Worldwide dissemination of the NDM-type carbapenemases in Gram-negative bacteria

Antimicrobial resistance and carbapenemase dissemination in Pseudomonas aeruginosa isolates from Libyan hospitals: a call for surveillance and intervention

Pseudomonas aeruginosa is a multidrug-resistant bacterium capable of forming biofilms. This study aimed to assess resistance of clinical isolates from Libyan hospitals to antipseudomonal antibiotics, the prevalence of selected extended-spectrum β-lactamases and carbapenemase genes among these isolates, and the microorganisms' capacity for alginate and biofilm production. Forty-five isolates were collected from four hospitals in Benghazi and Derna, Libya. Antimicrobial susceptibility was determined using agar disc diffusion. The presence of resistance genes (blaCTXM, blaTEM, blaSHV-1, blaGES-1, blaKPC, and blaNDM) was screened using PCR. Biofilm formation was quantified via the crystal violet assay, while alginate production was measured spectrophotometrically. Resistance to antipseudomonal antibiotics ranged from 48.9% to 75.6%. The most prevalent resistance gene was blaNDM (26.7%), followed by blaGES-1 (17.8%). Moreover, all isolates demonstrated varying degrees of biofilm-forming ability and alginate production. No statistically significant correlation was found between biofilm formation and alginate production. The dissemination of resistant genes in P. aeruginosa, particularly carbapenemases, is of great concern. This issue is compounded by the bacteria's biofilm-forming capability. Urgent intervention and continuous surveillance are imperative to prevent further deterioration and the catastrophic spread of resistance among these formidable bacteria.

Efficacy of aspergillomarasmine A/meropenem combinations with and without avibactam against bacterial strains producing multiple β-lactamases

The effectiveness of β-lactam antibiotics is increasingly threatened by resistant bacteria that harbor hydrolytic β-lactamase enzymes. Depending on the class of β-lactamase present, β-lactam hydrolysis can occur through one of two general molecular mechanisms. Metallo-β-lactamases (MBLs) require active site Zn2+ ions, whereas serine-β-lactamases (SBLs) deploy a catalytic serine residue. The result in both cases is drug inactivation via the opening of the β-lactam warhead of the antibiotic. MBLs confer resistance to most β-lactams and are non-susceptible to SBL inhibitors, including recently approved diazabicyclooctanes, such as avibactam; consequently, these enzymes represent a growing threat to public health. Aspergillomarasmine A (AMA), a fungal natural product, can rescue the activity of the β-lactam antibiotic meropenem against MBL-expressing bacterial strains. However, the effectiveness of this β-lactam/β-lactamase inhibitor combination against bacteria producing multiple β-lactamases remains unknown. We systematically investigated the efficacy of AMA/meropenem combination therapy with and without avibactam against 10 Escherichia coli and 10 Klebsiella pneumoniae laboratory strains tandemly expressing single MBL and SBL enzymes. Cell-based assays demonstrated that laboratory strains producing NDM-1 and KPC-2 carbapenemases were resistant to the AMA/meropenem combination but became drug-susceptible upon adding avibactam. We also probed these combinations against 30 clinical isolates expressing multiple β-lactamases. E. coli, Enterobacter cloacae, and K. pneumoniae clinical isolates were more susceptible to AMA, avibactam, and meropenem than Pseudomonas aeruginosa and Acinetobacter baumannii isolates. Overall, the results demonstrate that a triple combination of AMA/avibactam/meropenem has potential for empirical treatment of infections caused by multiple β-lactamase-producing bacteria, especially Enterobacterales.

Genomic study of Acinetobacter baumannii strains co-harboring bla OXA-58 and bla NDM-1 reveals a large multidrug-resistant plasmid encoding these carbapenemases in Brazil

Introduction

Acinetobacter baumannii contributes significantly to the global issue of multidrug-resistant (MDR) nosocomial infections. Often, these strains demonstrate resistance to carbapenems (MDR-CRAB), the first-line treatment for infections instigated by MDR A. baumannii. Our study focused on the antimicrobial susceptibility and genomic sequences related to plasmids from 12 clinical isolates of A. baumannii that carry both the blaOXA-58 and bla NDM-1 carbapenemase genes.

Methods

Whole-genome sequencing with long-read technology was employed for the characterization of an A. baumannii plasmid that harbors the bla OXA-58 and blaNDM-1 genes. The location of the bla OXA-58 and bla NDM-1 genes was confirmed through Southern blot hybridization assays. Antimicrobial susceptibility tests were conducted, and molecular characterization was performed using PCR and PFGE.

Results

Multilocus Sequence Typing analysis revealed considerable genetic diversity among bla OXA-58 and bla NDM-1 positive strains in Brazil. It was confirmed that these genes were located on a plasmid larger than 300 kb in isolates from the same hospital, which also carry other antimicrobial resistance genes. Different genetic contexts were observed for the co-occurrence of these carbapenemase-encoding genes in Brazilian strains.

Discussion

The propagation of bla OXA-58 and bla NDM-1 genes on the same plasmid, which also carries other resistance determinants, could potentially lead to the emergence of bacterial strains resistant to multiple classes of antimicrobials. Therefore, the characterization of these strains is of paramount importance for monitoring resistance evolution, curbing their rapid global dissemination, averting outbreaks, and optimizing therapy.

Molecular characterization of carbapenem and ceftazidime-avibactam-resistant Enterobacterales and horizontal spread of bla NDM-5 gene at a Lebanese medical center

Introduction

In the battle against multidrug-resistant bacterial infections, ceftazidime- avibactam (CZA) stands as a pivotal defense, particularly against carbapenemresistant (CR) Gram-negative pathogens. However, the rise in resistance against this drug poses a significant threat to its effectiveness, highlighting the critical need for in-depth studies about its resistance mechanisms.

Methods

This research focuses on the genomic characterization of CR- and CZA-resistant Escherichia coli (n=26) and Klebsiella pneumoniae (n=34) strains, harboring the blaNDM and/or blaOXA-48-like genes, at a major Lebanese tertiary care medical center, using whole genome sequencing (WGS).

Results

Our findings revealed a notable prevalence of blaNDM in all K. pneumoniae strains isolates, with 27 of these also harboring blaOXA-48. On the other hand, E. coli strains predominantly carried the blaNDM-5 gene. Whole genome sequencing (WGS) identified a predominance of ST383 among K. pneumoniae strains, which possessed a multi-replicon IncFIB-IncHI1B plasmid harboring the blaNDM-5. Additionally, various Inc group plasmids in K. pneumoniae across multiple sequence types were found to carry the blaNDM. Similarly, diverse STs of E. coli were observed to carry blaNDM-5 on different plasmids.

Discussion

The study underscores NDM carbapenemases as a paramount resistance mechanism in Lebanon,jeopardizing critical last-resort treatments. It also illuminates the role of varied sequence types and mobile genetic elements in the spread of NDM resistance,stressing the urgent need for strategies to mitigate this threat, especially in nosocomial infections.

New Delhi metallo-β-lactamases among extensively drug-resistant clinical isolates from Lahore, Pakistan

Aim: The study determines rates of carbapenem resistance (CR) and frequency of blaNDM in multidrug-resistance (MDR) or extensive drug resistance (XDR), and evaluates the potential of phenotypic tests for detecting NDM production. Materials & methods: Singleplex PCR was used to detect blaNDM. Phenotypic tests, including combination disc test (CDST) and modified Hodge test (MHT), were evaluated for NDM production. Results: Among 338 CR isolates, 47.63% were MDR, whereas 52.36% were XDR with 53.25% carrying blaNDM. MHT was found to be discriminative for detecting NDM production, whereas no significant association was observed for CDST. Conclusion: The high incidence of CR and MDR and XDR isolates possessing blaNDM presents an impending threat in therapeutics. Limitations of phenotypic tests suggest better testing, including molecular detection of the enzyme.

