Clinical Enterobacterales Isolates Research Articles

Usefulness of EUCAST rapid antibiotic susceptibility breakpoints and screening cut-off values directly from blood cultures for the inference of β-lactam resistance mechanisms in Enterobacterales.

Reducing the turnaround time for reporting antimicrobial susceptibility testing (AST) results is important for adjusting empirical treatments and may impact clinical outcomes of septic patients, particularly in settings with high antimicrobial resistance. Disc diffusion could be useful for inferring β-lactam resistance mechanisms. To evaluate the usefulness of EUCAST rapid AST (RAST) disc diffusion breakpoints for the screening of resistance mechanisms (sRAST) and interpretive reading of resistance phenotypes to infer ESBL and carbapenemases production in Enterobacterales. Blood cultures were artificially spiked with Enterobacterales clinical isolates with well-characterized β-lactam resistance mechanisms (n = 93), WT phenotypes (n = 26) and ATCC strains (n = 8). AST was performed by disc diffusion directly from blood cultures and inhibition zones were manually measured at 4, 6 and 8 h. To infer the presence of resistance mechanisms, EUCAST RAST breakpoints and screening cut-off values (sRAST) combined with the double-disc synergy test (DDS) for ESBLs or aztreonam susceptibility for carbapenemases detection were used. DDS together with sRAST detected all ESBL producers as early as at 4 h incubation. Cefotaxime was the antibiotic with the highest discriminatory power. The suspicion of carbapenemase production by sRAST at 8 h was possible in 73% of Klebsiella pneumoniae and in 100% of Escherichia coli carbapenemase-producing isolates. Phenotypic analysis improves the detection of some low hydrolytic carbapenemases (OXA-48 or KPC-3 mutants). Early detection of β-lactam resistance mechanisms directly from positive blood cultures was possible using sRAST together with the interpretive reading of antibiotic resistance phenotypes. Some carbapenemase types such as OXA-48 might be difficult to infer. Screening-positive isolates should be confirmed using an alternative technique.

Identification and characterization of plasmids carrying the mobile colistin resistance gene mcr-1 using optical DNA mapping.

Colistin is a last-resort antibiotic, but there has been a rapid increase in colistin resistance, threatening its use in the treatment of infections with carbapenem-resistant Enterobacterales (CRE). Plasmid-mediated colistin resistance, in particular the mcr-1 gene, has been identified and WGS is the go-to method in identifying plasmids carrying mcr-1 genes. The goal of this study is to demonstrate the use of optical DNA mapping (ODM), a fast, efficient and amplification-free technique, to characterize plasmids carrying mcr-1. ODM is a single-molecule technique, which we have demonstrated can be used for identifying plasmids harbouring antibiotic resistance genes. We here applied the technique to plasmids isolated from 12 clinical Enterobacterales isolates from patients at a major hospital in Thailand and verified our results using Nanopore long-read sequencing. We successfully identified plasmids encoding the mcr-1 gene and, for the first time, demonstrated the ability of ODM to identify resistance gene sites in small (∼30 kb) plasmids. We further identified bla CTX-M genes in different plasmids than the ones encoding mcr-1 in three of the isolates studied. Finally, we propose a cut-and-stretch assay, based on similar principles, but performed using surface-functionalized cover slips for DNA immobilization and an inexpensive microscope with basic functionalities, to identify the mcr-1 gene in a plasmid sample. Both ODM and the cut-and-stretch assay developed could be very useful in identifying plasmids encoding antibiotic resistance in hospitals and healthcare facilities. The cut-and-stretch assay is particularly useful in low- and middle-income countries, where existing techniques are limited.

1672. Antimicrobial Activity of Cefepime-Taniborbactam and Comparators Against Clinical Isolates from ICU and Non-ICU Patients; 2018-2020 Global Surveillance

Abstract Background Taniborbactam is a novel cyclic boronate-based broad-spectrum β-lactamase inhibitor with selective direct inhibitory activity against both serine- and metallo-β-lactamases. Taniborbactam restores the activity of cefepime against many difficult to treat organisms, including cephalosporin- and carbapenem-resistant Enterobacterales (EB) and P. aeruginosa (PA). The activity of cefepime-taniborbactam (FTB) and comparator agents was evaluated against clinical isolates of EB and PA from a 2018-2020 global surveillance study. Methods 16,742 isolates of EB and PA were collected from patients in wards designated ICU and non-ICU in 2018-2020. MICs of FTB and comparators were determined by the CLSI reference method. Resistant (R) phenotypes were based on 2022 CLSI breakpoints. Multidrug resistant (MDR) was defined as resistance to at least one agent from ≥3 drug classes. Provisional susceptible (S) breakpoints of ≤8 µg/mL and ≤16 µg/mL were applied for FTB for comparative purposes only. Results FTB had potent activity against EB, with MIC90s of 0.25 µg/mL for isolates from non-ICU patients and 0.5 µg/mL for isolates from ICU patients (Table). At least 99.2% of all EB from both wards were inhibited by ≤8 µg/mL FTB. FTB maintained activity against R phenotypes of EB in both ward types, with 90.3% to 98.1% of isolates inhibited at ≤8 µg/mL. FTB had potent activity against PA, with MIC90 values of 8 µg/mL and inhibiting ≥94.0% of isolates at ≤8 µg/mL for both ICU and non-ICU isolates. FTB maintained activity against R phenotypes of PA in both ward types, with 71.0% to 83.7% of isolates inhibited at ≤8 µg/mL and 84.7% to 92.5% inhibited at ≤16 µg/mL. %S to comparator agents against the R subsets ranged from 1.6% to 92.6% for EB, and 36.0% to 68.4% for PA. Against the particularly challenging subset of MDR PA from ICU patients, FTB was the most active agent tested as it inhibited 73.5/84.7% of isolates at ≤8/≤16 µg/mL compared to 43.1%S to CZA and 36.0%S to C/T. Conclusion Cefepime-taniborbactam demonstrated potent in vitro activity against EB and PA from ICU and non-ICU wards, including resistant subsets of isolates. This supports the continued development of FTB as a potential new treatment option for infections due to resistant Gram-negative pathogens. Disclosures All Authors: No reported disclosures.

