Carbapenemase-producing Enterobacterales infections: Recent advances in diagnosis and treatment

Rapid detection of Klebsiella pneumoniae based on one-tube RPA-CRISPR/Cas12a system

Klebsiella pneumoniae (KP) is a prevalent pathogen implicated in both community-acquired and nosocomial infections, often leading to severe clinical outcomes. The conventional methods for KP identification are characterized by intricacy and suboptimal efficiency. In this research, we have engineered a novel One-Tube RPA- CRISPR/Cas12a system, integrating recombinase polymerase amplification (RPA) method with the CRISPR/Cas12a diagnostic platform, to facilitate the detection of K. pneumoniae. To minimize the likelihood of aerosol-based contamination, the RPA components are positioned at the base of the tube, while the CRISPR/Cas12a components are placed at the tube's cap. The systems are combined post-RPA amplification through a brief centrifugation step, ensuring that RPA reactions are conducted independently to produce an adequate amount of target DNA before interaction with the CRISPR/Cas12a system. This method was validated using both fluorescent and lateral flow strip assays, achieving a limit of detection (LOD) of 100 copies/μL and 101 copies/μL respectively. The specificity for KP detection was found to be 100 %. Furthermore, the system demonstrated a positivity rate of 78 % (18/23) when directly extracting DNA from sputum samples, corroborated by culture and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). The simplicity and rapidity of the assay are augmented by a straightforward sample processing without extraction. The complete assay duration from specimen receipt to result is approximately 40 min, significantly reducing the turnaround time (TAT). Collectively, this system presents a streamlined, expeditious, and highly specific diagnostic approach for the detection of Klebsiella pneumoniae strains.

Antimicrobial resistance among imipenem-non-susceptible Escherichia coli and Klebsiella pneumoniae isolates, with an emphasis on novel β-lactam/β-lactamase inhibitor combinations and tetracycline derivatives: The Taiwan surveillance of antimicrobial resistance program, 2020-2022

BACKGROUND

To determine susceptibility of imipenem-non-susceptible Escherichia coli (INS-EC) and Klebsiella pneumoniae (INS-KP) isolates collected during 2020-2022 through a national surveillance program in Taiwan to novel antibiotics, and to compare the results with those obtained during 2012-2018.

METHODS

Minimum inhibitory concentrations were determined by broth microdilution methods. Genes encoding carbapenemases including blaKPC, metallo-β-lactamase (MBL) genes, and blaOXA-48 were detected via multiplex PCR. Data retrieved from our 2012-2018 study were used for comparison.

RESULTS

Of 3260 E. coli and 1457 K. pneumoniae isolates collected during 2020-2022, 0.9 % and 9.5 %, were INS-EC and INS-KP, respectively. Cefepime-zidebactam, ceftazidime-avibactam, imipenem-relebactam, and meropenem-vaborbactam were active against 100 %, 75.9 %, 65.5 %, and 79.3 % of 29 INS-EC isolates respectively; and against 100 %, 90.6 %, 64.5 %, and 67.4 % of 138 INS- KP isolates, respectively. Susceptibility was contingent upon carbapenemase types. Susceptibility rates of cefepime-zidebactam and ceftazidime-avibactam remained constant from 2012 to 2018 through 2020-2022 but those of imipenem-relebactam and meropenem-vaborbactam decreased significantly, which may be partially attributable to the increasing prevalence of blaOXA-48. Eighteen MBL-gene-positive isolates and two blaKPC-positive isolates were resistant to ceftazidime-avibactam, whereas all were susceptible to cefepime-zidebactam. Tigecycline had a higher susceptibility rate than eravacycline and omadacycline for K. pneumoniae isolates. Lascufloxacin and delafloxacin were effective against fewer than 10 % of INS isolates. Susceptibilities to novel tetracyclines and fluoroquinolones remained similar from 2012 to 2018 through 2020-2022.

CONCLUSIONS

This study highlights significant resistance patterns of INS-EC and INS-KP isolates in Taiwan. The declining susceptibility rates and the rising prevalence of genetic resistance determinants highlight the importance of ongoing surveillance and antimicrobial stewardship.

Insertion sequences in mgrB and mutations in two-component system genes confer high polymyxin resistance to carbapenem-resistant Enterobacter cloacae complex strains

Due to the complexity of identifying the Enterobacter cloacae complex (ECC) at the species level, little is known about the distribution of carbapenem-resistant ECC (CRECC). Plasmid-mediated mcr family genes are significant contributors to polymyxin resistance. The emergence of the mcr-9 gene has further complicated the landscape of polymyxin resistance in CRECC. Our study aimed to ascertain the prevalence of CRECC and the mcr-9 gene, and to elucidate the mechanisms underlying high-level resistance to polymyxin B (PB). In this study, we collected 212 non-replicating ECC strains, identifying 38 CRECC strains (17.9%, 38/212) and Enterobacter hormaechei (71.1%, 27/38) as the predominant endemic strains. Among these, 10 CRECC strains (36.3%, 10/38) were found to harbor the mcr-9 gene. Interestingly, the presence of mcr-9 did not significantly impact PB resistance or impose a fitness cost. While overexpression of mcr-9 can enhance PB resistance within a certain range and may incur fitness costs, it does not result in high-level PB resistance. The PB resistance of 17 CRECC strains was notably increased (from 16 to 128 mg/L), accompanied by mutations in the phoP/Q and mgrB genes. Notably, two novel insertion sequences, IS5D and IS1X2, were discovered within the mgrB gene. The inactivation of mgrB results in the loss of its negative regulatory effect on the two-component system. Protein structure predictions indicated that mutations in phoQ primarily affect the phosphatase (HAMP) and histidine kinase domains. This research significantly expands our comprehension of the complexities of PB resistance, highlighting the multifactorial nature of antibiotic resistance mechanisms.

Complete genome sequences of two verona integron-encoded metallo-ß-lactamase (VIM)-producing enterobacterales isolated from dogs in the United States

This announcement reports the complete genome sequences, created by combined Illumina and Oxford Nanopore sequencing, of two carbapenemase-producing Enterobacterales (Escherichia coli [LaAc-1-20] and Enterobacter hormaechei, strain 19632-21) isolated from dogs in the United States. Both isolates harbor a blaVIM-4 gene found on a 47 kb plasmid and on the bacterial chromosome, respectively.

Standard dose could be better! A multicenter study of tigecycline in patients with liver failure

BACKGROUND

High-dose (HD) tigecycline is often required for severe multidrug-resistant gram-negative infections in liver failure patients, despite package recommendations to halve the dose for those with severe liver impairment. This study evaluated the efficacy and safety of different tigecycline doses in this population.

RESEARCH DESIGN AND METHODS

A retrospective cohort of 192 patients with Child-Pugh grade C liver failure was divided into label-dose (LD), standard-dose (SD), and HD groups. Primary and secondary outcomes included microbial eradication, mortality, and adverse effects.

RESULTS

The SD group achieved higher microbial eradication than LD, with comparable efficacy to HD but fewer adverse events, such as fibrinogen requirements. High-dose treatment increased mortality risk (Hazard Ratio: 1.85, p = 0.062). Optimal microbial eradication and minimized adverse effects occurred with the SD group at 7 days of treatment.

CONCLUSIONS

Standard-dose tigecycline offers a balanced approach to microbial eradication and safety, making it preferable in liver failure patients.

