. coli was the most common infecting pathogen, present in 72.1% of ED-only infections and 51.4% of those admitted. 44.7% and 58.4% of ED-only and admitted patients, respectively, were resistant to at least 1 of the 5 drugs/classes examined (see table). We saw substantial regional variation; resistance to at least 3 of 5 drugs/classes across all patients ranged from 5.0% in West North Central region to 11.1% in East South Central region (national average: 9.1%).Resistance Rates by Drug/Drug Class and Hospital Admission Status ConclusionPatients with cUTI infections presenting to EDs in the US are frequently resistant to many commonly used oral antibiotics, even in patients not admitted to the hospital. Local epidemiology and resistance should be considered when making empiric treatment decisions in the ED. New oral options for cUTI patients are needed to address the growing challenge of resistance.DisclosuresThomas Lodise, PharmD, PhD, Paratek Pharmaceuticals, Inc. (Consultant) Teena Chopra, MD, MPH, Spero Therapeutics (Consultant, Advisor or Review Panel member) Brian Nathanson, PhD, Spero Therapeutics (Independent Contractor) Katherine Sulham, MPH, Spero Therapeutics (Independent Contractor)

Antimicrobial Susceptibility of Mycoplasma bovis Isolates from Veal, Dairy and Beef Herds.

Mycoplasma bovis is an important pathogen causing mostly pneumonia in calves and mastitis in dairy cattle. In the absence of an effective vaccine, antimicrobial therapy remains the main control measure. Antimicrobial use in veal calves is substantially higher than in conventional herds, but whether veal calves also harbor more resistant M. bovis strains is currently unknown. Therefore, we compared antimicrobial susceptibility test results of M. bovis isolates from different cattle sectors and genomic clusters. The minimum inhibitory concentration of nine antimicrobials was determined for 141 Belgian M. bovis isolates (29 dairy, 69 beef, 12 mixed, 31 veal farms), and was used to estimate the epidemiological cut-off. Acquired resistance was frequently observed for the macrolides, while no acquired resistance to oxytetracycline and doxycycline, minimal acquired resistance to florfenicol and tiamulin, and a limited acquired resistance to enrofloxacin was seen. M. bovis isolates from beef cattle or genomic cluster III had higher odds of being gamithromycin-resistant than those from dairy cattle or genomic clusters IV and V. In this study, no cattle industry could be identified as source of resistant M. bovis strains. A single guideline for antimicrobial use for M. bovis infections, with a small remark for gamithromycin, is likely sufficient.

Development of a method for creating antibiograms for use in companion animal private practices.

To identify a method for developing antibiograms for use in companion animal private practices (PPs). Reports (n = 532) of aerobic bacterial culture and antimicrobial susceptibility testing performed between January 1, 2018, and December 31, 2018, at 11 PPs and 1 academic primary care practice (APCP). Data extracted from reports included patient identification number, laboratory accession number, patient signalment, collection method, body site, and results of bacterial culture and antimicrobial susceptibility testing. A custom antibiogram was then constructed with the help of commonly available software by adapting methods used by human hospitals. Susceptibility patterns of bacteria isolated by PPs and the APCP were compared to identify challenges associated with collating data from multiple laboratories. 4 bacterial species (Escherichia coli, Proteus mirabilis, Pseudomonas aeruginosa, and Staphylococcus pseudintermedius) and 3 bacterial groups (Enterobacteriaceae, Enterococcus spp, and coagulase-positive Staphylococcus spp) met the minimum requirement of ≥ 15 isolates for construction of an antibiogram. For urine samples, 3 bacterial species and 2 bacterial groups met the minimum requirement of ≥ 10 isolates. For samples from skin, 2 bacterial species and 2 bacterial groups met the minimum requirement of ≥ 10 isolates. Patient signalment, sample source, and distribution of bacterial isolates were similar between PP and APCP patients. Results demonstrated that it was feasible to adapt existing guidelines for developing antibiograms in human medicine to the veterinary outpatient setting. Use of antibiograms could aid in empirical antimicrobial drug selection in a manner that supports antimicrobial stewardship principles.

Occurrence of Multi-Drug Resistant Escherichia Coli and Escherichia Coli O157:H7 in Meat and Swab Samples of Various Contact Surfaces at Abattoir and Butcher Shops in Jimma Town, Southwest District of Ethiopia.