1718. In Vitro Activity of Imipenem/Relebactam against Class C β-lactamase-Positive Enterobacterales in the Asia/Pacific Region: SMART 2018-2020

Abstract Background Imipenem/relebactam (IMR) is a combination of imipenem/cilastatin with the β-lactamase inhibitor relebactam, an inhibitor of class A and C β-lactamases. We evaluated the activity of IMR and comparators against AmpC- and extended-spectrum β-lactamase (ESBL)-producing E. coli and K. pneumoniae as well as against isolates of intrinsic AmpC-producing Enterobacterales species that were collected in 9 countries in Asia/Pacific as part of the global SMART surveillance program. Methods In 2018-2020, 48 clinical laboratories in Australia, Hong Kong, Malaysia, New Zealand, Philippines, South Korea, Taiwan, Thailand, and Vietnam each collected up to 250 consecutive, aerobic or facultative, gram-negative pathogens per year from patients with bloodstream, intraabdominal, lower respiratory tract, and urinary tract infections. MICs were determined using CLSI broth microdilution and interpreted with 2022 CLSI breakpoints. Isolates that were ertapenem- (2018 only), imipenem-, IMR-, or ceftolozane/tazobactam-nonsusceptible were screened by PCR and Sanger sequencing for β-lactamases. Results As shown in the table, IMR maintained activity against ≥96% K. pneumoniae and E. coli that carried ampC with or without ESBL as well as against those intrinsic ampC carriers (except S. marcescens, 92.7%) among which no additional β-lactamases other than ESBLs were identified. The addition of relebactam increased the susceptibility to imipenem alone by 8-55 percentage points for K. pneumoniae and E. coli carrying AmpC with or without ESBL. Among intrinsic ampC carriers, the largest increase was seen among K. aerogenes (28 percentage points). Relebactam restored susceptibility to 97.3% of imipenem-nonsusceptible (NS) ampC-positive K. pneumoniae (n=73) and to 95.7%, 98.6%, and 37.7% of imipenem-NS isolates of E. cloacae complex (n=92), K. aerogenes (n=147), and S. marcescens (n=61) that carried no acquired β-lactamases. Among the imipenem-NS S. marcescens isolates, 50.8% tested with an IMR MIC of 2 µg/mL, which would be susceptible according to EUCAST guidelines. Conclusion IMR showed strong activity against clinical Enterobacterales isolates that carried either acquired or intrinsic ampC with or without ESBL collected in Asia/Pacific. Disclosures Fakhar Siddiqui, MD, MBA, Merck & Co., Inc.: employee|Merck & Co., Inc.: Stocks/Bonds Katherine Young, M.S., Merck & Co., Inc.: Stocks/Bonds.

1678. Activity of mecillinam against urinary tract clinical isolates from the United States during 2017-2020 including isolates resistant to comparator antibiotics and multi-drug resistant isolates

Abstract Background Mecillinam is a first-in-class amidinopenicillin antibiotic, being the only β-lactam to exert its antibacterial activity through exclusive binding to penicillin-binding protein 2. Pivmecillinam is the oral prodrug of mecillinam recommended as a first-line therapy by the Infectious Disease Society of America guidelines for uncomplicated urinary tract infections (uUTIs) and is approved for the treatment of uUTI in Europe and Canada though not yet in the USA. To support the clinical development of mecillinam and pivmecillinam in the USA for the treatment of cUTI and uUTI, this study investigated the activity of mecillinam compared with other antibiotics against Enterobacterales isolates from patients with UTI in the US during 2017-2020 Methods A total of 3303 Enterobacterales clinical isolates from UTIs from hospitals throughout the USA during 2017-2020 were tested. MIC tests were performed by agar dilution in line with CLSI susceptibility testing standards. Results Overall, susceptibility was highest for fosfomycin (97.1% susceptible) and mecillinam (94.9% susceptible). Against isolates resistant to ceftriaxone, ciprofloxacin, fosfomycin, nitrofurantoin and trimethoprim/sulfamethoxazole susceptibility to mecillinam was high with 89.6 %, 90.9 %, 82.4 %, 86.7 % and 93.6 %, respectively. Only fosfomycin exhibited similar activity to mecillinam. The most active antibiotics against MDR Enterobacterales were fosfomycin (86% susceptible) and mecillinam (79.2 % susceptible). Of the 288 MDR Enterobacterales, the majority were E. coli (n = 128) and K. pneumoniae (n = 103). The most active agents against MDR E. coli and MDR K. pneumoniae were fosfomycin and mecillinam that had susceptibilities of 93.8 % and 92.2 % and 79.6 % and 72.8 %, respectively. Conclusion Mecillinam exhibited promising activity against the majority of Enterobacterales tested. The drug was notably active against isolates resistant to antibiotics in routine clinical use and notably was similarly active against many MDR isolates. The data from our study strongly support the clinical utility of mecillinam and pivmecillinam in the USA for the treatment of cUTI and uUTI. Disclosures Anne Santerre Henriksen, PhD, UTILITY therapeutics Ltd: Advisor/Consultant.