Phenotypic and genomic characterization of ST11-K1 CR-hvKP with highly homologous blaKPC-2-bearing plasmids in China

Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) strains present a significant global public health threat due to their high mortality rates. This study investigated the genomic characteristics of seven ST11-K1 CR-hvKP isolates harboring highly homologous KPC-2-encoding multidrug-resistance plasmids. The strains were isolated from a Chinese tertiary hospital between 2017 and 2020. Whole-genome sequencing and bioinformatic analysis revealed various antibiotic resistance genes (ARGs) and virulence determinants. The blaKPC-2-bearing plasmids that contain multiple antibiotic-resistance genes were also identified in these strains. ISfinder and Orifinder were applied to identify insertion sequences (IS) and conjugation-related factors among these blaKPC-2-bearing plasmids. The blaKPC-2 was highly consistent in seven blaKPC-2-bearing plasmids (ISKpn6-blaKPC-2-ISKpn27-ISYps3-IS26). In addition, we found a region composed of ISIR, Tn5393, and IS26. It was located upstream of the blaCTX-M-15 gene and presented in six blaKPC-2-bearing plasmids, with pCR-hvKP221-KPC-P3 as an exception. Conjugation experiments demonstrated the horizontal transfer of resistance plasmids pCR-hvKP128-KPC-P1 and pCR-hvKP132-KPC-P1 across species. Notably, pLVPK-like virulence plasmids carrying virulence gene clusters pCR-hvKP173-Vir-P1, and pCR-hvKP221-Vir-P1 were also detected. A fusional plasmid pCR-hvKP221-Vir-P2, which carries virulence gene clusters and ARGs, was also identified. Five CR-hvKP strains displayed enhanced biofilm formation and high virulence in vivo infection models. Phylogenetic and single nucleotide polymorphism (SNP) analyses indicated a close genetic relationship among the isolates, suggesting a subclade. These findings highlight the complex genetic profiles and potential transmission mechanisms of CR-hvKP strains.

IMPORTANCE

We reported seven CR-hvKP strains all carried a highly homologous blaKPC-2 integrated IncFⅡ-resistant plasmid, and two strains harbored virulence plasmids. Conjugation experiments confirmed the transferability of these plasmids, indicating a potential for resistance spread. Phylogenetic analysis clarified the relationship among the CR-hvKP isolates. This study provides insights into the phenotypic and genomic characteristics of seven ST11-K1 CR-hvKP strains. The high prevalence and potential for local outbreaks emphasize the need for effective control measures.

Modified Carba PBP test for rapid detection and differentiation between different classes of carbapenemases in Enterobacterales

An advanced biochemical assay named modified Carba PBP test was innovated to identify and differentiate distinct categories of clinically significant carbapenemases (Ambler classes A, B, and D) within the Enterobacterales. The mechanism of mCarba PBP hinges on two core attributes: (i) the hydrolysis of the meropenem substrate by various carbapenemases, (ii) the immobilized penicillin and free meropenem in their affinity to interact with a limited quantity of penicillin-binding protein (PBP). Specific inhibitors for class A (phenylboronic acid, PBA) and class B (ethylenediaminetetraacetic acid, EDTA) were employed to inhibit the hydrolysis activity of carbapenemase and facilitate the classification of carbapenemase classes within 25 min. A comprehensive evaluation was undertaken using 94 clinical Enterobacterales isolates, comprising 75 carbapenemase-producing strains and 19 non-carbapenemase-producing strains. Its overall specificity and sensitivity were 100% and 97.3%, respectively, including detection of all types of OXA-48-like carbapenemases. For precise carbapenemase type identification, the assay exhibited remarkable sensitivities for class A, class B, and class D detection at 94.7%, 100%, and 100%, respectively. This user-friendly test presents a promising tool for carbapenemase identification, refining the selection of β-lactam/β-endoenzyme inhibitor combinations for effectively treating infections due to carbapenemase-producing organisms.

In vivo development of resistance to novel β-lactam/β-lactamase inhibitor combinations in KPC-producing Klebsiella pneumoniae infections: a case series

INTRODUCTION

Understanding the dynamics that may characterize the emergence of KPC variants with resistance to novel β-lactam/β-lactamase inhibitor combinations (βL/βLICs) represents a challenge to be overcome in the appropriate use of recently introduced antibiotics.

METHODS

Retrospective case series describing development of multiple resistance to novel βL/βLICs in patients with KPC-producing Klebsiella pneumoniae (KPC-Kp) infections treated with these drugs. Clinical-microbiological investigation and characterization of longitudinal strains by Whole-Genome Sequencing were performed.

RESULTS

Four patients with KPC-Kp bloodstream infections were included. Most frequent clinical features were kidney disease, obesity, cardiac surgery as reason for admission, ICU stay, treatment with ceftazidime/avibactam, and pneumonia and/or acute kidney injury needing renal replacement therapy as KPC-Kp sepsis-associated complications. The development of resistance to ceftazidime/avibactam was observed in four longitudinal strains (three of which were co-resistant to aztreonam/avibactam and cefiderocol) following treatments with ceftazidime/avibactam (n = 3) or cefiderocol (n = 1). Resistance to meropenem/vaborbactam and imipenem/cilastatin/relebactam was observed in one case after exposure to ceftazidime/avibactam and imipenem/cilastatin/relebactam. Resistome analysis showed that resistance to novel βL/βLICs was related to specific mutations within blaKPC carbapenemase gene (D179Y mutation [KPC-33]; deletion Δ242-GT-243 [KPC-14]) in three longitudinal strains, while porin loss (truncated OmpK35 and OmpK36 porins) was observed in one case.

CONCLUSION

Therapy with novel βL/βLICs or cefiderocol may lead to the selection of resistant mutants in the presence of factors influencing the achievement of PK/PD targets. KPC variants are mainly associated with resistance to ceftazidime/avibactam, and some of them (e.g. KPC-14) may also be associated with reduced susceptibility to aztreonam/avibactam and/or cefiderocol. Loss of function of the OmpK35 and OmpK36 porins appears to play a role in the development of resistance to meropenem/vaborbactam and/or imipenem/relebactam, but other mechanisms may also be involved.

Novel agents in development for the treatment of resistant Gram-negative infections

INTRODUCTION

Several novel agents are in advanced stages of clinical development, potentially expanding our treatment options against third- and fourth-generation cephalosporin-resistant and carbapenem-resistant Gram-negative bacteria (GNB), including those pathogens for which the current number of effective treatments is limited.

AREAS COVERED

This review focuses on agents that have completed or ongoing phase-3 studies. A PubMed search was conducted up to 31 May 2024.

EXPERT OPINION

Novel agents in late-stage clinical development belong to the β-lactam or β-lactam/β-lactamase inhibitor combinations class and display variable antimicrobial activity depending on the specific β-lactamases expressed by GNB, particularly carbapenemases. While many of these novel agents demonstrate in vitro activity against carbapenem-resistant GNB, their efficacy has mainly been evaluated in phase-3 randomized controlled trials (RCT) for infections caused by carbapenem-susceptible GNB. Although evidence from real-world observational studies is generally less robust than that from RCT, it could be crucial for updating clinical guidelines on treating carbapenem-resistant GNB with these new agents in the absence of dedicated RCT.

Performance of Ertapenem-Supplemented MacConkey Agar (MacErt) for Detecting Carbapenemase-Producing Enterobacterales