BackgroundRaw meat is one of the commonly consumed traditional diets in Ethiopia. However, unhygienic processing and distribution practices are risky for contamination of meat leading to human infection. This study was conducted to assess the presence of multi-drug resistant E. coli with special emphasis on E. coli O157:H7 from meat of cattle and swab samples at abattoir houses and butcher shops in Jimma town, Southwest district of Ethiopia.MethodologyA cross-sectional descriptive study was conducted from April to July, 2018. The isolation and identification processes passed through enrichment of samples with modified tryptone soy broth (mTSB), streaked onto MacConkey agar and Cefixime-tellurite sorbitol MacConkey agar, biochemical testing (indole and TSI), followed by latex agglutination testing.ResultsOut of 505 samples, 102 (20.2%) and 27 (5.4%) were positive for E. coli and E. coli O157:H7, respectively. Of these, 55 (19.3%) and 47 (21.4%) of E. coli and 17 (6.0%) and 10 (4.5%) of E. coli O157:H7 were isolated from the abattoir and butcher shop samples, respectively. A significant difference in the occurrences was observed among sample sources. Antimicrobial susceptibility test results showed that, 92.2% to 96.1% of E. coli and 85.5% to 96.3% of E. coli O157:H7 were susceptible to third generation cephalosporin, ciprofloxacin, gentamycin, kanamycin, streptomycin, and chloramphenicol. About 91.2% and 97.1% of E. coli and 88.9% and 92.6% of E. coli 0157:H7 were resistant to ampicillin and erythromycin, respectively. A total of 57 (44.2%) E. coli and E. coli O157:H7 isolates were resistant to three or more classes of antibiotics. All abattoir and butcher shop workers did not have any formal education or training certificates on food safety, and unhygienic practices were also observed.ConclusionThe presence of E. coli and E. coli O157:H7 including multi-drug resistant isolates in raw meat highlights how the current meat processing and distribution practice was unhygienic. Therefore, strategies in the prevention and control of food-borne infections that could be caused by multi-drug resistant strains will depend greatly on hygienic processing and distribution practices of meat.

Proficiency Testing Performances Analysis of Microbiology Laboratories Participating in Cambodia Antimicrobial Resistance (AMR) Surveillance System

Background: The WHO recommends the establishment of sustainable and evidence-based surveillance systems are recommended for the prevention of microbial resistance. For these surveillance systems, all medical microbiology laboratories are required to participate an external quality assessment (EQA) program that covers antimicrobial susceptibility testing (AST). Clinical microbiology EQA panels with 3 isolates have been provided 3 times per year to antimicrobial resistance (AMR) sentinel laboratories in Cambodia since 2012. We evaluated the performance of laboratory testing implemented between 2016 and 2019, based on 4 years EQA results to highlight the main sources of unsatisfactory analytical processes and to suggest areas for improvement. Methods: We analyzed the results of microbiology EQA in 7 AMR surveillance sentinel laboratories from 2016 to 2019, which were coordinated by the National Institute of Public Health (NIPH) under the program of Pacific Paramedical Training Centre (PPTC) from New Zealand. All participating laboratories were required to identify bacteria to the species level, to verify AST results, and to answer a case study question on parasitology. Feedback results and appropriate corrective actions were reviewed to identify the root cause of nonconformity and to suggest areas for improvement. Results: Proficiency test results of participating laboratories from 9 cycles with 27 isolates were analyzed. The overall average of EQA result was 94.0%. The laboratories failed to identify the isolated pathogens in 7.0% of the tests and failed to interpret the inhibition zone of AST (ie, resistant, intermediate or susceptible) in 6.0% of tested strains. The main causes of erroneous of PT results were either preanalytical (ie, handling of the samples, timing of analysis, equipment and reagent management), analytical (ie, quality control, unsuitable methods, confusion of samples, or errors of confirmation), or postanalytical mistakes (eg, interpretation guideline, cross-checking of results, or the information management system). Followed by the root causes, internal quality control and inventory management were the highest-priority suggestions for improvement. Conclusions: All participating laboratories showed good performance on EQA for evidence-based AMR surveillance. The national antimicrobial resistance data quality is sufficiently good and the data should be shared on national and international platforms. However, the regular monitoring of national AMR surveillance system should be conducted for continued quality improvement.Funding: NoneDisclosures: None

Is Only Clarithromycin Susceptibility Important for the Successful Eradication of Helicobacter pylori?

Resistance to clarithromycin and other antibiotics included in the eradication regimen, such as amoxicillin and metronidazole, is important for Helicobacter pylori (H. pylori) eradication. The aim of this study was to investigate the correlation between the results of antimicrobial susceptibility testing and the eradication rate, as well as to understand the importance of antimicrobial susceptibility testing in H. pylori eradication. We retrospectively reviewed the electronic medical records of 1862 patients who underwent gastric biopsy for the culture of H. pylori during upper endoscopy from March 2015 to June 2019. We tried to find a correlation between the results of the antimicrobial susceptibility testing and the eradication rate in patients who received standard triple or concomitant therapy. A total of 247 patients exhibited positive results for culture and underwent antimicrobial susceptibility testing. Of these, 146 received eradication therapy, with follow-up tests after treatment. In the standard triple therapy, patients who were susceptible to both clarithromycin and amoxicillin exhibited significantly higher eradication rates (85.9%) than those susceptible to clarithromycin and resistant to amoxicillin (75.0%) or those resistant to clarithromycin and susceptible to amoxicillin (44.4%) (p = 0.013). In the concomitant therapy, patients who were susceptible to both clarithromycin and metronidazole had significantly higher eradication rates (96.3%) than those susceptible to clarithromycin and resistant to metronidazole (88.9%) or those resistant to clarithromycin and susceptible to metronidazole (50.0%) (p = 0.016). There was a correlation between the results of antimicrobial susceptibility testing and the eradication rate for H. pylori. In addition to clarithromycin, susceptibility to amoxicillin and metronidazole is also important for the successful eradication of H. pylori.