659. In Vitro Activity of Ceftazidime-Avibactam and Comparator Agents against Enterobacterales Collected from Patients with Bloodstream Infections (BSI) as Part of the ATLAS (India) Surveillance Program, 2019-2020

Abstract Background Ceftazidime-avibactam (CAZ-AVI) is indicated for patients with bacteremia that occurs in association complicated intra-abdominal infection (cIAI), complicated urinary tract infection (cUTI) and hospital-acquired pneumonia (HAP). The present report evaluated the in vitro activity of CAZ-AVI and comparators against Enterobacterales clinical isolates collected from BSI as part of the ATLAS (The Antimicrobial Testing Leadership and Surveillance) surveillance program in 2019-2020 from India. Methods A total of 2126 Enterobacterales (493 from blood samples) non-duplicate clinically significant isolates, were collected from 2019-2020. In vitro activity of Ceftazidime-avibactam and its comparators were assessed against Enterobacterales blood isolates. Results Overall susceptibility to the β -lactam/β -lactamase inhibitor (BL-BLI) was 60 -76% for Enterobacterales. with highest susceptibility to Ceftazidime-avibactam. Overall highest susceptibility (97%) was noted for Tigecycline for Enterobacterales(n=476).The susceptibility to colistin was lower(83%) in Enterobacterales (n=409). Among 168 CR-Enterobacterales (CRE), Ceftazidime avibactam showed 29% susceptibility (n=49) while susceptibility to Tigecycline was 96%(n=161) followed by Colistin at 84%(n=141). Molecular analysis for CRE isolates showed 55 % (n=93) to be OXA-48 like producers (with or without NDM) ,68%(n=114)to be NDM producers (with or without OXA- 48) and 30%(n=51) to be co producers of OXA-48 like & NDM. In vitro activity of commonly used antibiotics against Enterobacterales, blood isolates (2019-2020) Conclusion Caz-Avi showed overall good susceptibility against the blood isolates tested hence it may be a valuable therapeutic option for treating BSI caused by MBL-negative Enterobacterales. Tigecycline followed by Colistin showed the highest susceptibilities. Tigecycline attains very low plasma concentrations and is not licensed for use in blood stream infections, while the use of colistin may be limited by the lack of CLSI susceptibility breakpoints and safety concerns. Disclosures Abhisek Routray, PhD, Pfizer India Limited: Advisor/Consultant Akshata Mane, MD, Pfizer India Limited: Advisor/Consultant|Pfizer India Limited: Stocks/Bonds.

Increasing trends of colistin resistance in patients at high-risk of carbapenem-resistant Enterobacteriaceae

Introduction Occurrence of colistin-resistant Enterobacteriaceae in response to the unregulated use of this antibiotic has been documented. This study reports an investigation of colistin resistance rates among carbapenem-resistant enterobacterial clinical isolates. Methods A total of 196 multidrug-resistant Enterobacteriaceae isolates (Klebsiella pneumoniae (n = 100), Escherichia coli (n = 89) and Enterobacter cloacae (n = 7) were selected from Gram-negative isolates over one year. Susceptibility to antimicrobials was determined using Vitek2. Broth microdilution method was used to detect colistin antimicrobial susceptibility. Identification of ESBL and carbapenemases were both done phenotypically and by PCR. Results All the studied isolates showed multidrug-resistant phenotypes with 51.5% resistance to carbapenems (meropenem, imipenem). Very low resistance rates towards tigecycline (n = 9) 4.6% were found. Thirty-nine isolates (19.9%) showed reduced susceptibility to colistin among the MDR isolates. Sixty-four isolates (32.7%) were ESBL producers. Hundred isolates (51%) were carbapenemase producers using Carba NP test. The PCR amplification results revealed that 40 isolates (20%) harboured NDM-1 and 40 isolates contained OXA-48-like gene. Coexistence of both (NDM-1 and OXA-48-like) was observed in nine (4.59%) isolates. A Statistically significant relationship was observed between carbapenem resistance and each of the followings; OXA-48 producers (p= .009), amikacin resistance (p = .000), gentamicin resistance (p = .032), tobramycin resistance (p = .000), and tigecycline resistance (p-value ≤ .001). A statistical significance was detected between ESBL-producing isolates and carbapenem susceptible isolates ESBL producers with p = 0.000. Conclusion An alarming sign is the increasing colistin resistance rates among carbapenem-resistant isolates. Aminoglycosides are still a therapeutic option to decrease the use of colistin and avoid further development of resistance. KEY MESSAGES High rates of colistin resistance among carbapenem-resistant Enterobacteriaceae. The choice of antibiotic is significantly associated with the clinical site of infection. Aminoglycosides are offered choices for treating multiple drug-resistant Enterobacteriaceae to preserve the colistin and carbapenems.