Background and objectives Antimicrobial resistance (AMR) is a growing global threat, with carbapenemase-producing Enterobacterales (CPEs) representing a critical public health challenge. Rapid and accurate detection of CPEs is essential for controlling fatal bacterial AMR infections. This study evaluated the performance of MacConkey media supplemented with ertapenem (MacErt1 and MacErt2) for the detection of CPEs. Methods We formulated the media by supplementing MacConkey agar with ertapenem to final concentrations of 0.5 mg/L (MacErt1) and 1 mg/L (MacErt2). The media were assessed using a panel of 26 characterized Enterobacterales, including CPEs harboring oxacillinase (OXA)-48, OXA-181, New Delhi metallo-beta-lactamase (NDM)-5, and Klebsiella pneumoniae carbapenemase (KPC). All isolates were cultured on Mueller Hinton agar and incubated overnight at 36°C. Inocula were prepared and adjusted to a 0.5 McFarland standard. Ten microliter loops were used to streak MacErt1 and MacErt2 plates, which were then incubated overnight. After validation, MacErt1 was employed for the detection of CPEs in wastewater. A volume of 10 mL of wastewater was filtered, and the membrane was placed on MacErt agar, followed by overnight incubation. Grown colonies were identified using the Biotyper Sirius 2 MALDI-TOF (Bremen, Germany: Bruker), and the presence of carbapenem resistance genes was determined by lateral flow immunoassay (LFIA) tests and PCR. Results MacErt1 exhibited excellent sensitivity (100%) for all tested CPEs and a specificity of 77%. In contrast, MacErt2 demonstrated an overall sensitivity of 83%, primarily due to reduced sensitivity for OXA-181. However, it was 100% sensitive for detecting NDM, KPC, and OXA-48 producers. MacErt2 also maintained excellent specificity at 93%. The application of MacErt1 to wastewater samples resulted in 100% positivity and allowed the isolation of 124 CPEs among 150 examined isolates, predominantly NDM producers, followed by OXA-48-like and NDM+OXA-48-like strains. None of the isolates tested positive for blaKPC, blaVIM, or blaIMP. Conclusion This study demonstrated the efficacy of MacErt media for selectively detecting CPEs. MacErt1 exhibited 100% sensitivity for various CPEs and a specificity of 77%. MacErt2 showed 93% specificity and 100% sensitivity for NDM and KPC producers, making it suitable for targeted detection. These findings suggest that MacErt media provide an effective in-house solution for CPE surveillance, serving as a valuable tool in the ongoing battle against AMR.

Direct Klebsiella pneumoniae Carbapenem Resistance and Carbapenemases Genotype Prediction by Al-MOF/TiO2@Au Cubic Heterostructures-Assisted Intact Bacterial Cells Metabolic Analysis

Carbapenem-resistant Klebsiella pneumoniae (CRKP) infections pose a significant threat to human health. Fast and accurate prediction of K. pneumoniae carbapenem resistance and carbapenemase genotype is critical for guiding antibiotic treatment and reducing mortality rates. In this study, we present a novel method using Al-MOF/TiO2@Au cubic heterostructures for the metabolic analysis of intact bacterial cells, enabling rapid diagnosis of CRKP and its carbapenemases genotype. The Al-MOF/TiO2@Au cubic composites display strong light absorption and high surface area, facilitating the in situ effective extraction of metabolic fingerprints from intact bacterial cells. Utilizing this method, we rapidly and sensitively extracted metabolic fingerprints from 169 clinical isolates of K. pneumoniae obtained from patients. Machine learning analysis of the metabolic fingerprint changes successfully distinguishes CRKP from the sensitive strains, achieving the high area under the curve (AUC) values of 1.00 in both training and testing sets based on the 254 m/z features, respectively. Additionally, this platform enables rapid carbapenemase genotype discrimination of CRKP for precision antibiotic therapy. Our strategy holds great potential for swift diagnosis of CRKP and carbapenemase genotype discrimination, guiding effective management of CRKP bacterial infections in both hospital and community settings.

Evaluation of blaOXA-48-like point mutation carbapenemase-producing Enterobacterales in Prapokklao Hospital, Thailand

Carbapenemase-producing Enterobacterales (CPE) isolates increasingly carry oxacillinase-48 (OXA-48)-like enzymes encoded by blaOXA-48-like, which can confer high levels of carbapenem resistance. This aims to determine the prevalence of CPE and genetic variation among blaOXA-48-like-carrying isolates recovered from Prapokklao Hospital in Chanthaburi Province, Thailand in 2016-2017. In total, 122 carbapenem-resistant Enterobacterales (CRE) isolates were recovered from clinical samples. CRE were evaluated using standard biochemical tests and MIC test strips. Carbapenemase production was assessed through the modified Hodge test (MHT), modified carbapenem inactivation method (mCIM), and EDTA-modified carbapenem inactivation method (eCIM). Detection of blaOXA-48-like mutations was conducted via PCR and confirmed by Sanger sequencing. Among these CRE isolates, 72 (59.02%), 44 (36.07%), 3 (2.46%), and 3 (2.46%) were Klebsiella pneumoniae, Escherichia coli, Enterobacter aerogenes, and Enterobacter cloacae, respectively. The MHT identified carbapenemase production in 108 isolates (88.52%). Based on the mCIM, 81 isolates (66.39%) were carbapenemase producers. Seventy-three isolates (59.84%) were eCIM-positive, indicating metallo-β-lactamase production. Three distinct genetic variants of the blaOXA-48-like gene were identified among the isolates, including the wild-type and two point mutation types harboring the mutations E168Q and S171A (mutation type 1) and E168Q, S171A, and R214S (mutation type 2). Multiple-sequence alignment and in silico analysis revealed variation of R214 located in the β5-β6 loop. This study identified blaOXA-48-like point mutation groups and carbapenemase production, predominantly metallo-β-lactamases, among CRE isolates, especially K. pneumoniae and E. coli. These findings highlight the importance of implementing stringent infection control measures and active antimicrobial resistance surveillance to combat the spread of difficult-to-treat, metallo-β-lactamase-producing CRE in healthcare settings.

IMPORTANCE

In this study, we aimed to investigate genetic variation and CPE among blaOXA-48-like carrying isolates recovered from Prapokklao Hospital, Chanthaburi Province, Thailand, during 2016-2017. A total of 122 carbapenem-resistant Enterobacterales (CRE) were recovered from clinical samples in Prapokklao Hospital. All CRE samples were confirmed by standard biochemical tests and minimum inhibitory concentration (MIC) test strips (E-test). The carbapenemase production was determined using the modified Hodge test (MHT), the modified carbapenem inactivation method (mCIM), and EDTA-CIM (eCIM). Three single mutations (E168Q, S171A, and R214S) were characterized in this study. This mutation might reflect the hydrolysis of the modified β-lactam spectrum, especially carbapenem, by OXA-48-like. Our report provides evidence of the blaOXA-48-like point mutation and carbapenemase-producing phenotype of CRE detected in this healthcare setting. Effective control measures and active surveillance of drug resistance in nosocomial pathogens are crucial for controlling diseases associated with difficult-to-treat bacteria.

High prevalence of colonization with extended-spectrum β-lactamase-producing and multidrug-resistant Enterobacterales in the community in Addis Ababa Ethiopia: risk factors, carbapenem resistance, and molecular characterization

BACKGROUND

Globally, extended-spectrum beta-lactamase-producing and carbapenem-resistant Enterobacterales are major causes of hospital-acquired infections and there are increasing concerns about their role in community-acquired infections.

OBJECTIVE

We aimed to investigate the prevalence of extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) and Carbapenemase-producing-Carbapenemresistant-Enterobacterales (CP-CRE) and associated factors in community settings in Gulele sub city, Addis Ababa, Ethiopia.

METHODS

A cross-sectional study was conducted among 261 healthy individuals. Stool samples were collected and processed using standard microbiological methods. Antimicrobial susceptibility and phenotypic ESBL and carbapenemase tests were performed. Antibiotic resistance genes were detected by Polymerase Chain Reaction (PCR).

RESULTS

The colonization rate of ESBL-PE and CP-CRE were 31.4% (82/261, 95% CI: 25.91-37.48) and 0.8% (2/261, 95% CI: 0.13-3.1), respectively by phenotypic method. Molecular detection of genes for ESBL-PE was 27.9% (73/261, 95% CI:22.7-33.9), and for CP-CRE was 0.8% (2/261, 95% CI: 0.13-3.1). The most prevalent genes were blaTEM [76.7% (56/73)] and blaCTX-M [45.2% (33/73)]. Previous antibiotic use (AOR:2.04, 95%CI: 1.35-4.41, P:0.041) and age between 42 and 53 years old (AOR:3.00, 95%CI:1.12-7.48, P:0.019) were significantly associated with ESBL-PE colonization.