Does the presence of multiple β-lactamases in Gram-negative bacilli impact the results of antimicrobial susceptibility tests and extended-spectrum β-lactamase and carbapenemase confirmation methods?

ObjectivesMany multidrug-resistant Gram-negative bacilli (MDR-GNB) harbour multiple β-lactamases. The aim of this study was to assess the impact of multiple β-lactamase carriage on the accuracy of susceptibility tests and extended-spectrum β-lactamase (ESBL) and carbapenemase confirmation methods. MethodsA total of 50 MDR-GNB, of which 29 carried multiple β-lactamases, underwent broth microdilution (BMD) and disk diffusion (DD) testing as well as confirmation tests for ESBLs and carbapenemases. Whole-genome sequencing (WGS) was used for β-lactamase gene identification. ResultsCategorical agreement of BMD and DD testing results ranged from 86.5 to 97.7% for 10 β-lactam agents. BMD and DD algorithms for ESBL detection were highly variable; 6 of 8 positive strains carried an ESBL plus a carbapenemase or an AmpC enzyme, which may confound antimicrobial selection. The sensitivity and specificity of the modified carbapenem inactivation method (mCIM) were both 100%, whilst mCIM and EDTA-modified carbapenem inactivation method (eCIM) when used together to differentiate serine from metallo-β-lactamase carriage were both 96%. Xpert® Carba-R results (in vitro diagnostic test) were consistent with WGS results. Predicting phenotypic carbapenem resistance from WGS data overall showed 100% specificity but only 66.7% sensitivity for Enterobacterales isolates that were non-susceptible to imipenem and meropenem. ConclusionsMultiple β-lactamases in MDR-GNB does not impact DD results, the utility of mCIM/eCIM tests, or Xpert Carba-R results. However, ESBL algorithms produced inconsistent results and predicting carbapenem resistance from WGS data was problematic in such strains.

Performance of a multiplex polymerase chain reaction panel for identifying bacterial pathogens causing pneumonia in critically ill patients with COVID-19

The FilmArray® Pneumonia Plus (FA-PP) panel can provide rapid identifications and semiquantitative results for many pathogens. We performed a prospective single-center study in 43 critically ill patients with coronavirus disease 2019 (COVID-19) in which we performed 96 FA-PP tests and cultures of blind bronchoalveolar lavage (BBAL). FA-PP detected 1 or more pathogens in 32% (31/96 of samples), whereas culture methods detected at least 1 pathogen in 35% (34/96 of samples). The most prevalent bacteria detected were Pseudomonas aeruginosa (n = 14) and Staphylococcus aureus (n = 11) on both FA-PP and culture. The FA-PP results from BBAL in critically ill patients with COVID-19 were consistent with bacterial culture findings for bacteria present in the FA-PP panel, showing sensitivity, specificity, and positive and negative predictive value of 95%, 99%, 82%, and 100%, respectively. Median turnaround time for FA-PP was 5.5 h, which was significantly shorter than for standard culture (26 h) and antimicrobial susceptibility testing results (57 h).

Clinical Performance and Impact of Accelerate Pheno for Gram-negative Bacteremia in Hospitalized Children

PurposeAccelerate Pheno provides rapid identification and antimicrobial susceptibility tests (ASTs) of pathogens that cause blood stream infections (BSIs). The study objective was to assess the accuracy of the Accelerate Pheno platform and its impact on antimicrobial modification in children with gram-negative BSIs. MethodsA retrospective review was conducted of patients at a children's hospital with gram-negative BSIs from November 2018 to November 2019. Proportion of agreement between Accelerate Pheno and standard of care (SOC) was determined for organism identification (matrix-assisted laser desorption ionization time-of-flight mass spectrometry) and susceptibilities (MicroScan). Time from culture collection to Gram stain, identification and AST by the Accelerate Pheno method, and AST results by MicroScan were calculated. Antibiotic modifications and opportunities to optimize antimicrobial stewardship were recorded. FindingsOf 115 BSIs from 90 patients, 90 monomicrobial gram-negative BSIs with an organism included on the Accelerate Pheno panel were found. Compared with SOC, the organism was correctly identified in 90 patients (100%). Overall, 5 of 732 ASTs (0.7%) reported susceptible by Accelerate Pheno were resistant by SOC, and 8 of 109 (7.3%) reported resistant by Accelerate Pheno were susceptible by SOC. On the basis of the Accelerate Pheno AST results, antibiotic spectrum was increased in 10 of 11 instances to correct organism-drug mismatch and narrowed in 16 of 33 instances. Median times from culture collection to reporting of Gram stain, Accelerate Pheno identification, Accelerate Pheno AST, and SOC AST were 12.6, 14.6, 19.9, and 60.6 h, respectively. Median time to optimal therapy was 21.8 h for infections with actionable AST data. ImplicationsAccelerate Pheno was accurate and decreased time to optimal therapy by almost 40 h for children with gram-negative BSIs. Antibiotic spectrum was increased in multiple instances, but opportunities to decrease spectrum were underused.