In vitro activity of aztreonam in combination with newly developed β-lactamase inhibitors against MDR Enterobacterales and Pseudomonas aeruginosa producing metallo-β-lactamases.

To evaluate the in vitro activity of aztreonam in combination with novel β-lactamase inhibitors, namely avibactam, nacubactam, taniborbactam and zidebactam, against MDR MBL-producing Enterobacterales and Pseudomonas aeruginosa clinical isolates. MIC values of aztreonam, aztreonam/β-lactam inhibitor but also cefiderocol as comparator were determined for 64 and 39 clinical Enterobacterales or P. aeruginosa isolates, respectively, producing representative MBLs, i.e. derivatives of NDM (n = 64), VIM (n = 32), IMP (n = 8) and SPM (n = 2). MICs were also determined for Escherichia coli TOP10 and P. aeruginosa PAO1 harbouring recombinant plasmids producing the different β-lactamases under isogenic backgrounds (n = 22 and n = 11, respectively). Fifty percent inhibitory concentrations were additionally determined for the abovementioned β-lactamase inhibitors using β-lactamase crude extracts. The susceptibility rate for aztreonam was 17.1% among MBL-producing Enterobacterales, while it was very high with aztreonam/zidebactam (98.4%), and to a lower extent with aztreonam/nacubactam (84.4%) and aztreonam/taniborbactam (75%), compared with aztreonam/avibactam (70.3%) and cefiderocol (39.1%). Among MBL-producing P. aeruginosa isolates, the susceptibility rates were 53.8% with aztreonam, 66.7% with aztreonam/nacubactam and aztreonam/taniborbactam combinations, and 69.2% with aztreonam/avibactam, aztreonam/zidebactam and cefiderocol. Altogether, these results showed that combinations including aztreonam and novel β-lactamase inhibitors, such as zidebactam, nacubactam or taniborbactam, have a very significant in vitro activity against MDR MBL-producing Enterobacterales clinical isolates, the aztreonam/zidebactam combination being the best option. On the other hand, aztreonam/zidebactam is equivalent to aztreonam/avibactam and cefiderocol among MBL-producing P. aeruginosa isolates.

Ceftibuten-Ledaborbactam Activity against Multidrug-Resistant and Extended-Spectrum-β-Lactamase-Positive Clinical Isolates of Enterobacterales from a 2018-2020 Global Surveillance Collection.

Ceftibuten-ledaborbactam etzadroxil is a cephalosporin-boronate β-lactamase inhibitor prodrug combination under development as an oral treatment for complicated urinary tract infections caused by multidrug-resistant (MDR) Enterobacterales producing serine β-lactamases (Ambler class A, C, and D). In vivo, ledaborbactam etzadroxil (formerly VNRX-7145) is cleaved to the active inhibitor ledaborbactam (formerly VNRX-5236). To more completely define the breadth of ceftibuten-ledaborbactam's activity against important antimicrobial-resistant pathogens, we assessed its in vitro activity against phenotypic and genotypic subsets from a 2018-2020 global culture collection of 3,889 clinical isolates of Enterobacterales, including MDR organisms, extended-spectrum-β-lactamase (ESBL)-positive organisms, and organisms that are nonsusceptible and resistant to other antimicrobials. MICs were determined by CLSI broth microdilution and interpreted using both CLSI and EUCAST breakpoints. Ledaborbactam was tested at a fixed concentration of 4 μg/mL. β-Lactamase genes were characterized by PCR followed by Sanger sequencing or whole-genome sequencing for selected β-lactam-resistant isolate subsets. At ≤1 μg/mL, ceftibuten-ledaborbactam (MIC90, 0.25 μg/mL) inhibited 89.7% of MDR isolates, 98.3% of isolates with a presumptive ESBL-positive phenotype, and 92.6% of trimethoprim-sulfamethoxazole-nonsusceptible, 91.7% of levofloxacin-nonsusceptible, 88.1% of amoxicillin-clavulanate-nonsusceptible, 85.7% of ceftibuten-resistant (MIC >1 μg/mL), and 54.1% of carbapenem-nonsusceptible isolates. Against specific ESBL genotype-positive isolates (AmpC negative, serine carbapenemase negative, and metallo-β-lactamase negative), ceftibuten-ledaborbactam inhibited 96.3% of CTX-M-9 group (MIC90, 0.25 μg/mL), 91.5% of CTX-M-1 group (MIC90, 0.5 μg/mL), and 88.2% of SHV-positive (MIC90, 2 μg/mL) isolates at ≤1 μg/mL. Against specific serine carbapenemase genotype-positive isolates, ceftibuten-ledaborbactam inhibited 85.9% of KPC-positive (MIC90, 2 μg/mL) and 82.9% of OXA-48-group-positive (MIC90, 2 μg/mL) isolates at ≤1 μg/mL. Continued development of ceftibuten-ledaborbactam appears warranted.