CONCLUSION

Intestinal colonization by ESBL-PE harboring the associated antibiotic resistance genes was substantially high but with low CP-CRE. Continued surveillance of community-level carriage of antimicrobial resistance Enterobacterales is warranted.

Investigation of in vitro susceptibility and resistance mechanisms to amikacin among diverse carbapenemase-producing Enterobacteriaceae

OBJECTIVE

This study aims to assess the in vitro drug susceptibility of various Carbapenemase-Producing Enterobacteriaceae (CPE) genotypes and elucidate the underlying mechanisms of amikacin resistance.

METHODS

A total of 72 unique CPE strains were collected from the Second Hospital of Jiaxing between 2019 and 2022, including 51 strains of Klebsiella pneumoniae, 11 strains of Escherichia coli, 6 strains of Enterobacter cloacae, 2 strains of Klebsiella aerogenes, 1 strain of Citrobacter freundii, and 1strain of Citrobacter werkmanii. Among these strains, 24 carried blaKPC gene, 20 carried blaNDM gene, 23 carried blaOXA-48-like gene, and 5 carried both blaKPC and blaNDM. We measured the in vitro activity of amikacin and other common antibiotics. Strains carrying blaOXA-48-like gene were selected for whole genome sequencing (WGS) via next-generation sequencing to identify genes related to antimicrobial resistance (AMR) and virulence factor (VF).

RESULTS

Out of the 72 CPE strains tested, 41.7% exhibited resistance to amikacin. The drug resistance rates for K. pneumoniae, E. coli, and Enterobacter spp. were 51.0%, 27.3%, and 10.0%, respectively. The majority of the CPE strains (> 90%) displayed resistance to cephalosporins and carbapenems, while most of them were sensitive to polymyxin B and tigecycline (97.2% and 94.4%). The amikacin resistance rate was 100% for strains carrying blaOXA-48, 20.8% for those with blaKPC, 5.0% for those with blaNDM, and 20.0% for those with both blaKPC and blaNDM. These differences were statistically significant (P < 0.05). Through sequencing, we detected aminoglycoside resistance genes rmtF and aac(6')-Ib, VF genes iucABCD and rmpA2 in OXA-48-producing multidrug resistance and highly virulent strains. These genes were located on a IncFIB- and IncHI1B-type plasmid, respectively. Both plasmids were highly homologous to the plasmid from OXA-232 strains in Zhejiang province and Shanghai province. Integration of these resistance genes into the IncFIB plasmid, facilitated by the IS6 and/or Tn3 transposons, resulted in OXA232-producing K. pneumoniae with amikacin resistance.

CONCLUSION

This study identified significant amikacin resistance in CPE strains, particularly in those carrying the blaOXA-48 gene. Resistance genes rmtF and aac(6')-Ib were identified on plasmids. These results highlight the need for careful monitoring of amikacin resistance.

In vitro Synergistic and Bactericidal Effects of Aztreonam in Combination with Ceftazidime/ Avibactam, Meropenem/Vaborbactam and Imipenem/Relebactam Against Dual-Carbapenemase-Producing Enterobacterales

Objective

Our aim was to elucidate the resistance mechanisms and assess the combined synergistic and bactericidal activities of aztreonam in combination with ceftazidime/avibactam (CZA), meropenem/vaborbactam (MEV), and imipenem/relebactam (IMR) against Enterobacterales strains producing dual carbapenemases.

Methods

Species identification, antimicrobial susceptibility testing and determination of carbapenemase type were performed for these strains. Plasmid sizes, plasmid conjugation abilities and the localization of carbapenemase genes were investigated. Whole-genome sequencing was performed for all strains and their molecular characteristics were analyzed. In vitro synergistic and bactericidal activities of the combination of aztreonam with CZA, MEV and IMR against these strains were determined using checkerboard assay and time-kill curve assay.

Results

A total of 12 Enterobacterales strains producing dual-carbapenemases were collected, including nine K. pneumoniae, two P. rettgeri, and one E. hormaechei. The most common dual-carbapenemase gene pattern observed was bla (KPC-2+NDM-5) (n=4), followed by bla KPC-2+IMP-26 (n=3), bla (KPC-2+NDM-1) (n=2), bla (KPC-2+IMP-4) (n=1), bla (NDM-1+IMP-4) (n=1) and bla (KPC-2+KPC-2) (n=1). In each strain, the carbapenemase genes were found to be located on two distinct plasmids which were capable of conjugating from the original strain to the receipt strain E. coli J53. The results of the checkerboard synergy analysis consistently revealed good synergistic effects of the combination of ATM with CZA, MEV and IMR. Except for one strain, all strains exhibited significant synergistic activity and bactericidal activity between 2 and 8 hours.

Conclusion

Dual-carbapenemase-producing Enterobacterales posed a significant threat to clinical anti-infection treatment. However, the combination of ATM with innovative β-lactam/β-lactamase inhibitor compounds had proven to be an effective treatment option.

Chemical sensors for the early diagnosis of bacterial resistance to β-lactam antibiotics

β-Lactamases are bacterial enzymes that inactivate β-lactam antibiotics and, as such, are the most prevalent cause of antibiotic resistance in Gram-negative bacteria. The ever-increasing production and worldwide dissemination of bacterial strains producing carbapenemases is currently a global health concern. These enzymes catalyze the hydrolysis of carbapenems - the β-lactam antibiotics with the broadest spectrum of activity that are often considered as drugs of last resort. The incidence of carbapenem-resistant pathogens such as Pseudomonas aeruginosa, Acinetobacter baumannii and carbapenemase or extended spectrum beta-lactamase (ESBL)-producing Enterobacterales, which are frequent in clinical settings, is worrisome since, in some cases, no therapies are available. These include all metallo-β-lactamases (VIM, IMP, NDM, SMP, and L1), and serine-carbapenemases of classes A (KPC, SME, IMI, and GES), and of classes D (OXA-23, OXA-24/40, OXA-48 and OXA-58). Consequently, the early diagnosis of bacterial strains harboring carbapenemases is a pivotal task in clinical microbiology in order to track antibiotic bacterial resistance and to improve the worldwide management of infectious diseases. Recent research efforts on the development of chromogenic and fluorescent chemical sensors for the specific and sensitive detection and quantification of β-lactamase production in multidrug-resistant pathogens are summarized herein. Studies to circumvent the main limitations of the phenotypic and molecular methods are discussed. Recently reported chromogenic and fluorogenic cephalosporin- and carbapenem-based β-lactamase substrates will be reviewed as alternative options to the currently available nitrocefin and related compounds, a chromogenic cephalosporin-based reagent widely used in clinical microbiology laboratories. The scope of these new chemical sensors, along with the synthetic approaches to synthesize them, is also summarized.

Delivery of endolysin across outer membrane of Gram-negative bacteria using translocation domain of botulinum neurotoxin

The emergence of multidrug-resistant pathogens has outpaced the development of new antibiotics, leading to renewed interest in endolysins. Endolysins have been investigated as novel biocontrol agents for Gram-positive bacteria. However, their efficacy against Gram-negative species is limited by the barrier presented by their outer membrane, which prevents endolysin access to the peptidoglycan substrate. Here, we used the translocation domain of botulinum neurotoxin to deliver endolysin across the outer membrane of Gram-negative bacteria. The translocation domain selectively interacts with and penetrates membranes composed of anionic lipids, which have been used in nature to deliver various proteins into animal cells. In addition to the botulinum neurotoxin translocation domain, we have fused bacteriophage-derived receptor binding protein to endolysins. This allows the attached protein to efficiently bind to a broad spectrum of Gram-negative bacteria. By attaching these target-binding and translocation machineries to endolysins, we aimed to develop an engineered endolysin with broad-spectrum targeting and enhanced antibacterial activity against Gram-negative species. To validate our strategy, we designed engineered endolysins using two well-known endolysins, T5 and LysPA26, and tested them against 23 strains from six species of Gram-negative bacteria, confirming that our machinery can act broadly. In particular, we observed a 2.32 log reduction in 30 min with only 0.5 µM against an Acinetobacter baumannii isolate. We also used the SpyTag/SpyCatcher system to easily attach target-binding proteins, thereby improving its target-binding ability. Overall, our newly developed endolysin engineering strategy may be a promising approach to control multidrug-resistant Gram-negative bacterial strains.