IncX3 plasmid-mediated spread of blaNDM gene in Enterobacteriaceae among children in China

OBJECTIVES

The blaNDM gene was prevalent among children and became the predominant cause of severe infection in infants and children. This study aimed to investigate the epidemiology and molecular characteristics of blaNDM in Enterobacteriaceae among children in China.

METHODS

Carbapenem-resistant Enterobacteriaceae (CRE) were collected in the Children's Hospital of Fudan University from January 2016 to December 2022. Five carbapenemase genes (blaKPC, blaNDM, blaVIM, blaIMP, blaOXA-48) were screened by PCR method. Multilocus sequence typing (MLST) was conducted for phylogenetic analyses. blaNDM-carrying plasmids were typed by PCR-based Incompatibility (Inc) typing method. Moreover, plasmid comparison was performed with 213 publicly available IncX3 plasmids.

RESULTS

A total of 330 CRE strains were enrolled, 96.4% of which carried carbapenemase genes. blaNDM gene accounted for 64.8% (214 strains) and included four variants, including blaNDM-1 (59.8%), blaNDM-5 (39.3%), blaNDM-7 (0.5%), and blaNDM-9 (0.5%). There were no predominant MLST lineages of blaNDM carrying strains. IncX3 was the major plasmid carrying blaNDM-1 (68.0%) and blaNDM-5 (72.6%) and was dominant in blaNDM-Klebsiella penumoniae (79.8%), blaNDM-Escherichia coli (58.2%), and blaNDM-Enterobacter cloacae (61.0%), respectively. Most (79.0%) clinical IncX3 plasmids in the world carried blaNDM, and the prevalence of blaNDM in IncX3 plasmids was more common in China (95.8%) than other countries (58.1%, P <0.01).

CONCLUSION

blaNDM is highly prevalent in CRE among children in China. The spread of blaNDM was mainly mediated by IncX3 plasmids. Surveillance and infection control on the spread of blaNDM among children are important.

Emergence and genomic chion of Proteus mirabilis harboring blaNDM-1 in Korean companion dogs

Proteus mirabilis is a commensal bacterium dwelling in the gastrointestinal (GI) tract of humans and animals. Although New Delhi metallo-β-lactamase 1 (NDM-1) producing P. mirabilis is emerging as a threat, its epidemiology in our society remains largely unknown. LHPm1, the first P. mirabilis isolate harboring NDM-1, was detected from a companion dog that resides with a human owner. The whole-genome study revealed 20 different antimicrobial resistance (AMR) genes against various classes of antimicrobial agents, which corresponded to the MIC results. Genomic regions, including MDR genes, were identified with multiple variations and visualized in a comparative manner. In the whole-genome epidemiological analysis, multiple phylogroups were identified, revealing the genetic relationship of LHPm1 with other P. mirabilis strains carrying various AMR genes. These genetic findings offer comprehensive insights into NDM-1-producing P. mirabilis, underscoring the need for urgent control measures and surveillance programs using a "one health approach".

The evosystem: A centerpiece for evolutionary studies

In this paper, we redefine the target of evolutionary explanations by proposing the "evosystem" as an alternative to populations, lineages and species. Evosystems account for changes in the distribution of heritable variation within individual Darwinian populations (evolution by natural selection, drift, or constructive neutral evolution), but also for changes in the networks of interactions within or between Darwinian populations and changes in the abiotic environment (whether these changes are caused by the organic entities or not). The evosystem can thereby become a centerpiece for a redefined evolutionary science, that is, evolutionary studies, that apprehends through a single framework the variety of evolutionary processes that lie at various scales. To illustrate the importance of this broadened perspective on evolution, we use a case of antimicrobial resistance evolution: the spread of the blaNDM gene family and the related resistance to carbapenem antibiotics observed globally, and show how evolutionary studies can contribute to answering contemporary socially relevant challenges.

Identification and characterization of CIM-1, a carbapenemase that adds to the family of resistance factors against last resort antibiotics

The increasing rate of carbapenem-resistant bacteria within healthcare environments is an issue of great concern that needs urgent attention. This resistance is driven by metallo-β-lactamases (MBLs), which can catalyse the hydrolysis of almost all clinically available β-lactams and are resistant to all the clinically utilized β-lactamase inhibitors. In this study, an uncharacterized MBL is identified in a multidrug resistant isolate of the opportunistic pathogen, Chryseobacterium indologenes. Sequence analysis predicts this MBL (CIM-1) to be a lipoprotein with an atypical lipobox. Characterization of CIM-1 reveals it to be a high-affinity carbapenemase with a broad spectrum of activity that includes all cephalosporins and carbapenems. Results also shown that CIM-1 is potentially a membrane-associated MBL with an uncharacterized lipobox. Using prediction tools, we also identify more potentially lipidated MBLs with non-canonical lipoboxes highlighting the necessity of further investigation of lipidated MBLs.

Evaluation of the French novel disc diffusion-based algorithm for the phenotypic screening of carbapenemase-producing Enterobacterales

OBJECTIVES

The early identification of carbapenemase-producing Enterobacterales (CPE) is required to prevent their spread and initiate proper therapy. Accordingly, it is crucial to develop efficient algorithms using susceptibility testing results to discriminate non-carbapenemase producers (non-CPE) from those that require complementary tests. In 2022, to adapt its recommendations to the evolution of CPE epidemiology (increased prevalence of OXA-244 producers), the Antibiogram Committee of the French Society of Microbiology (CA-SFM) proposed a new algorithm for the screening of CPE. We compared this algorithm to the former algorithm (2015-2021).

METHODS

From July 2022 to January 2023, all nonduplicate enterobacterial isolates referred to French National Reference Centre for carbapenemase detection (n = 518) were subjected to the former CA-SFM algorithm (2015 to 2021) using inhibition diameters of ertapenem, ticarcillin-clavulanate, temocillin and meropenem or imipenem, and the novel CA-SFM algorithm (since 2022) using inhibition diameters of ceftazidime-avibactam, temocillin, and meropenem or imipenem.

RESULTS

Sensitivity, specificity, negative predictive value, and positive predictive value were of 80.8% (CI95 76.3%-84.6%), 66.2% (58.1%-73.5%), 59.3% (51.5%-66.6%), and 85.0% (80.7% - 88.5%) for the old CA-SFM algorithm and 97.8% (95.5%-99.0%), 45.5% (37.5%-53.7%), 89.7% (80.3%-95.2%), and 80.9% (76.9%-84.4%) for the novel CA-SFM algorithm.

DISCUSSION

The novel CA-SFM algorithm possesses the best performance for the screening of CPE particularly in countries with a high prevalence of OXA-48-like producers.

The metallo-β-lactamases strike back: emergence of taniborbactam escape variants

Metallo-β-lactamases (MBLs) have evolved relatively rapidly to become an international public health threat. There are no clinically available β-lactamase inhibitors with activity against MBLs. This may change with the introduction of cefepime-taniborbactam. Herein, we review three manuscripts (S. I. Drusin, C. Le Terrier, L. Poirel, R. A. Bonomo, et al., Antimicrob Agents Chemother 68:e01168-23, 2024, https://doi.org/10.1128/aac.01168-23; C. Le Terrier, C. Viguier, P. Nordmann, A. J. Vila, and L. Poirel, Antimicrob Agents Chemother 68:e00991-23, 2024, https://doi.org/10.1128/aac.00991-23; D. Ono, M. F. Mojica, C. R. Bethel, Y. Ishii, et al., Antimicrob Agents Chemother 68:e01332-23, 2024, https://doi.org/10.1128/aac.01332-23) in which investigators describe elegant experiments to explore MBL/taniborbactam interactions and modifications to MBLs, in response, to reduce the affinity of taniborbactam. Challenges with MBL inhibition will not disappear; rather, they will evolve commensurate with advancements in medicinal chemistry.