Activity of meropenem/vaborbactam and comparators against non-carbapenemase-producing carbapenem-resistant Enterobacterales isolates from Europe.

BackgroundCarbapenem-resistant Enterobacterales (CRE) isolates have disseminated worldwide. CREs usually produce a carbapenemase; however, some isolates are negative for known carbapenemases. In this study, we evaluated the activity of meropenem/vaborbactam and comparators against CREs without a carbapenemase (nonCP CREs) collected from European hospitals from 2016 to 2019.Materials and methods23 043 Enterobacterales clinical isolates were collected in 41 hospitals located in 20 countries. Susceptibility (S) testing was performed using the broth microdilution method. CLSI/EUCAST (2021) interpretive criteria were used. 978 CREs were identified with MICs >2 mg/L to meropenem or imipenem. Whole-genome sequencing was performed on each CRE isolate. 125 isolates were negative for carbapenemase genes, including blaKPC, blaNDM, blaIMP, blaVIM and blaOXA-48-like. NonCP CRE isolates were analysed for the presence of other β-lactamases, multilocus sequence types (ST) and mutations in outer membrane protein (OMP) sequences.ResultsMost nonCP CRE were Klebsiella pneumoniae (KPN; n = 97/125). 84.0% of nonCP CRE (n = 105) were from Poland, including 88 KPN. The most common β-lactamase was blaCTX-M-15 in 92/125 isolates. OMP disruptions or alterations were noted among 76 KPN. Among KPN isolates that had MLST typing, 30 belonged to ST11, 18 to ST152 and 17 to ST147, while 13 other STs were observed. Susceptibility to meropenem/vaborbactam was 96.0/97.6% (CLSI/EUCAST) while meropenem was 2.4/8.0%S.ConclusionsMeropenem/vaborbactam had potent in vitro activity against CRE isolates that lacked known carbapenemases. Resistance mechanisms observed among nonCP CREs included acquired β-lactamases and OMP alterations. These results indicate that meropenem/vaborbactam may be a useful treatment for infections caused by nonCP CREs.

Dominant Carbapenemase-Encoding Plasmids in Clinical Enterobacterales Isolates and Hypervirulent Klebsiella pneumoniae, Singapore.

Dissemination of carbapenemase-encoding plasmids by horizontal gene transfer in multidrug-resistant bacteria is the major driver of rising carbapenem-resistance, but the conjugative mechanics and evolution of clinically relevant plasmids are not yet clear. We performed whole-genome sequencing on 1,215 clinical Enterobacterales isolates collected in Singapore during 2010–2015. We identified 1,126 carbapenemase-encoding plasmids and discovered pKPC2 is becoming the dominant plasmid in Singapore, overtaking an earlier dominant plasmid, pNDM1. pKPC2 frequently conjugates with many Enterobacterales species, including hypervirulent Klebsiella pneumoniae, and maintains stability in vitro without selection pressure and minimal adaptive sequence changes. Furthermore, capsule and decreasing taxonomic relatedness between donor and recipient pairs are greater conjugation barriers for pNDM1 than pKPC2. The low fitness costs pKPC2 exerts in Enterobacterales species indicate previously undetected carriage selection in other ecological settings. The ease of conjugation and stability of pKPC2 in hypervirulent K. pneumoniae could fuel spread into the community.

Susceptibility of Meropenem-Resistant and/or Carbapenemase-Producing Clinical Isolates of Enterobacterales (Enterobacteriaceae) and Pseudomonas aeruginosa to Ceftazidime-Avibactam and Ceftolozane-Tazobactam as Assessed by In Vitro Testing Methods.

This study aimed to assess the comparability of in vitro susceptibility testing methods to ceftazidime-avibactam (CZA) and ceftolozane-tazobactam (C/T). Meropenem-resistant and/or carbapenemase-producing clinical isolates of Enterobacterales (Enterobacteriaceae) and Pseudomonas aeruginosa were tested by both bioMérieux ETEST and VITEK-2 AST-N397 card and compared with a Micronaut AST-system broth microdilution (BMD) method. CZA and C/T MICs were interpreted using EUCAST breakpoints. Of the 153 Enterobacteriaceae isolates, 55.6% and 0.0% (VITEK 2) and 56.9% and 0.0% (ETEST and BMD) were susceptible to CZA and C/T, respectively. Of 52 P. aeruginosa isolates, 50.0% and 40.4% (VITEK 2, ETEST, and BMD) were susceptible to CZA and C/T, respectively. The essential agreement (EA) was 96.1% (197/205; VITEK 2 versus BMD) and 95.6% (196/205; ETEST versus BMD) for CZA testing, whereas EA was 98.0% (201/205; VITEK 2 versus BMD) and 96.6% (198/205; ETEST versus BMD) for C/T testing. The categorical agreement (CA) was 98.0% (201/205; VITEK 2 versus BMD) and 100% (ETEST versus BMD) for CZA testing, whereas CA was 100% (VITEK 2 versus BMD) and 100% (ETEST versus BMD) for C/T testing. Categorical errors regarded four Enterobacteriaceae isolates. VITEK 2 and ETEST yielded equivalent CZA and C/T susceptibility testing results, compared to the BMD method, in such a clinical context.