Comparison of three colloidal gold immunoassays and GeneXpert Carba-R for the detection of Klebsiella pneumoniae blaKPC-2 variants

The increasing use of ceftazidime-avibactam has led to the emergence of a wide range of ceftazidime-avibactam-resistant blaKPC-2 variants. Particularly, the conventional carbapenemase phenotypic assay exhibited a high false-negative rate for KPC-2 variants. In this study, three colloidal gold immunoassays, including the Gold Mountainriver CGI test, Dynamiker CGI test and NG-Test CARBA5, and GeneXpert Carba-R, were used to detect the presence of KPC-2 carbapenemase and its various variants in 42 Klebsiella pneumoniae strains. These strains covered blaKPC-2 (13/42) and 16 other blaKPC-2 variants including blaKPC-12 (1/42), blaKPC-23 (1/42), blaKPC-25 (1/42), blaKPC-33 (6/42), blaKPC-35 (1/42), blaKPC-44 (1/42), blaKPC-71 (1/42), blaKPC-76 (8/42), blaKPC-78 (1/42), blaKPC-79 (1/42), blaKPC-100 (1/42), blaKPC-127 (1/42), blaKPC-128 (1/42), blaKPC-144 (1/42), blaKPC-157 (2/42), and blaKPC-180 (1/42). For KPC-2 strains, all four assays showed 100% negative percentage agreement (NPA) and 100% positive percentage agreement (PPA) with sequencing results. For all 16 KPC-2 variants, GeneXpert Carba-R showed 100% NPA and 100% PPA, and the three colloidal gold immunoassays showed 100% NPA, while the PPAs of the Gold Mountainriver CGI test, Dynamiker CGI test, and NG-Test CARBA5 were 87.5%, 87.5%, and 68.8%, respectively. We also found a correlation between the mutation site in the amino acid of the variants and false-negative results by colloidal gold immunoassays. In conclusion, the GeneXpert Carba-R has been proven to be a reliable method in detecting KPC-2 and its variants, and the colloidal gold immunoassay tests offer a practical and cost-effective approach for their detection. For the sample with a negative result by a colloidal gold immunoassay test but not matching the drug-resistant phenotype, it is recommended to retest using another type of kit or the GeneXpert Carba-R assay, which can significantly improve the accuracy of detection.

Ceftolozane/tazobactam: Literature review of its activity on Taiwanese isolates before its launch in Taiwan (2012-2021)

Ceftolozane, a novel cephalosporin, combined with tazobactam, a known β-lactamase inhibitor, shows robust antipseudomonal activity, although it doesn't cover carbapenemases. Our review of data from 2012 to 2021 in Taiwan highlights TOL/TAZ's in-vitro performance. TOL/TAZ is most effective against Pseudomonas aeruginosa (91.3-94.4 % susceptible, with an MIC <4 μg/mL). It also demonstrates good activity against Enterobacterales, including Escherichia coli (88-94.3 % susceptible), Klebsiella pneumoniae (72.6-84.1 % susceptible), Citrobacter koseri (93.3 % susceptible), Klebsiella oxytoca (98.1-100 % susceptible), and Proteus mirabilis (100 % susceptible). However, its efficacy varies among species typically associated with chromosomally-mediated AmpC production, such as Morganella morganii (100 % susceptible), Serratia marcescens (81.3-90.0 % susceptible), Enterobacter cloacae species complex (76.6-76.7 % susceptible), Klebsiella aerogenes (66.7-89.6% susceptible), and Citrobacter freundii (60.0 % susceptible). For carbapenem-nonsusceptible isolates, TOL/TAZ is less effective against K. pneumoniae and E. coli (susceptibility <10 %) but remains useful for P. aeruginosa (susceptibility 81.3-91.8 %). In conclusion, TOL/TAZ shows potent activity against P. aeruginosa and carbapenem-susceptible Enterobacterales in Taiwan.

Global epidemiology and antimicrobial resistance of Enterobacterales harbouring genes encoding OXA-48-like carbapenemases: insights from the results of the Antimicrobial Testing Leadership and Surveillance (ATLAS) programme 2018-2021

OBJECTIVES

The recent emergence of carbapenem-resistant Enterobacterales poses a major and escalating threat to global public health. This study aimed to analyse the global distribution and antimicrobial resistance of Enterobacterales harbouring variant OXA-48-like carbapenemase-related genes.

METHODS

Enterobacterales isolates were collected from the Antimicrobial Testing Leadership and Surveillance (ATLAS) programme during 2018-2021. Comprehensive antimicrobial susceptibility testing and β-lactamase gene detection were also conducted, along with statistical analysis of the collected data.

RESULTS

Among the 72 244 isolates, 1934 Enterobacterales isolates were identified to harbour blaOXA-48-like genes, predominantly Klebsiella spp. (86.9%). High rates of multidrug resistance were observed, with only ceftazidime/avibactam and tigecycline showing favourable susceptibility. A discrepancy between the genotype and phenotype of carbapenem resistance was evident: 16.8% (233 out of 1384) of the Enterobacterales isolates with blaOXA-48-like genes exhibited susceptibility to meropenem. Specifically, 37.4% (64/95) of Escherichia coli strains with blaOXA-48-like genes displayed meropenem susceptibility, while the corresponding percentages for Klebsiella pneumoniae and Enterobacter cloacae complex were 25.2% (160/1184) and 0% (0/36), respectively (P < 0.05). Geographical analysis revealed that the highest prevalence of blaOXA-48-like genes occurred in Asia, the Middle East and Eastern Europe. The proportion of K. pneumoniae isolates harbouring blaOXA-232 increased from 23.9% in 2018 to 56.0% in 2021. By contrast, the proportion of blaOXA-48 decreased among K. pneumoniae isolates during 2018-2021.

CONCLUSIONS

This study underscores the widespread and increasing prevalence of blaOXA-48-like genes in Enterobacterales and emphasizes the need for enhanced surveillance, improved diagnostic methods and tailored antibiotic stewardship to combat the spread of these resistant pathogens.

Characterization of carbapenemase-producing Enterobacterales from rectal swabs of patients in the intensive care units of a tertiary hospital in Cali-Colombia

Background

Carbapenemase-producing Enterobacterales (CPE) represents a significant threat to global health. This study aimed to characterize clinically and molecularly the CPE isolated from rectal swabs of patients in the intensive care units (ICUs) of a tertiary hospital in Cali, Colombia.

Methods

This was a cross-sectional observational study. Rectal swabs from patients admitted to the ICUs were collected. Bacterial identification and carbapenemase production were determined using phenotypic and molecular methods. Demographic and clinical data were extracted from electronic medical records.

Results

The study included 223 patients. Thirty-six patients (36/223, 16.14 %) were found to be colonized or infected by CPE. Factors such as prolonged stay in the ICU, previous exposure to carbapenem antibiotics, use of invasive procedures, and admission due to trauma were associated with CPE. Klebsiella pneumoniae (52.5 %) was the most prevalent microorganism, and the dominant carbapenemases identified were KPC (57.8 %) and NDM (37.8 %).

Conclusion

Distinguishing carbapenemase subtypes can provide crucial insights for controlling dissemination in ICUs in Cali, Colombia.

Comparison of ERIC carbapenem-resistant Enterobacteriaceae test, BD Phoenix CPO detect panel, and NG-test CARBA 5 for the detection of main carbapenemase types of carbapenem-resistant Enterobacterales

BACKGROUND

This study aimed to assess the performance of three commercial panels, the ERIC Carbapenem-Resistant Enterobacteriaceae Test (ERIC CRE test), the NG-Test CARBA 5 (NG CARBA 5), and the BD Phoenix CPO Detect Panel (CPO panel), for the detection of main types of carbapenemases among carbapenem-resistant Enterobacterales (CRE).