An overview on recent advances of reversible fluorescent probes and their biological applications

Due to the simplicity and low detection limit, fluorescent probes are widely used in both analytical sensing and optical imaging. Compared to conventional fluorescent probes, reversibility endows the reversible fluorescent probe outstanding advantages and special properties, making reversible fluorescent probes with capable of quantitative, repetitive or circulatory. Reversible fluorescent probes can also monitor the concentration dynamics of target analytes in real time, such as metal ions, proteins and enzymes, as well as intracellular redox processes, which have been widely applied in various fields. This review summarized the types and excellent properties of reversible fluorescent probes designed and developed in recent years. It also summarized the applications of reversible fluorescent probe in fluorescence imaging, biological testing, monitoring redox cycles, and proposed the remaining challenges and future development directions of the reversible fluorescent probe. This review provided comprehensive overview of reversible fluorescent probe, which may provide valuable references for the design and fabrication of the reversible fluorescent probe.

Characterization of Klebsiella pneumoniae carrying the blaNDM-1 gene in IncX3 plasmids and the rare In1765 in an IncFIB-IncHI1B plasmid

Background

Today, the blaNDM gene is widely distributed on several plasmids from a variety of Gram-negative bacteria, primarily in transposons and gene cassettes within their multidrug-resistant (MDR) regions. This has led to the global dissemination of the blaNDM gene.

Methods

The determination of class A beta-lactamase, class B and D carbapenemases was performed according to the recommendations of the Clinical and Laboratory Standards Institute (CLSI). Antimicrobial susceptibility testing was performed using both the BioMerieux VITEK2 system and antibiotic paper diffusion methods. Plasmid transfer was then evaluated by conjugation experiments and plasmid electroporation assays. To comprehensively analyze the complete genome of K. pneumoniae strain F11 and to investigate the presence of mobile genetic elements associated with antibiotic resistance and virulence genes, Nanopore and Illumina sequencing platforms were used, and bioinformatics methods were applied to analyze the obtained data.

Results

Our findings revealed that K. pneumoniae strain F11 carried class A beta-lactamase and classes B+D carbapenemases, and exhibited resistance to commonly used antibiotics, particularly tigecycline and ceftazidime/avibactam, due to the presence of relevant resistance genes. Plasmid transfer assays demonstrated successful recovery of plasmids pA_F11 and pB_F11, with average conjugation frequencies of 2.91×10-4 and 1.56×10-4, respectively. However, plasmids pC_F11 and pD_F11 failed in both conjugation and electroporation experiments. The MDR region of plasmid pA_F11 contained rare In1765, TnAs2, and TnAs3 elements. The MDR2 region of plasmid pB_F11 functioned as a mobile genetic "island" and lacked the blaNDM-1 gene, serving as a "bridge" connecting the early composite structure of bleMBL and blaNDM-1 to the recent composite structure. Additionally, the MDR1 region of plasmid pB_F11 comprised In27, TnAs1, TnAs3, and Tn2; and plasmid pC_F11 harbored the recent composite structure of bleMBL and blaNDM-1 within Tn3000 which partially contained partial Tn125.

Conclusion

This study demonstrated that complex combinations of transposons and integron overlaps, along with the synergistic effects of different drug resistance and virulence genes, led to a lack of effective therapeutic agents for strain F11, therefore its dissemination and prevalence should be strictly controlled.

Occurrence and characterization of β-lactamase-producing bacteria in biomedical wastewater and in silico enhancement of antibiotic efficacy

Wastewater discharged from hospitals is a recognized contributor to the dissemination of antibiotic-resistant bacteria and their associated genetic traits into the environment. This study focused on the analysis of β-lactamase-producing pathogenic bacteria within untreated biomedical wastewater originating from various hospitals in Dhaka City, Bangladesh, as well as in silico evaluation and structural activity relationship mentioned antibiotics were evaluated. In silico drug design techniques were applied to identify the relationship with how the functional group impacts the binding energy. Out of the 184 isolates obtained from well-established hospital sewage discharge points in Dhaka, 89 were identified as β-lactamase positive. These bacteria were subjected to antimicrobial susceptibility testing using the VITEK-2 assay, and their profiles of extended-spectrum beta-lactamase (ESBL) production were determined through molecular methodologies. Among the β-lactamase-positive isolates, considerable resistance was observed, particularly against ampicillin, Ceftriaxone, Cefuroxime, and Meropenem. The predominant resistant species included Escherichia coli, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter cloacae. The study identified the prevalence of ESBL-producing genes, with blaNDM-1 being the most prevalent, followed by blaOXA-1, blaSHV, blaCTX-M, and blaKPC. None of the isolates carried the blaTEM gene. In addition to characterizing these bacteria, the research explored ways to enhance the binding energy of four existing antibiotics as new inhibitors through computational studies. The findings revealed significant improvements in binding energy. Specifically, Meropenem initially exhibited a binding energy of -7.5 kcal/mol, notably increasing to -8.3 kcal/mol after modification. With an initial binding energy was only -7.9 kcal/mol, Ampicillin experienced an enhancement, reaching -8.0 kcal/mol post-modification. Similarly, Ceftriaxone, with an initial binding energy of -8.2 kcal/mol, increased to -8.5 kcal/mol following structural adjustments. Finally, Cefuroxime, initially registering a binding energy of -7.1 kcal/mol, substantially increased to -8.9 kcal/mol after modification. This finding establishes a foundation for future investigations in the development of modified antibiotics to address the issue of antibiotic resistance. It presents prospective remedies for the persistent problem of antibiotic-resistant bacteria in healthcare and the environment.

Characterization of class 1 integrons in metallo-β-lactamase-producing Acinetobacter baumannii isolates from hospital environment

BACKGROUND AND OBJECTIVE

The emergence and widespread dissemination of antibiotic resistance in A. baumannii, has become a globally challenge. The increasing hospital outbreaks by multi-drug resistant (MDR) A. baumannii strains, shows the necessity of continuous monitoring to find sources of resistant strains in hospitals. This study aimed to identify the presence of class 1 integrons and metallo-β-lactamase (MBL) related genes in A. baumannii isolates from hospital environment.

METHODS

In order to identify A. baumannii isolates, a total of 297 environmental samples were collected from burn wards and intensive care units (ICUs) of two university hospitals. Resistance to common antibiotics was studied by disk diffusion method and microbroth dilution assay was used to determine the minimum inhibitory concentrations (MICs) of imipenem, colistin and tigecycline. The A. baumannii isolates were studied by polymerase chain reaction (PCR) for the presence of class 1 integrons (intI1, intl CS) and metallo-β-lactamases (MBLs) (blaIMP, blaVIM, blaNDM) genes.

RESULTS

A. baumannii was identified in 68/297 (22.9%) of hospital environment. All A. baumannii strains were multidrug-resistant (MDR), but none of them were resistant to colistin, tigecycline and ampicillin-sulbactam. All (100%) and 38 (95.0%) of A. baumannii isolates from ICUs and burn wards were imipenem resistant respectively. Class 1 integrons was identified in 30/40 (75.0%) and 23/28 (82.1%) isolates from burn wards and ICUs respectively. Two different types of gene cassettes were identified, which included: arr-2, ereC, aadA1, cmlA5 and arr2, cmlA5. MBL genes including blaVIM and blaIMP were detected in 26/28 (92.8%), 27/28(96.4%) and 39/40 (97.5%) and 31/40 (77.5%) of the isolates from the ICUs and the burn wards respectively. None of the isolates contained the blaNDM-1 gene.