MALDI-TOF mass spectrometry for direct KPC detection among Enterobacterales.

In this study, we evaluate a method for the KPC enzyme detection, using MALDI-TOF MS, for Enterobacterales. A total of 300 clinical Enterobacterales isolates were selected. The collection included 259 carbapenemase-producing (157 KPC and 102 non-KPC) and 41 carbapenemase non-producing isolates. Bacterial proteins were extracted from Mueller-Hinton agar plates using formic acid, isopropyl alcohol, and water (17:33:50). Samples were prepared with a double layer of synapinic acid. Analyses were performed using a Microflex LT mass spectrometer (Bruker Daltonics) and flexAnalysis 4.0 software (Bruker Daltonics). Statistical analyses were performed using SPSS Software. A distinctive peak at m/z 28,643-28,731 was found in all 157 KPC-producing isolates, and it was consistently absent in the 143 KPC non-producing group. KPC-producing peak intensities ranged from 77 to 3893. Considering an intensity cutoff value ≥ 120 for the presence of KPC, this methodology presented 98.09% and 97.90% of sensitivity and specificity, respectively.

Comparing the activity of novel antibiotic agents against carbapenem-resistant Enterobacterales clinical isolates.

We compared the activity of 8 novel β-lactam and tetracycline-derivative antibiotics against a cohort of clinical carbapenem-resistant Enterobacterales (CRE) isolates and investigated the incremental susceptibility benefit of the addition of an aminoglycoside, fluoroquinolone, or polymyxin to the β-lactam agents to assist with empiric antibiotic decision making. A collection of consecutive CRE clinical isolates from unique patients at 3 US hospitals (2016-2021) was assembled. Broth microdilution was performed to obtain antimicrobial susceptibility testing results. Mechanisms of carbapenem resistance were investigated through short-read and long-read whole-genome sequencing. Of the 603 CRE isolates, 276 (46%) were carbapenemase producing and 327 (54%) were non-carbapenemase producing, respectively. The organisms most frequently identified were Klebsiella pneumoniae (38%), Enterobacter cloacae complex (26%), and Escherichia coli (16%). We obtained the following percent susceptibility to novel β-lactam agents: ceftazidime-avibactam (95%), meropenem-vaborbactam (92%), imipenem-relebactam (84%), and cefiderocol (92%). Aminoglycosides and the polymyxins provided greater incremental coverage as second agents, compared to fluoroquinolones. Amikacin and plazomicin exhibited the greatest additive value. Ceftazidime-avibactam, meropenem-vaborbactam, and cefiderocol were active against 94% of the 220 KPC-producing isolates. Cefiderocol was active against 83% of the 29 NDM-producing isolates. Ceftazidime-avibactam had 100% activity against the 9 OXA-48-like-producing isolates. Tigecycline had the highest activity compared to other tetracyclines against KPC, NDM, or OXA-48-like-producing isolates. Selection among novel agents requires a nuanced understanding of the molecular epidemiology of CRE. This work provides insights into the comparative activity of novel agents and the additive value of a second antibiotic for empiric antibiotic decision making.

Two Newly Isolated Enterobacter-Specific Bacteriophages: Biological Properties and Stability Studies.

In an era of antibiotic therapy crisis caused by spreading antimicrobial resistance, and when recurrent urinary tract infections constitute a serious social and medical problem, the isolation and complex characterization of phages with a potential therapeutic application represents a promising solution. It is an inevitable, and even a necessary direction in the development of current phage research. In this paper, we present two newly isolated myoviruses that show lytic activity against multidrug-resistant clinical isolates of Enterobacter spp. (E. cloacae, E. hormaechei, and E. kobei), the genomes of which belong to a poorly represented phage group. Both phages were classified as part of the Tevenvirinae subfamily (Entb_43 was recognized as Karamvirus and Entb_45 as Kanagawavirus). Phage lytic spectra ranging from 40 to 60% were obtained. The most effective phage-to-bacteria ratios (MOI = 0.01 and MOI = 0.001) for both the phage amplification and their lytic activity against planktonic bacteria were also estimated. Complete adsorption to host cells were obtained after about 20 min for Entb_43 and 10 min for Entb_45. The phage lysates retained their initial titers even during six months of storage at both −70 °C and 4 °C, whereas storage at 37 °C caused a complete loss in their activity. We showed that phages retained their activity after incubation with solutions of silver and copper nanoparticles, which may indicate possible synergistic antibacterial activity. Moreover, a significant reduction in phage titers was observed after incubation with a disinfectant containing octenidinum dihydrochloridum and phenoxyethanol, as well as with 70% ethanol. The observed maintenance of phage activity during incubation in a urine sample, along with other described properties, may suggest a therapeutic potential of phages at the infection site after intravesical administration.