METHODS

We collected 502 isolates of carbapenem-resistant Enterobacterales (CRE) demonstrating intermediate or resistant profiles to at least one carbapenem antibiotic (ertapenem, imipenem, meropenem, or doripenem). Carbapenemase genes and their specific types were identified through multiplex PCR and sequencing methods. Subsequently, the ERIC CRE test, CPO panel, and NG CARBA 5 assay were conducted on these isolates, and the results were compared with those obtained from multiplex PCR.

RESULTS

The results indicated that the ERIC CRE test exhibited an overall sensitivity and specificity of 98.1% and 93.6%, respectively, which were comparable to 99.1% and 90.6% for the NG CARBA 5. However, the CPO panel demonstrated a sensitivity of only 56.2% in identifying Ambler classes, exhibiting the poorest sensitivity for class A. Moreover, while the ERIC CRE test outperformed the NG CARBA 5 in identifying multi-gene isolates with multiple carbapenemase-encoding genes, the CPO panel failed to accurately classify these isolates.

CONCLUSIONS

Our findings support the utilization of the ERIC CRE test as one of the methods for detecting carbapenemases in clinical laboratories. Nonetheless, further optimization is imperative for the CPO panel to enhance its accuracy in determining carbapenemase classification and address limitations in detecting multi-gene isolates.

Development of a Simple Method to Detect the Carbapenemase-Producing Genes blaNDM, blaOXA-48-like, blaIMP, blaKPC, and blaVIM Using a LAMP Method with Lateral Flow DNA Chromatography

Infections by carbapenemase-producing Enterobacterales constitute a global public health threat. The rapid and efficient diagnosis of Enterobacterales infection is critical for prompt treatment and infection control, especially in hospital settings. We developed a novel loop-mediated isothermal amplification (LAMP) method combined with DNA chromatography to identify five major groups of carbapenemase-producing genes (blaNDM, blaOXA-48-like, blaIMP, blaKPC, and blaVIM). This method uses DNA-DNA hybridization-based detection in which LAMP products can be easily visualized as colored lines. No specific technical expertise, expensive equipment, or special facilities are required for this method, allowing its broad application. Here, 73 bacteria collections including strains with carbapenemase-producing genes were tested. Compared to sequencing results, LAMP DNA chromatography for five carbapenemase-producing genes had a sensitivity and specificity of 100% and >97%, respectively. This newly developed method can be a valuable rapid diagnostic test to guide appropriate treatments and infection control measures, especially in resource-limited settings.

Epidemiology and antimicrobial susceptibility profiles of Enterobacterales causing bloodstream infections before and during COVID-19 pandemic: Results of the Study for Monitoring Antimicrobial Resistance Trends (SMART) in Taiwan, 2018-2021

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic has contributed to the spread of antimicrobial resistance, including carbapenem-resistant Enterobacterales.

METHODS

This study utilized data from the Study for Monitoring Antimicrobial Resistance Trends (SMART) surveillance program in Taiwan. Enterobacterales from patients with bloodstream infections (BSIs) were collected and subjected to antimicrobial susceptibility testing and β-lactamase gene detection using a multiplex PCR assay. Statistical analysis was conducted to compare susceptibility rates and resistance genes between time periods before (2018-2019) and during the COVID-19 pandemic (2020-2021).

RESULTS

A total of 1231 Enterobacterales isolates were collected, predominantly Escherichia coli (55.6%) and Klebsiella pneumoniae (29.2%). The proportion of nosocomial BSIs increased during the COVID-19 pandemic (55.5% vs. 61.7%, p < 0.05). Overall, susceptibility rates for most antimicrobial agents decreased, with Enterobacterales from nosocomial BSIs showing significantly lower susceptibility rates than those from community-acquired BSIs. Among 123 Enterobacterales isolates that underwent molecular resistance mechanism detection, ESBL, AmpC β-lactamase, and carbapenemase genes were detected in 43.1%, 48.8% and 16.3% of the tested isolates, respectively. The prevalence of carbapenemase genes among carbapenem-resistant Enterobacterales increased during the pandemic, although the difference was not statistically significant. Two novel β-lactamase inhibitor combinations, imipenem-relebactam and meropenem-vaborbactam, preserved good efficacy against Enterobacterales. However, imipenem-relebactam showed lower in vitro activity against imipenem-non-susceptible Enterobacterales than that of meropenem-vaborbactam.

CONCLUSIONS

The COVID-19 pandemic appears to be associated with a general decrease in antimicrobial susceptibility rates among Enterobacterales causing BSIs in Taiwan. Continuous surveillance is crucial to monitor antimicrobial resistance during the pandemic and in the future.

Multiplex detection of the big five carbapenemase genes using solid-phase recombinase polymerase amplification

Five carbapenemase enzymes, coined the 'big five', have been identified as the biggest threat to worldwide antibiotic resistance based on their broad substrate affinity and global prevalence. Here we show the development of a molecular detection method for the gene sequences from the five carbapenemases utilising the isothermal amplification method of recombinase polymerase amplification (RPA). We demonstrate the successful detection of each of the big five carbapenemase genes with femtomolar detection limits using a spatially separated multiplex amplification strategy. The approach uses tailed oligonucleotides for hybridisation, reducing the complexity and cost of the assay compared to classical RPA detection strategies. The reporter probe, horseradish peroxidase, generates the measureable output on a benchtop microplate reader, but more notably, our study leverages the power of a portable Raman spectrometer, enabling up to a 19-fold enhancement in the limit of detection. Significantly, the development approach employed a solid-phase RPA format, wherein the forward primers targeting each of the five carbapenemase genes are immobilised to a streptavidin-coated microplate. The adoption of this solid-phase methodology is pivotal for achieving a successful developmental pathway when employing this streamlined approach. The assay takes 2 hours until result, including a 40 minutes RPA amplification step at 37 °C. This is the first example of using solid-phase RPA for the detection of the big five and represents a milestone towards the developments of an automated point-of-care diagnostic for the big five using RPA.

Prediction of methicillin-resistant Staphylococcus aureus and carbapenem-resistant Klebsiella pneumoniae from flagged blood cultures by combining rapid Sepsityper MALDI-TOF mass spectrometry with machine learning

This study investigated combination of the Rapid Sepsityper Kit and a machine learning (ML)-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) approach for rapid prediction of methicillin-resistant Staphylococcus aureus (MRSA) and carbapenem-resistant Klebsiella pneumoniae (CRKP) from positive blood culture bottles. The study involved 461 patients with monomicrobial bloodstream infections. Species identification was performed using the conventional MALDI-TOF MS Biotyper system and the Rapid Sepsityper protocol. The data underwent preprocessing steps, and ML models were trained using preprocessed MALDI-TOF data and corresponding labels. The interpretability of the model was enhanced using SHapely Additive exPlanations values to identify significant features. In total, 44 S. aureus isolates comprising 406 MALDI-TOF MS files and 126 K. pneumoniae isolates comprising 1249 MALDI-TOF MS files were evaluated. This study demonstrated the feasibility of predicting MRSA among S. aureus and CRKP among K. pneumoniae isolates using MALDI-TOF MS and Sepsityper. Accuracy, area under the receiver operating characteristic curve, and F1 score for MRSA/methicillin-susceptible S. aureus were 0.875, 0.898 and 0.904, respectively; for CRKP/carbapenem-susceptible K. pneumoniae, these values were 0.766, 0.828 and 0.795, respectively. In conclusion, the novel ML-based MALDI-TOF MS approach enables rapid identification of MRSA and CRKP from flagged blood cultures within 1 h. This enables earlier initiation of targeted antimicrobial therapy, reducing deaths due to sepsis. The favourable performance and reduced turnaround time of this method suggest its potential as a rapid detection strategy in clinical microbiology laboratories, ultimately improving patient outcomes.