CONCLUSION

The findings of the present study showed that the isolation rate of MBL producing carbapenem-resistant A. baumannii (CRAB) was relatively high in the environmental surface of burn wards and ICUs, which can be considered as a potential source of outbreaks in hospitalized patients.

First report of New Delhi metallo-β-lactamase-1-producing Acinetobacter soli in Japan

New Delhi metallo-β-lactamase (NDM)-producing gram-negative rods, including Acinetobacter species, are a global problem but have rarely been isolated in Japan. To our knowledge, this is the first study to isolate an NDM-1-producing Acinetobacter soli strain, KUH106, in Japan. We analyzed this strain using next-generation sequencing to examine the plasmid carrying NDM-1. This plasmid, named pKUH106_NDM1, is 41,135 bp in length and contains genetic contexts with the structure ISAba14-aph(3')-VI-ISAba125-blaNDM-1ble-MBL. Comparative analysis of the plasmid revealed that it resembled the plasmids of Acinetobacter detected in various countries, such as the A. soli isolate from Taiwan and the Acinetobacter baumannii isolate from a healthcare facility in Osaka Prefecture, Japan. These results suggest that blaNDM-1 may spread via this plasmid in Acinetobacter species. This phenomenon needs to be confirmed through the genetic analysis of A. baumannii and other carbapenem-resistant Acinetobacter species. In particular, blaNDM-1 and other resistance genes must be investigated, and the spread of these genes in the community must be cautioned.

Multidrug-resistant Escherichia coli isolated from patients and surrounding hospital environments in Bangladesh: A molecular approach for the determination of pathogenicity and resistance

Extended spectrum β-lactamase producing Escherichia coli (ESBL E. coli) is a primary concern for hospital and community healthcare settings, often linked to an increased incidence of nosocomial infections. This study investigated the characteristics of ESBL E. coli isolated from hospital environments and clinical samples. In total, 117 ESBL E. coli isolates were obtained. The isolates were subjected to molecular analysis for the presence of resistance and virulence genes, antibiotic susceptibility testing, quantitative adherence assay, ERIC-PCR for phylogenetic analysis and whole genome sequencing of four highly drug resistant isolates. Out of the 117 isolates, 68.4% were positive for blaCTX-M, 39.3% for blaTEM, 30.8% for blaNDM-1, 13.7% for blaOXA and 1.7% for blaSHV gene. Upon screening for diarrheagenic genes, no isolates were found to harbour any of the tested genes. In the case of extraintestinal pathogenic E. coli (ExPEC) virulence factors, 7.6%, 11%, 5.9%, 4.3% and 21.2% of isolates harbored the focG, kpsMII, sfaS, afa and iutA genes, respectively. At a temperature of 25°C, 14.5% of isolates exhibited strong biofilm formation with 21.4% and 28.2% exhibiting moderate and weak biofilm formation respectively, whereas 35.9% were non-biofilm formers. On the other hand at 37°C, 2.6% of isolates showed strong biofilm formation with 3.4% and 31.6% showing moderate and weak biofilm formation respectively, whereas, 62.4% were non-biofilm formers. Regarding antibiotic susceptibility testing, all isolates were found to be multidrug-resistant (MDR), with 30 isolates being highly drug resistant. ERIC-PCR resulted in 12 clusters, with cluster E-10 containing the maximum number of isolates. Hierarchical clustering and correlation analysis revealed associations between environmental and clinical isolates, indicating likely transmission and dissemination from the hospital environment to the patients. The whole genome sequencing of four highly drug resistant ExPEC isolates showed the presence of various antimicrobial resistance genes, virulence factors and mobile genetic elements, with isolates harbouring the plasmid incompatibility group IncF (FII, FIB, FIA). The sequenced isolates were identified as human pathogens with a 93.3% average score. This study suggests that ESBL producing E. coli are prevalent in the healthcare settings of Bangladesh, acting as a potential reservoir for AMR bacteria. This information may have a profound effect on treatment, and improvements in public healthcare policies are a necessity to combat the increased incidences of hospital-acquired infections in the country.

Severe infections caused by difficult-to-treat Gram-negative bacteria

PURPOSE OF REVIEW

Antimicrobial resistance (AMR) in Gram-negative bacteria (GNB) poses a significant global health concern, contributing to increased infections, mortality rates, and healthcare costs. This review discusses the main clinical manifestations, therapeutic options, and recent findings in managing antibiotic-resistant GNB, with a focus on difficult-to-treat infections.

RECENT FINDINGS

Difficult-to-treat resistance (DTR) is a novel classification that identifies GNB exhibiting intermediate or resistant phenotypes to first-line agents in the carbapenem, beta-lactam, and fluoroquinolone categories. The main pathogens implicated in severe infections include DTR Enterobacterales, DTR Pseudomonas aeruginosa , and DTR Acinetobacter baumannii. Although the clinical implications of DTR strains are still under investigation, certain studies have linked them to prolonged hospital stays and poor patient outcomes.

SUMMARY

Severe infections caused by DTR-GNB pose a formidable challenge for healthcare providers and represent a growing global health issue. The proper administration and optimization of novel antibiotics at our disposal are of paramount importance for combating bacterial resistance and improving patient prognosis.

Emergence and rapid dissemination of highly resistant NDM-14-producing Klebsiella pneumoniae ST147, France, 2022

BackgroundSince 2021, an emergence of New Delhi metallo-β-lactamase (NDM)-14-producing Klebsiella pneumoniae has been identified in France. This variant with increased carbapenemase activity was not previously detected in Enterobacterales.AimWe investigated the rapid dissemination of NDM-14 producers among patients in hospitals in France.MethodsAll NDM-14-producing non-duplicate clinical isolates identified in France until June 2022 (n = 37) were analysed by whole genome sequencing. The phylogeny of NDM-14-producers among all K. pneumoniae sequence type (ST) 147 reported in France since 2014 (n = 431) was performed. Antimicrobial susceptibility testing, conjugation experiments, clonal relationship and molecular clock analysis were performed.ResultsThe 37 NDM-14 producers recovered in France until 2022 belonged to K. pneumoniae ST147. The dissemination of NDM-14-producing K. pneumoniae was linked to a single clone, likely imported from Morocco and responsible for several outbreaks in France. The gene bla NDM-14 was harboured on a 54 kilobase non-conjugative IncFIB plasmid that shared high homology with a known bla NDM-1-carrying plasmid. Using Bayesian analysis, we estimated that the NDM-14-producing K. pneumoniae ST147 clone appeared in 2020. The evolutionary rate of this clone was estimated to 5.61 single nucleotide polymorphisms per genome per year. The NDM-14 producers were highly resistant to all antimicrobials tested except to colistin, cefiderocol (minimum inhibitory concentration 2 mg/L) and the combination of aztreonam/avibactam.ConclusionHighly resistant NDM-14 producing K. pneumoniae can rapidly spread in healthcare settings. Surveillance and thorough investigations of hospital outbreaks are critical to evaluate and limit the dissemination of this clone.