In vitro activity of aztreonam/avibactam against isolates of Enterobacterales collected globally from ATLAS in 2019

Objectives: Infections caused by drug-resistant Enterobacterales including those producing metallo-β-lactamases (MBLs) are particularly challenging due to limited therapeutic options. The drug combination aztreonam/avibactam (ATM-AVI) is under clinical development for treating serious infections caused by these strains. This study assessed the in vitro activity of ATM-AVI against Enterobacterales isolates collected globally in the ATLAS surveillance programme in 2019. Methods: Clinical isolates of Enterobacterales (N = 18 713) including Citrobacter freundii, Citrobacter koseri, Enterobacter cloacae complex, Escherichia coli, Klebsiella aerogenes, Klebsiella oxytoca, Klebsiella pneumoniae, Proteus mirabilis, and Serratia marcescens collected from 232 sites in 2019 were analysed. Antimicrobial susceptibility testing was performed by reference broth microdilution. A pharmacokinetic/pharmacodynamic based breakpoint of 8 mg/L was considered for ATM-AVI activity. Results: ATM-AVI demonstrated potent antimicrobial activity against all Enterobacterales, with 99.9% isolates inhibited at MIC ≤8 mg/L (MIC90, 0.25 mg/L). MICs ≤8 mg/L (>99.0%) were noted for ATM-AVI across regions worldwide. Among other antimicrobials, amikacin, colistin, imipenem, meropenem, and tigecycline were also active (susceptibility >85.0%) against Enterobacterales. Activity of ATM-AVI was sustained against multidrug-resistant, extended-spectrum β-lactamase producing, and carbapenem-resistant isolates (susceptibility >99%; MIC90, 0.25–0.5 mg/L). Importantly, potent activity for ATM-AVI (>99.0%; MIC90, 0.5 mg/L) was noted among MBL-positive isolates and those producing other carbapenemases, such as KPC and OXA-48. Conclusion: Our results demonstrated that ATM-AVI was highly active against a recent collection of Enterobacterales isolates, including those producing MBLs either alone or in combination with other carbapenemases. Thus, ATM-AVI represents a potential option for treating infections caused by antibiotic-resistant Enterobacterales including MBL-producing strains.

Performance evaluation of colistin rapid NP test for detection of colistin resistance in colistin resistant Enterobacterales

BackgroundCarbapenem-resistant Enterobacterales (CRE) have become a global threat, with colistin being the last resort for treatment. CLSI and EUCAST recommend broth microdilution (BMD) as the reference method for colistin susceptibility testing. Nordmann and Poirel have developed a simple and rapid Polymyxin NP test as an alternative to BMD for screening of colistin-resistant Enterobacterale (CoRE) isolates. This study aimed to evaluate the performance of the colistin rapid NP (CRNP) test for the detection of colistin resistance. MethodsCRNP test was performed on thirty-one clinical Enterobacterales isolates [Klebsiella pneumoniae (21), Enterobacter spp, (9) and Escherichia coli (1), which were resistant to Colistin by the reference BMD method. The results of the NP test were interpreted after 4hr by the change in color of NP solution (original orange to yellow as a result of bacterial growth) and compared with that of BMD. ResultsThe CRNP test could accurately detect 26/31 of the colistin resistant Enterobacterale isolates, and thus had an overall categorical agreement of 83.8%. Out of thirty-one CoRE isolates, five Enterobacter spp. 5/31 (16.1%) could not be detected by the CRNP test giving a false-negative result. Excluding those five Enterobacter spp. the categorical agreement (CA) of the CRNP test with BMD was 100%. The overall very major error (VME) of the CRNP test was 16% but decreased to < 3% when Enterobacter spp. (5) were excluded. ConclusionThe CRNP test is technically less demanding, yields faster results compared to the reference BMD method, and has 100% agreement with reference BMD in Enterobacterales except for Enterobacter spp.

Antimicrobial susceptibility profiles of clinically important bacterial pathogens at the Kamuzu Central Hospital in Lilongwe, Malawi.

The aim of this prospective study was to ascertain antimicrobial resistance (AMR) in clinical bacterial pathogens from in-hospital adult patients at a tertiary hospital in Lilongwe, Malawi. Clinical specimens (blood culture, pus, urine and cerebrospinal fluid) collected during June to December 2017 were examined for bacterial growth in standard aerobic conditions. One specimen per patient was included. Antimicrobial susceptibility testing (AST) was performed using the disk diffusion method and interpreted according to EUCAST guidelines. A total of 694 specimens were collected during the study period, of which 336 (48%) specimen yielded visible bacterial growth. Of the 336 specimens, a total of 411 phenotypically different isolates were recovered. Of the 411 isolates, 84 isolates (20%) were excluded and the remaining 327 (80%) were further characterised. The characterised isolates were identified as ESKAPE pathogens (n=195/327; 60%), Escherichia coli (n=92/327; 28%), Proteus mirabilis (n=33/327; 10) or Salmonella spp. (n=7/327; 2%) and were included for further analysis. The excluded isolates (n=84) comprised of coagulase-negative staphylococci (n=25), streptococci (n=33), and low-prevalence Gram-negative bacilli (n=26). E. coli (n=92; 28%) and S. aureus (n=86; 26%) were the most dominant species. A multidrug resistant (MDR) extended spectrum β- lactamase (ESBL)-positive phenotype was detected in Klebsiella pneumoniae (n=20/29; 69%) and E. coli (n=49/92; 53%). One third of the Pseudomonas aeruginosa isolates were resistant to meropenem (MEM), but did not appear to be carbapenemase-producers. Methicillin resistant Staphylococcus aureus (MRSA) was molecularly confirmed in 10.5% of S. aureus (n=9/86). The high proportion of the MDR ESBL-phenotype in clinical isolates of Enterobacterales, strongly limits antimicrobial treatment options and has consequences for empirical and targeted antimicrobial treatment as well as clinical microbiology services and hospital infection control. There is need for a continuous surveillance and an antimicrobial stewardship (AMS) program to contain and prevent the spread of AMR.