Antibiotic-Resistant ESKAPE Pathogens and COVID-19: The Pandemic beyond the Pandemic

Antibacterial resistance is a renewed public health plague in modern times, and the COVID-19 pandemic has rekindled this problem. Changes in antibiotic prescribing behavior, misinformation, financial hardship, environmental impact, and governance gaps have generally enhanced the misuse and improper access to antibiotics during the COVID-19 pandemic. These determinants, intersected with antibacterial resistance in the current pandemic, may amplify the potential for a future antibacterial resistance pandemic. The occurrence of infections with multidrug-resistant (MDR), extensively drug-resistant (XDR), difficult-to-treat drug-resistant (DTR), carbapenem-resistant (CR), and pan-drug-resistant (PDR) bacteria is still increasing. The aim of this review is to highlight the state of the art of antibacterial resistance worldwide, focusing on the most important pathogens, namely Enterobacterales, Acinetobacter baumannii, and Klebsiella pneumoniae, and their resistance to the most common antibiotics.

Recent Advances in Colorimetric Tests for the Detection of Infectious Diseases and Antimicrobial Resistance

Diagnosis of infection-causing microorganisms with sensitive, rapid, selective and economical diagnostic tests is critical to start the right treatment. With these tests, the spread of infections can be prevented. In addition to that, the detection of antimicrobial resistance also makes a significant contribution to public health. In recent years, different types of diagnostic tests have been developed as alternatives to traditional diagnostic tests used in clinics. In particular, colorimetric tests, which minimize the need for an instrument, have advantages owing to their cost effectiveness, rapid response and naked-eye detection and practical use. In this review, we especially focused on pH indicators and nanomaterial-based colorimetric tests in detection of infection-causing microorganisms and antimicrobial resistance.

An overview of gram-negative bacteria with difficult-to-treat resistance: definition, prevalence, and treatment options

INTRODUCTION

Difficult-to-treat resistance (DTR) is a newly proposed resistance phenotype characterized by resistance to all first-line drugs. The emergence of DTR as a new resistance phenotype has significant implications for clinical practice. This new concept has the potential to be widely used instead of traditional phenotypes.

AREAS COVERED

This study carried out a detailed analysis about the definition, application, and evolution of various resistance phenotypes. We collected all the research articles on Gram-negative bacteria with difficult-to-treat resistance (GNB-DTR), analyzed the DTR in each region and each bacterial species. The advantages and doubts of DTR, the dilemma of GNB-DTR infections and the potential therapeutic strategies are summarized in the review.

EXPERT OPINION

Available studies show that the prevalence of GNB-DTR is not optimistic. Unlike traditional resistance phenotypes, DTR is more closely aligned with the clinical treatment perspective and can help with the prompt selection of an appropriate treatment plan. Currently, potential treatment options for GNB-DTR include a number of second-line drugs and novel antibiotics. However, the definition of first-line drugs is inherently dynamic. Therefore, the DTR concept based on first-line drugs needs to be continuously updated and refined, considering the emergence of new antibiotics, resistance characteristics, and pathogen prevalence in different regions.

An Overview of Cefiderocol's Therapeutic Potential and Underlying Resistance Mechanisms

Antimicrobial resistance continues to increase globally and treatment of difficult-to-treat (DTT) infections, mostly associated with carbapenem-resistant (CR) Pseudomonas aeruginosa, CR Acinetobacter baumannii, and CR- and third-generation-cephalosporins-resistant Enterobacterales remains a challenge for the clinician. The recent approval of cefiderocol has broaden the armamentarium for the treatment of patients with DTT infections. Cefiderocol is a siderophore cephalosporin that has shown excellent antibacterial activity, in part due to its innovative way of cell permeation. It is relatively stable compared to most commonly found carbapenamases. However, some resistant mechanisms to cefiderocol have already been identified and reduced susceptibility has developed during patient treatment, highlighting that the clinical use of cefiderocol must be rational. In this review, we summarize the current available treatments against the former resistant bacteria, and we revise and discuss the mechanism of action of cefiderocol, underlying the biological function of siderophores, the therapeutic potential of cefiderocol, and the mechanisms of resistance reported so far.

ESKAPE and Beyond: The Burden of Coinfections in the COVID-19 Pandemic

The ESKAPE group constitute a threat to public health, since these microorganisms are associated with severe infections in hospitals and have a direct relationship with high mortality rates. The presence of these bacteria in hospitals had a direct impact on the incidence of healthcare-associated coinfections in the SARS-CoV-2 pandemic. In recent years, these pathogens have shown resistance to multiple antibiotic families. The presence of high-risk clones within this group of bacteria contributes to the spread of resistance mechanisms worldwide. In the pandemic, these pathogens were implicated in coinfections in severely ill COVID-19 patients. The aim of this review is to describe the main microorganisms of the ESKAPE group involved in coinfections in COVID-19 patients, addressing mainly antimicrobial resistance mechanisms, epidemiology, and high-risk clones.

Clonal Spread of Hospital-Acquired NDM-1-Producing Klebsiella pneumoniae and Escherichia coli in an Italian Neonatal Surgery Unit: A Retrospective Study

This article reports a rapid and unexpected spread of colonization cases of NDM-1 carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in a neonatal surgical unit (NSU) at Bambino Gesù Children's Hospital in Rome, Italy. Between the 16th of November 2020 and the 18th of January 2021, a total of 20 NDM-1 carbapenemase-producing K. pneumoniae (n = 8) and E. coli (n = 12) were isolated from 17 out of 230 stool samples collected from neonates admitted in the aforementioned ward and time period by an active surveillance culture program routinely in place to monitor the prevalence of colonization/infection with multidrug-resistant Gram-negative microorganisms. All strains were characterized by antimicrobial susceptibility testing, detection of resistance determinants, PCR-based replicon typing (PBRT) and multilocus-sequence typing (MLST). All isolates were highly resistant to most of the tested antibiotics, and molecular characterization revealed that all of them harbored the bla_NDM-1 gene. Overall, IncA/C was the most common Inc group (n = 20/20), followed by IncFIA (n = 17/20), IncFIIK (n = 14/20) and IncFII (n = 11/20). MLST analysis was performed on all 20 carbapenemase-producing Enterobacterales (CPE) strains, revealing three different Sequence Types (STs) among E. coli isolates, with the prevalence of ST131 (n = 10/12; 83%). Additionally, among the 8 K. pneumoniae strains we found 2 STs with the prevalence of ST37 (n = 7/8; 87.5%). Although patient results were positive for CPE colonization during their hospital stay, infection control interventions prevented their dissemination in the ward and no cases of infection were recorded in the same time period.

Geographic patterns of global isolates of carbapenem-resistant Klebsiella pneumoniae and the activity of ceftazidime/avibactam, meropenem/vaborbactam, and comparators against these isolates: Results from the Antimicrobial Testing Leadership and Surveillance (ATLAS) program, 2020

Carbapenem-resistant Enterobacterales (CRE) are a growing threat to public health. This study was conducted to determine the prevalence of carbapenem-resistant Klebsiella pneumoniae (CR-KP) and the associated carbapenemase genes using data from the Antimicrobial Testing Leadership and Surveillance (ATLAS) program, 2020. Minimum inhibitory concentrations (MICs) were determined using the broth microdilution method, and carbapenemase genes were detected using multiplex polymerase chain reaction (PCR). Clinical and Laboratory Standards Institute breakpoints were used for interpretation of susceptibility. A total of 6753 K. pneumoniae isolates were collected from 57 countries in six regions worldwide. Of these, 1118 (16.6%) were CR-KP isolates. Among 1079 of the tested CR-KP isolates, 1017 (94.3%) had at least one of the class A (41.0%, 417/1017), B (39.3%, 400/1017), and D (38.8%, 395/1017) carbapenemase genes. The resistance patterns and associated genes differed significantly between the participating countries. India, Greece, and Argentina had the highest rates of carbapenem resistance. Susceptibility to the β-lactamase inhibitor combination, ceftazidime/avibactam was greater than that to meropenem/vaborbactam in all K. pneumoniae (93.7% vs. 90.3%, P < 0.05), CR-KP (63.3% vs. 41.5%, P < 0.05), CR-KP with genes for Klebsiella pneumoniae carbapenemase-like carbapenemase (99.5% vs. 96.0%, P < 0.05), oxacillinase-like carbapenemase (98.7% vs. 4.6%, P < 0.05), and CR-KP without carbapenemase genes (93.5% vs. 79.0%, P < 0.05). CR-KP was the only exception with class B carbapenemase, with susceptibility rates of 1.4% and 9.4% to ceftazidime/avibactam and meropenem/vaborbactam, respectively (P < 0.05). Overall, surveillance results are important for guiding empirical antimicrobial therapy in different regions and for monitoring the global transmission of CR-KP with varying resistance mechanisms.