Infection Prevention Control Strategies of New Delhi Metallo-β-lactamase Producing Klebsiella pneumoniae

The spread of multi-drug resistant organisms (MDROs) is increasing at an alarming rate worldwide. Among these, Carbapenemase-producing New Delhi Metallo-β-lactamase (NDM) poses a significant clinical threat, and appropriate measures must be taken to prevent or limit its penetration into still-free territories. The present report describes two independent cases of patients from Ukraine colonized by NDM-producing Klebsiella pneumoniae and admitted to two separate wards of an acute university hospital in a territory not yet affected by Carbapenemase producers of this class. Moreover, this report illustrates the infection prevention control (IPC) strategies promptly implemented by the IPC operational team to verify the possible spread of the microorganism in the ward and avoid any possible further contamination. The identification of genes coding for Carbapenemases, performed using real-time PCR, revealed no other cases within the wards involved. These cases emphasize the importance of early case recognition of multidrug-resistant bacteria, the necessity of effective inter-hospital communication, the need for effective antimicrobial stewardship protocol, and the importance of adequate IPC policies. Additionally, we highlight the need to improve screening procedures in the case of patients from countries with a high prevalence of MDRO, as essential measures to prevent potential nosocomial outbreaks and/or endemization.

Active Surveillance of Antimicrobial Resistance and Carbapenemase-Encoding Genes According to Sites of Care and Age Groups in Mexico: Results from the INVIFAR Network

We analyzed the antimicrobial resistance (AMR) data of 6519 clinical isolates of Escherichia coli (n = 3985), Klebsiella pneumoniae (n = 775), Acinetobacter baumannii (n = 163), Pseudomonas aeruginosa (n = 781), Enterococcus faecium (n = 124), and Staphylococcus aureus (n = 691) from 43 centers in Mexico. AMR assays were performed using commercial microdilution systems (37/43) and the disk diffusion susceptibility method (6/43). The presence of carbapenemase-encoding genes was assessed using PCR. Data from centers regarding site of care, patient age, and clinical specimen were collected. According to the site of care, the highest AMR was observed in E. coli, K. pneumoniae, and P. aeruginosa isolates from ICU patients. In contrast, in A. baumannii, higher AMR was observed in isolates from hospitalized non-ICU patients. According to age group, the highest AMR was observed in the ≥60 years age group for E. coli, E. faecium, and S. aureus, and in the 19-59 years age group for A. baumannii and P. aeruginosa. According to clinical specimen type, a higher AMR was observed in E. coli, K. pneumoniae, and P. aeruginosa isolates from blood specimens. The most frequently detected carbapenemase-encoding gene in E. coli was blaNDM (84%).

Complete-genome sequencing and comparative genomic characterization of blaNDM-5 carrying Citrobacter freundii isolates from a patient with multiple infections

BACKGROUND

The emergence and wide spread of carbapenemase-producing Enterobacteriaceae (CPE) poses a growing threat to global public health. However, clinically derived carbapenemase-producing Citrobacter causing multiple infections has rarely been investigated. Here we first report the isolation and comparative genomics of two blaNDM-5 carrying Citrobacter freundii (C. freundii) isolates from a patient with bloodstream and urinary tract infections.

RESULTS

Antimicrobial susceptibility testing showed that both blaNDM-5 carrying C. freundii isolates were multidrug-resistant. Positive modified carbapenem inactivation method (mCIM) and EDTA-carbapenem inactivation method (eCIM) results suggested metallo-carbapenemase production. PCR and sequencing confirmed that both metallo-carbapenemase producers were blaNDM-5 positive. Genotyping and comparative genomics analyses revealed that both isolates exhibited a high level of genetic similarity. Plasmid analysis confirmed that the blaNDM-5 resistance gene is located on IncX3 plasmid with a length of 46,161 bp, and could successfully be transferred to the recipient Escherichia coli EC600 strain. A conserved structure sequence (ISAba125-IS5-blaNDM-5-trpF-IS26-umuD-ISKox3) was found in the upstream and downstream of the blaNDM-5 gene.

CONCLUSIONS

The data presented in this study showed that the conjugative blaNDM-5 plasmid possesses a certain ability to horizontal transfer. The dissemination of NDM-5-producing C. freundii isolates should be of close concern in future clinical surveillance. To our knowledge, this is the first study to characterize C. freundii strains carrying the blaNDM-5 gene from one single patient with multiple infections.

Comparative Genomics Identified PenR E151V Substitution Associated with Carbapenem-Resistance Burkholderia cepacia Complex and a Novel Burkholderia cepacia Complex Specific OXA-1043 Subgroup

Purpose

Burkholderia cepacia complex (Bcc) is a known significant opportunistic pathogen causing morbidity and mortality, particularly in those with cystic fibrosis, chronic granulomatous disease, or immunocompromising host. Mortality of Bcc bloodstream infections among non-cystic fibrosis patients remained high. The antibiotic treatment for Bcc infection is quite challenging due to its intrinsic resistance to most antibiotics, and the resistance to carbapenems was the biggest concern among them. We aimed to realize the mechanism of carbapenem resistance in Bcc.

Patients and Methods

Ten strains of Bcc were identified by the MALDI-TOF MS, and the drug susceptibility test was using VITEK 2 system. The Burkholderia cepacia complex genomes were sequenced via Nanopore GridIon. We also downloaded another ninety-five strains of Bcc from the National Center for Biotechnology Information database to evaluate the divergence between carbapenem-resistance and carbapenem-sensitive strains.

Results

The genetic organization between carbapenem-sensitive and carbapenem-resistant strains of Bcc showed no difference. However, in the carbapenem-sensitive strain, E151V substitution in PenR was detected. In addition, a novel specific OXA family subgroup, blaOXA-1043 in Burkholderia cenocepacia was discovered.

Conclusion

The E151V substitution in PenR may be associated with carbapenem-sensitive in Bcc. Moreover, the V151E mutation in PenR may be related to the activation of PenB, leading to Bcc resistance to carbapenems. Besides, a novel OXA family subgroup, blaOXA-1043, was found in Burkholderia cenocepacia, which differs from the previous OXA family.

Acinetobacter baumannii Carbapenemase Producers in Morocco: Genetic Diversity

INTRODUCTION

 Carbapenem resistance in Acinetobacter baumannii (A. baumannii) is a public health problem worldwide. Although carbapenem resistance is emerging in Morocco, few studies have shown the epidemiological profile of carbapenemase genes in Moroccan healthcare facilities. The aim of this study was to characterize the molecular profile of the carbapenemase enzyme in Acinetobacter baumannii from clinical isolates.

METHODS

Clinical strains isolated in the laboratory from various samples were subjected to several phenotypic tests. Antibiotic susceptibility and identification were tested using Phoenix 100 (Becton Dickinson Co., Sparks, MD, USA) and Api 20 (bioMérieux, Marcy-l'Etoile, France). Simple phenotypic assays were used to detect carbapenemase oxacillinase (OXA) and metallo-β-lactamase (MBL) production, including the modified Hodge test (MHT) and ethylenediaminetetraacetic acid (EDTA) test. The detection of carbapenemase genes was performed by multiplex and simple polymerase chain reaction (PCR).

RESULTS

A total of 140 strains or 100% of isolates contained OXA-51 and ISbA1 sequences, 89% contained OXA-23 and OXA-58 sequences, and 1% contained OXA-24 sequence. The MBL genes were predominated by Verona integron-encoded metallo-β-lactamase (VIM) (56%), followed by Seoul imipenemase (SIM) (39%), German imipenemase (GIM) (37%), São Paulo metallo-β-lactamase (SPM) (13%), imipenemase (IMP) (11%), and New Delhi metallo-β-lactamase (NDM) (4%). Guyana extended-spectrum β-lactamase (GES) was not found in any isolation.

CONCLUSION

Our study shows a high frequency of carbapenem resistance in Acinetobacter baumannii, as it reports a high molecular diversity of carbapenemase-encoding genes, mainly dominated by the carbapenemase ISaba1/OXA-23, which represents an emerging threat in our hospital.