A Longitudinal Nine-Year Study of the Molecular Epidemiology of Carbapenemase-Producing Enterobacterales Isolated From a Regional Hospital in Taiwan: Predominance of Carbapenemase KPC-2 and OXA-48.

Enterobacterales clinical isolates are now being resistant to clinically achievable concentrations of most commonly used antibiotics that makes treatment of hospitalized patients very challenging. We hereby determine the molecular characteristics of carbapenemase genes in carbapenem-resistant Enterobacterales (CRE) isolates in Taiwan. A total of 455 CRE isolates were identified between August 2011 to July 2020. Minimum inhibitory concentrations for selected carbapenems were tested using Vitek 2, and carbapenemase genes were determined using polymerase chain reaction in combination with sequencing. Phenotypic detection of carbapenemase was determined by modified carbapenem inactivation method (mCIM) and EDTA-modified carbapenem inactivation method (eCIM) to validate our PCR screening results. Pulsed-field gel electrophoresis (PFGE) was used to determine the clonality of carbapenemase-producing Enterobacterales (CPE) isolates, and the transferability of carbapenemase-carrying plasmids was determined by conjugation assays. A slight increase in carbapenem-resistant E. coli (CREC) was observed, however, the prevalence of carbapenem-resistant K. pneumoniae (CRKP) was steady, during 2011–2020. The dominant species among our CRE was K. pneumoniae (270/455, 59.3%), followed by E. coli (81/455, 17.8%), Morganella morganii (32/455, 7.0%), and Enterobacter cloacae (25/455, 5.5%). From 2011 to 2020, the total percentage of CPE increased steadily, accounting for 61.0% of CRE in 2020. Moreover, 122 of 455 CRE isolates (26.8%) were CPE. Among the CPE isolates, the dominant carbapenemase gene was blaOXA–48–like (54/122, 44.3%), and the second most common carbapenemase gene was blaKPC–2 (47/122, 38.5%). The sensitivity and specificity for mCIM to detect carbapenemase in the 455 isolates were both 100% in this study. The PFGE results showed that 39 carbapenemase-producing E. coli and 69 carbapenemase-producing K. pneumoniae isolates carrying blaKPC–2 and/or blaNDM–5 could be classified into 5 and 12 clusters, respectively. In conclusion, our results showed an increase in CPE isolates in Taiwan. Moreover, the distribution of carbapenemase and antimicrobial susceptibility in CPE were associated with PFGE typing.

Activity of cefepime/taniborbactam and comparators against whole genome sequenced ertapenem-non-susceptible Enterobacterales clinical isolates: CANWARD 2007-19.

ObjectivesThis study assessed in vitro activities of cefepime/taniborbactam and comparator antimicrobial agents against ertapenem-non-susceptible Enterobacterales (ENSE) clinical isolates collected from the CANWARD study 2007–19, and associations between MIC and various mechanisms of β-lactam resistance identified using WGS.MethodsA total of 179 ENSE (MIC ≥ 1 mg/L) isolates underwent susceptibility testing using reference CLSI broth microdilution. WGS was performed using the Illumina NextSeq platform. Carbapenemases, ESBLs and other β-lactamases were identified using ResFinder 4.0. Alterations in ompC/F and ftsI (PBP3) were identified by comparing extracted sequences to the appropriate NCBI reference gene. Porin alterations were analysed with Provean v1.1.3. Specific alterations of interest in PBP3 included a YRIN or YRIK insertion after P333.ResultsCefepime/taniborbactam was highly active (MIC50/MIC90, 0.5/2 mg/L; 177/179 isolates inhibited at ≤ 8 mg/L) against ENSE with various antimicrobial resistance phenotypes. Thirteen (7.3%) of the 179 ENSE isolates demonstrated cefepime/taniborbactam MIC values ≥ 4 mg/L and possessed combinations of β-lactam resistance mechanisms, including a carbapenemase and/or ESBL and/or other β-lactamase genes, as well as alterations in OmpC and/or OmpF and/or PBP3. Of the two Escherichia coli isolates that demonstrated a cefepime/taniborbactam MIC of 32 mg/L, one possessed NDM-5, OXA-181 and TEM-1B, an OmpC alteration and P333_Y334insYRIN in PBP3, while the second contained CTX-M-71, a truncated OmpF and a large alteration in OmpC (F182_R195delinsMTTNGRDDVFE).ConclusionsCefepime/taniborbactam was highly active against ENSE with various antimicrobial resistance phenotypes/genotypes. ENSE isolates with cefepime/taniborbactam MIC values ≥ 4 mg/L possessed combinations of β-lactam resistance mechanisms, including β-lactamase genes, as well as alterations in OmpC and/or OmpF and/or PBP3.