Genomic Characterization of an Extensively Drug-Resistant Extra-Intestinal Pathogenic (ExPEC) Escherichia coli Clinical Isolate Co-Producing Two Carbapenemases and a 16S rRNA Methylase

An extensively drug-resistant Escherichia coli clinical isolate (N1606) belonging to Sequence Type 361 was recovered from the urine of a patient hospitalized in Switzerland. The strain showed resistance to virtually all β-lactams including the latest generation antibiotics cefiderocol and aztreonam-avibactam. Whole genome sequencing revealed that it possessed two carbapenemase-encoding genes, namely bla_NDM-5 and bla_KPC-3, and a series of additional β-lactamase genes, including bla_CTX-M-15 and bla_SHV-11 encoding extended-spectrum β-lactamases (ESBLs), bla_CMY-145 encoding an AmpC-type cephalosporinase, and bla_OXA-1 encoding a narrow-spectrum class D ß-lactamase. Most of these resistance genes were located on plasmids (IncFII-FIA, IncX3, IncIγ, IncFII). That strain exhibited also a four amino-acid insertion in its penicillin-binding protein 3 (PBP3) sequence, namely corresponding to YRIN. Complete genome analysis revealed that this E. coli isolate carried virulence factors (sitA, gad, hra, terC, traT, and cia) and many other non-β-lactam resistance determinants including rmtB, tet(A), dfrA17 (two copies), aadA1, aadA5 (two copies), sul1 (two copies), qacE (two copies), qepA, mdf(A), catA1, erm(B), mph(A), and qnrS1, being susceptible only to tigecycline, colistin and fosfomycin. In conclusion, we described here the phenotypic and genome characteristics of an extensively drug-resistant (XDR) E. coli ST361 being recognized as an emerging clone worldwide.

Antibiotics for multidrug-resistant gram-negative bacteria

Background: Increase in antimicrobial-resistant bacteria continues to be challenge to physicians. Particularly, multidrug-resistant (MDR) gram-negative bacilli (GNB), such as extended-spectrum beta-lactamase (ESBL)-producers and carbapenem-resistant pathogens, are becoming a major human health problem globally.Current Concepts: Gram-negative bacteria have developed resistance via mechanisms encoding AmpC beta-lactamases, ESBLs, and carbapenemases. The therapeutic options available for these pathogens are extremely limited. Infection by MDR bacteria is associated with ineffective antimicrobial therapy, which poses a major threat to the survival of patients with serious infections. Physicians should be familiar with the local epidemiology of MDR bacterial infections and the available therapeutic options. Carbapenems are considered as the drugs of choice for treating ESBL or AmpC-producers. However, increased use of carbapenems in response to an increased prevalence of MDR pathogens could be associated with the rapid emergence of carbapenem resistance. Therefore, there is an ongoing quest for carbapenem-sparing regimens for the treatment of MDR-GNB. Treatment of MDR-GNB infections need not be limited to carbapenems as novel antimicrobial agents are now available.Discussion and Conclusion: This comprehensive review aims to describe therapeutic options available for MDR-GNB infections in Korea, a country with a high prevalence of MDR pathogens. Recently developed antimicrobial agents that should be urgently introduced in Korea include ceftolozane-tazobactam, ceftazidime-avibactam, meropenem-vaborbactam, imipenem-relebactam, and cefiderocol. These drugs have been shown to be effective against carbapenem-resistant Enterobacterales, carbapenem-resistant Pseudomonas aeruginosa, and Acinetobacter baumannii.

Genomic Analysis of a Highly Virulent NDM-1-Producing Escherichia coli ST162 Infecting a Pygmy Sperm Whale (Kogia breviceps) in South America

Carbapenemase-producing Enterobacterales are rapidly spreading and adapting to different environments beyond hospital settings. During COVID-19 lockdown, a carbapenem-resistant NDM-1-positive Escherichia coli isolate (BA01 strain) was recovered from a pygmy sperm whale (Kogia breviceps), which was found stranded on the southern coast of Brazil. BA01 strain belonged to the global sequence type (ST) 162 and carried the bla_NDM–1, besides other medically important antimicrobial resistance genes. Additionally, genes associated with resistance to heavy metals, biocides, and glyphosate were also detected. Halophilic behavior (tolerance to > 10% NaCl) of BA01 strain was confirmed by tolerance tests of NaCl minimal inhibitory concentration, whereas halotolerance associated genes katE and nhaA, which encodes for catalase and Na⁺/H⁺ antiporter cytoplasmic membrane, respectively, were in silico confirmed. Phylogenomics clustered BA01 with poultry- and human-associated ST162 lineages circulating in European and Asian countries. Important virulence genes, including the astA (a gene encoding an enterotoxin associated with human and animal infections) were detected, whereas in vivo experiments using the Galleria mellonella infection model confirmed the virulent behavior of the BA01 strain. WHO critical priority carbapenemase-producing pathogens in coastal water are an emerging threat that deserves the urgent need to assess the role of the aquatic environment in its global epidemiology.

Efficacy and Safety of Oral Fosfomycin-Trometamol in Male Urinary Tract Infections with Multidrug-Resistant Enterobacterales

BACKGROUND

Antimicrobial drugs to treat male urinary tract infection (UTI) with multidrug-resistant Enterobacterales are limited. We studied oral fosfomycin-trometamol (FT) in this situation. The objective was to assess the clinical cure rate in patients presenting UTIs treated with oral FT.

METHODS

We conducted a single-center observational retrospective study from January 2017 to August 2018. The primary endpoint was clinical cure; and the secondary endpoints were incidence of recurrences, oral FT safety, and microbiological cure.

RESULTS

Sixteen male patients were included, presenting 21 UTI episodes. Fourteen patients (88%) have at least one underlying urologic disorder. We described 4 episodes of acute UTI and 17 episodes of chronic bacterial prostatitis (CBP). Sixteen out of twenty-one Enterobacterales were extended spectrum beta-lactamase (ESBL)-producers and all the patients presented a resistance to fluoroquinolones and trimethoprim/sulfamethoxazole. In acute UTI, the regimen was a daily dose of oral FT for a mean duration of 2.5 weeks (+/-7.0 days). Clinical and microbiological recovery was achieved in all patients, with no recurrence after 5.3 months follow-up on average (+/-10.4 days). In CBP, the regimen was one oral dose of fosfomycin every 24-48 h, for a mean duration of 5.5 weeks/UTI episodes (+/-15.3 days). Clinical and microbiological recovery was found in 16/17 cases. Seven of the twelve patients with CBP had relapsed and 3/12 had had a new episode of infection after an average follow-up of 5.8 months. Only 6/21 of patients presented minor or moderate adverse effects, such as digestive disorders.

CONCLUSIONS

FT could be an alternative option to carbapenems in the treatment of multidrug-resistant Enterobacterales infections for male UTIs.