Probable Three-Species In Vivo Transfer of blaNDM-1 in a Single Patient in Greece: Occurrence of NDM-1-Producing Klebsiella pneumoniae, Proteus mirabilis, and Morganella morganii

NDM carbapenemase-encoding genes disseminate commonly among Enterobacterales through transferable plasmids carrying additional resistance determinants. Apart from the intra-species dissemination, the inter-species exchange of plasmids seems to play an additional important role in the spread of bla_NDM. We here present the genetics related to the isolation of three species (Klebsiella pneumoniae, Proteus mirabilis, and Morganella morganii) harboring the bla_NDM-1 gene from a single patient in Greece. Bacterial identification and antimicrobial susceptibility testing were performed using the Vitek2. Whole genome sequencing and bioinformatic tools were used to identify resistance genes and plasmids. Bla_NDM-1 harboring plasmids were found in all three isolates. Moreover, the plasmid constructs of the respective incomplete or circular contigs showed that the bla_NDM-1 and its neighboring genes form a cluster that was found in all isolates. Our microbiological findings, together with the patient's history, suggest the in vivo transfer of the bla_NDM-1-containing cluster through three different species in a single patient.

An NDM-Producing Escherichia coli Clinical Isolate Exhibiting Resistance to Cefiderocol and the Combination of Ceftazidime-Avibactam and Aztreonam: Another Step Toward Pan-β-Lactam Resistance

Background

Cefiderocol and ceftazidime-avibactam plus aztreonam (CZA-ATM) are preferred treatment regimens for New Delhi metallo-β-lactamase (NDM)-producing infections.

Methods

We report the case of a US patient who traveled to India to receive a renal transplant. He subsequently experienced pyelonephritis by an NDM-producing Escherichia coli. Broth microdilution and the broth disk elution method indicated resistance to all β-lactams, including cefiderocol and CZA-ATM. Whole-genome sequencing investigations were undertaken to identify resistance mechanisms.

Results

An E. coli isolate belonging to sequence type (ST) 167 containing a bla_NDM-5 gene was identified on a plasmid of the IncFIA/IncFIB/IncFIC replicon groups. When compared with the genome of another ST167 E. coli clinical isolate containing bla_NDM-5 and exhibiting susceptibility to cefiderocol and CZA-ATM, a 12-base pair insertion in ftsI, translating to a 4-amino acid duplication in PBP3, was identified. Moreover, a bla_CMY-59 gene was harbored on an IncI-γ replicon type, and frameshift mutations were identified in the cirA iron transport gene.

Conclusions

This is the first clinical case of a US patient harboring an NDM-producing isolate exhibiting resistance to all available β-lactam agents. The isolate's unexpected resistance to cefiderocol and CZA-ATM was likely due to a combination of (1) a modified PBP3 (increased MICs to both regimens), (2) truncated iron-binding protein (increased cefiderocol MIC), and (3) a bla_CMY gene (reduced CZA-ATM activity). E. coli ST167 clinical isolates harboring bla_NDM-5 genes are a recognized international high-risk clone. When coupled with the additional mechanisms identified in our patient's isolate, which is not uncommon for this high-risk clone, pan-β-lactam resistance may occur.

Emergence of Carbapenem-Resistant Gram-Negative Isolates in Hospital Settings in Djibouti

Introduction: The antimicrobial resistance (AMR) of bacteria is increasing rapidly against all classes of antibiotics, with the increasing detection of carbapenem-resistant isolates. However, while growing prevalence has been reported around the world, data on the prevalence of carbapenem resistance in developing countries are fairly limited. In this study, we investigated and determined the resistance rate to carbapenems among multidrug-resistant Gram-negative bacteria (MDR-GNB) isolated in Djibouti and characterized their resistance mechanisms. Results: Of the 256 isolates, 235 (91.8%) were identified as Gram-negative bacteria (GNB). Of these GNBs, 225 (95.7%) isolates exhibited a multidrug resistance phenotype, and 20 (8.5%) isolates were resistant to carbapenems, including 13 Escherichia coli, 4 Acinetobacter baumannii, 2 Klebsiella pneumoniae and 1 Proteus mirabilis. The most predominant GNB in this hospital setting were E. coli and K. pneumoniae species. Carbapenemase genes such as bla_OXA-48 and bla_NDM-5 were identified, respectively, in six and four E. coli isolates, whereas the carbapenemase bla_NDM-1 was identified in three E. coli, two K. pneumoniae, one P. mirabilis and one A. baumannii. Moreover, three A. baumannii isolates co-hosted bla_OXA-23 and bla_NDM-1. Materials and Methods: A total of 256 clinical strains collected between 2019 and 2020 were identified using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). Antibiotic susceptibility testing was performed using disk diffusion and E-test methods. Real-time polymerase chain reaction (RT-PCR), standard PCR and sequencing were used to investigate genes encoding for extended-spectrum-β-lactamases, carbapenemases and colistin resistance genes. Conclusions: We report, for the first time, the presence of MDR-GNB clinical isolates and the emergence of carbapenem-resistant isolates in Djibouti. In addition to performing antimicrobial susceptibility testing, we recommend phenotypic and molecular screening to track the spread of carbapenemase genes among clinical GNB isolates.

Bloodstream infections due to Carbapenem-Resistant Enterobacteriaceae in hematological patients: assessment of risk factors for mortality and treatment options

PURPOSE

Bloodstream infection (BSI) caused by Carbapenem-Resistant Enterobacteriaceae (CRE) are associated with poor outcomes in hematological patients. The aim of this study was to identify risk factors for mortality and evaluate the value of epidemiological feature of carbapenemases in guiding antimicrobial treatment options.

METHODS

Hematological patients with monomicrobial CRE BSI between January 2012 and April 2021 were included. The primary outcome was all-cause mortality 30 days after BSI onset.

RESULTS

A total of 94 patients were documented in the study period. Escherichia coli was the most common Enterobacteriaceae, followed by Klebsiella pneumoniae. 66 CRE strains were tested for carbapenemase genes, and 81.8% (54/66) were positive, including NDM (36/54), KPC (16/54), IMP (1/54). Besides, one E. coli isolate was found to express both NDM and OXA-48-like genes. Overall, 28 patients received an antimicrobial treatment containing ceftazidime-avibactam (CAZ-AVI), of which 21 cases were combined with aztreonam. The remaining 66 patients were treated with other active antibiotics (OAAs). The 30-day mortality rate was 28.7% (27/94) for all patients, and was only 7.1% ((2/28) for patients treated with CAZ-AVI. In multivariate analysis, the presence of septic shock at BSI onset (OR 10.526, 95% CI 1.376-76.923) and pulmonary infection (OR 6.289, 95% CI 1.351-29.412) were independently risk factors for 30-day mortality. Comparing different antimicrobial regimens, CAZ-AVI showed a significant survive benefit than OAAs (OR 0.068, 95% CI 0.007-0.651).

CONCLUSION

CAZ-AVI-containing regimen is superior to OAAs for CRE BSI. As the predominance of blaNDM in our center, we recommend the combination with aztreonam when choose CAZ-AVI.

Carbapenemase-producing Klebsiella pneumoniae in community settings: a cross-sectional study in Belgrade, Serbia

Aim: The types of carbapenemases and clonal relatedness among community isolates of carbapenemase-producing Klebsiella pneumoniae in Belgrade, Serbia, were determined. Materials & methods: During the period 2016-2020, K. pneumoniae community isolates were screened for carbapenemases, and carbapenemase production was confirmed by multiplex PCR. Clonality was determined based on genetic profiles obtained by enterobacterial repetitive intergenic consensus PCR. Results: Carbapenemase genes were detected in 114 of 4800 isolates (2.4%). The most frequent gene was blaOXA-48-like. Most isolates (70.5%) were grouped in ten clusters. Cluster 11 contained 16.4% of all blaOXA-48-like-positive isolates, and all blaKPC-positive isolates were grouped in one cluster. Conclusion: Laboratory-based detection and surveillance are highly recommended in order to control the spread of resistance in community settings.

Aprosamine Derivatives Active against Multidrug-Resistant Gram-Negative Bacteria

Novel aprosamine derivatives were synthesized for the development of aminoglycoside antibiotics active against multidrug-resistant Gram-negative bacteria. The synthesis of aprosamine derivatives involved glycosylation at the C-8' position and subsequent modification (epimerization and deoxygenation at the C-5 position and 1-N-acylation) of the 2-deoxystreptamine moiety. All 8'-β-glycosylated aprosamine derivatives (3a-h) showed excellent antibacterial activity against carbapenem-resistant Enterobacteriaceae and 16S ribosomal RNA methyltransferase-producing multidrug-resistant Gram-negative bacteria compared to the clinical drug, arbekacin. The antibacterial activity of 5-epi (6a-d) and 5-deoxy derivatives (8a,b and 8h) of β-glycosylated aprosamine was further enhanced. On the other hand, the derivatives (10a,b and 10h) in which the amino group at the C-1 position was acylated with (S)-4-amino-2-hydroxybutyric acid showed excellent activity (MICs 0.25-0.5 μg/mL) against resistant bacteria that produce the aminoglycoside-modifying enzyme, aminoglycoside 3-N-acetyltransferase IV, which induces high resistance against parent apramycin (MIC > 64 μg/mL). In particular, 8b and 8h showed approximately 2- to 8-fold antibacterial activity against carbapenem-resistant Enterobacteriaceae and 8- to 16-fold antibacterial activity against resistant Gram-positive bacteria, such as methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci, compared to apramycin. Our results showed that aprosamine derivatives have immense potential in the development of therapeutic agents for multidrug-resistant bacteria.

Detection of Carbapenem-resistance in CRE by Comparative Assessment of RAPIDEC® CARBA NP and Xpert™Carba-R Assay

Introduction

Carbapenem-resistant Enterobacteriaceae (CRE) infections resist nearly most available antimicrobials, resulting in poor clinical outcomes. Saudi Arabia has a relatively high CRE prevalence. This study aims to evaluate the sensitivity of Rapidec Carba NP test and GeneXpert Carba-R assay compared with conventional manners for detection of carbapenemase-producing Enterobacteriaceae.

Methods

This is a cross-sectional study including a total of 90 CRE isolates examined at two tertiary hospitals in KSA from October 2020 to December 2021. Gram-negative Enterobacteriaceae were identified by using Vitek 2 system and were furtherly tested for imipenem and meropenem susceptibility by E- test strips, followed by Rapidec Carba NP test and the Xpert™Carba-R assay.

Results

Carbapenem-resistant K. pneumoniae (78.9%) and carbapenem-resistant E. coli (14.4%) were the two most common isolates species. Colistin (98.9%) and tigecycline (88.9%) were the most effective antibiotics against CRE isolates, followed by amikacin (52.2%), gentamicin (33.3%), cotrimoxazole (15.6%), and ciprofloxacin (8.9%). blaOXA-48 was the predominant carbapenemase gene (44.4%), followed by blaNDM (32.2%). blaKPC gene was not detected. The Rapidec Carba NP and the Xpert™Carba-R demonstrated an overall sensitivity of 69.3% and 88%, respectively, in comparison to gold standard detection of meropenem and imipenem resistance by Vitek 2 system and E- test strips.

Discussion

RAPIDEC^® CARBA NP may be a beneficial screening test for detecting CRE, but for confirmation of the results, Xpert Carba-R assay is more sensitive, significantly lowering the turnaround time compared to reference traditional methods. The information on carbapenemase genes may be used for epidemiologic purposes and outbreak management.

The shared NDM-positive strains in the hospital and connecting aquatic environments

The spread of antibiotic-resistant priority pathogens outside hospital settings is, both, a significant public health concern and an environmental problem. In recent years, New Delhi Metallo-β-lactamase (NDM)-positive strains have caused nosocomial infections with high mortality and poor prognosis worldwide. Our study investigated the links of NDM-positive strains between the hospital and the connecting river system in Jinan city, Eastern China by using NDM-producing Escherichia coli (NDM-EC) as an indicator via whole genome sequencing. Thirteen NDM-EC isolates were detected from 187 river water and sediment samples, while 9 isolates were identified from patients at the local hospital. All NDM-EC isolates were resistant to imipenem, meropenem, cefotaxime, cefoxitin, ampicillin, tetracycline, fosfomycin, piperacillin-tazobactam. The bla_NDM-5 (n = 20) and bla_NDM-9 (n = 2) genes were identified, which were predominantly on IncX3 plasmids (n = 13), followed by IncFII plasmids (n = 5) and IncFIA plasmids (n = 2). Conjugation experiments showed that 21 isolates could transfer NDM-harboring plasmids. The well-conserved bla_NDM-5 genetic environment (ISAba125-bla_NDM-5/9-ble_MBL-trpF-dsbD-IS26) of these plasmids suggested a common genetic origin. Nine sequence types (STs) were detected, including three international high-risk clones ST167 (n = 8), ST410 (n = 1), and ST617 (n = 1). Phylogenetic analysis showed ST167 E. coli from the river was genotypically related to clinical isolates recovered from patients. Furthermore, ST167 isolates showed high genetic similarities with other clinical strains from geographically distinct regions. The genetic concordance between isolates from different sampling sites in the same river (ST218 clone), and different rivers (ST448 clone) raises concerns regarding the rapid dissemination of NDM-EC in the aquatic environment. The emergence and spread of the clinically relevant NDM-positive strains, especially for E. coli ST167 clone, an international high-risk clone associated with multi-resistance and virulence capacity, within and between the hospital and aquatic environments were elucidated, highlighting the need for attention and action.

Characterization of NDM-5-Producing Escherichia coli Strains Isolated from Pediatric Patients with Bloodstream Infections in a Chinese Hospital

Escherichia coli (E. coli) bloodstream infections (BSIs) are among the most predominant causes of death in infants and children worldwide. NDM-5 (New Delhi Metallo-lactamase-5) is responsible for one of the main mechanisms of carbapenem resistance in E. coli. To analyze the phenotypic and genomic characteristics of NDM-5-producing E. coli from bloodstream infections (BSIs), a total of 114 E. coli strains was collected from a children's hospital in Jiangsu province, China. Eight blaNDM-5-carrying E. coli strains were identified which were all carbapenem-resistant and carried diverse antimicrobial resistance genes apart from blaNDM-5. They belonged to six distinct sequence types (STs) and serotypes including one each for ST38/O7:H8, ST58/O?:H37, ST131/O25:H4, ST156/O11:H25 and ST361/O9:H30 and three strains are originating from a single clone belonging to ST410/O?:H9. Apart from blaNDM-5, the E. coli strains isolated from BSIs also carried other β-lactamase genes, including blaCMY-2 (n = 4), blaCTX-M-14 (n = 2), blaCTX-M-15 (n = 3), blaCTX-M-65 (n = 1), blaOXA-1 (n = 4) and blaTEM-1B (n = 5). The blaNDM-5 genes were located on three different types of plasmids, which were IncFII/I1 (n = 1), IncX3 (n = 4) and IncFIA/FIB/FII/Q1 (n = 3). The former two types were conjugatively transferable at frequencies of 10-3 and 10-6, respectively. The dissemination of NDM-producing strains, which exhibit resistance to the last-line antibiotics, carbapenems, may increase the muti-antimicrobial resistance burden among E. coli BSIs and further threaten public health.

Whole-Genome Sequencing Snapshot of Clinically Relevant Carbapenem-Resistant Gram-Negative Bacteria from Wastewater in Serbia

Wastewater (WW) is considered a source of antibiotic-resistant bacteria with clinical relevance and may, thus, be important for their dissemination into the environment, especially in countries with poor WW treatment. To obtain an overview of the occurrence and characteristics of carbapenem-resistant Gram-negative bacteria (CR-GNB) in WW of Belgrade, we investigated samples from the four main sewer outlets prior to effluent into international rivers, the Sava and the Danube. Thirty-four CR-GNB isolates were selected for antimicrobial susceptibility testing (AST) and whole-genome sequencing (WGS). AST revealed that all isolates were multidrug-resistant. WGS showed that they belonged to eight different species and 25 different sequence types (STs), seven of which were new. ST101 K. pneumoniae (bla_CTX-M-15/bla_OXA-48) with novel plasmid p101_srb was the most frequent isolate, detected at nearly all the sampling sites. The most frequent resistance genes to aminoglycosides, quinolones, trimethroprim-sulfamethoxazole, tetracycline and fosfomycin were aac(6')-Ib-cr (55.9%), oqxA (32.3%), dfrA14 (47.1%), sul1 (52.9%), tet(A) (23.5%) and fosA (50%), respectively. Acquired resistance to colistin via chromosomal-mediated mechanisms was detected in K. pneumoniae (mutations in mgrB and basRS) and P. aeruginosa (mutation in basRS), while a plasmid-mediated mechanism was confirmed in the E. cloacae complex (mcr-9.1 gene). The highest number of virulence genes (>300) was recorded in P. aeruginosa isolates. Further research is needed to systematically track the occurrence and distribution of these bacteria so as to mitigate their threat.

Various mobile genetic elements carrying optrA in Enterococcus faecium and Enterococcus faecalis isolates from swine within the same farm

OBJECTIVES

In this study, the distribution of the oxazolidinone/phenicol resistance gene optrA and the mobile genetic elements involved in its dissemination were analysed among enterococcal isolates from a farrow-to-finish swine farm.

METHODS

Enterococcus faecium and Enterococcus faecalis isolates were obtained from all pig production stages in the farm. The optrA-carrying E. faecium and E. faecalis isolates were subjected to PFGE and antimicrobial susceptibility testing. Complete sequences of the genetically unrelated optrA-carrying E. faecium and E. faecalis isolates were determined using Illumina HiSeq and MinION platforms.

RESULTS

The optrA gene was present in 12.2% (23/188) of the E. faecium and E. faecalis isolates, most of which originated from nursery and finishing stages. The 23 optrA-positive Enterococcus isolates represented 15 PFGE types. WGS of representative isolates of the 15 PFGE types showed that optrA was carried by diverse genetic elements either located in the chromosomal DNA or on plasmids. A novel optrA-bearing genetic element was identified on two distinct multi-resistance plasmids from E. faecium. Two new hybrid plasmids carrying several resistance genes were found in two E. faecalis isolates. pC25-1-like plasmids and chromosomally integrated Tn6674 and Tn6823-like transposons were prevalent in the remaining Enterococcus isolates.

CONCLUSIONS

The gene optrA was found in genetically unrelated E. faecium and E. faecalis isolates from the same farm. Analysis of the genetic contexts of optrA suggested that horizontal transfer including different plasmids and transposons played a key role in the dissemination of optrA in this farm.

Recent Approaches for Downplaying Antibiotic Resistance: Molecular Mechanisms

Antimicrobial resistance (AMR) is a ubiquitous public health menace. AMR emergence causes complications in treating infections contributing to an upsurge in the mortality rate. The epidemic of AMR in sync with a high utilization rate of antimicrobial drugs signifies an alarming situation for the fleet recovery of both animals and humans. The emergence of resistant species calls for new treatments and therapeutics. Current records propose that health drug dependency, veterinary medicine, agricultural application, and vaccination reluctance are the primary etymology of AMR gene emergence and spread. Recently, several encouraging avenues have been presented to contest resistance, such as antivirulent therapy, passive immunization, antimicrobial peptides, vaccines, phage therapy, and botanical and liposomal nanoparticles. Most of these therapies are used as cutting-edge methodologies to downplay antibacterial drugs to subdue the resistance pressure, which is a featured motive of discussion in this review article. AMR can fade away through the potential use of current cutting-edge therapeutics, advancement in antimicrobial susceptibility testing, new diagnostic testing, prompt clinical response, and probing of new pharmacodynamic properties of antimicrobials. It also needs to promote future research on contemporary methods to maintain host homeostasis after infections caused by AMR. Referable to the microbial ability to break resistance, there is a great ultimatum for using not only appropriate and advanced antimicrobial drugs but also other neoteric diverse cutting-edge therapeutics.

Molecular epidemiology and genomic insights into the transmission of carbapenem-resistant NDM-producing Escherichia coli

Escherichia coli is a leading cause of nosocomial infections. Carbapenem-resistant E. coli (CREC), which has been frequently isolated in recent years because of the widespread use of carbapenems, poses a significant challenge to clinical anti-infection treatment. In this study, a total of 27 CREC strains were identified from a set of 795 E. coli isolates collected over a two-year period from a tertiary hospital in China. Whole-genome sequencing revealed that 17 strains carried the bla _NDM-5 gene, 5 strains carried the bla _NDM-1 gene, 1 strain carried the bla _NDM-7 gene, and the remaining 4 strains carried the bla _KPC-2 gene. All 23 NDM-producing E. coli strains were resistant to all antibiotics except tigecycline, colistin, and cefiderocol. Nine different sequence types (STs) were identified, with ST410 and ST167 being the most prevalent. All of the bla _NDM genes were located on conjugatable plasmids. We identified five different plasmid replicon types ranging in size from 20 kb to 200 kb, with the IncX3-type plasmid, 46 kb in size, being a key factor in facilitating the horizontal transmission of the bla _NDM gene in E. coli. The structure surrounding the bla _NDM gene was relatively conserved and mainly contained the following structures: IS3000-ISAbal25-IS5-bla _NDM-ble _MBL-trpF-dsbC-IS26. However, the plasmid backbone structure was highly variable, which indicates that the bla _NDM gene has already spread horizontally among different types of plasmids. In addition, we discovered two copies of the bla _NDM-5 gene in a single plasmid (pEC29-NDM-5), with an identical structure around the gene and the complete sequence of the class 1 integron. Our findings detail the prevalence of CREC in a tertiary hospital in China, and the emergence of multiple copies of the bla _NDM-5 gene on a single plasmid needs our attention.

Genomic analysis of chromosomal cointegrated bla NDM-1-carrying ICE and bla RSA-1-carrying IME from clinical multidrug resistant Aeromonas caviae

Introduction

The objective of this study is to thoroughly analyze the detailed genomic characteristics of clinical strain 211703 of Aeromonas caviae, which co-carrying bla _RSA-1 and bla _NDM-1 genes. 211703 was isolated from the patient's cerebrospinal fluid drainage sample in a Chinese tertiary hospital.

Methods

Carbapenemase NDM was detected by the immunocolloidal gold technique. The MIC values were determined by VITEK2. The whole genome sequence of 211703 was analyzed using phylogenetics, genomic comparison, and extensive dissection.

Results

This study revealed that 211703 only contained a single 4.78 Mb chromosome (61.8% GC content), and no plasmids were discovered in 211703. 15 different types of resistant genes were detected in the genome of 211703, including bla _RSA-1 harbored on integrative and mobilizable element (IME) Tn7413a, and bla _NDM-1 harbored on integrative and conjugative element (ICE). The ICE and IME were all carried on the chromosome of 211703 (c211703). Detailed comparison of related IMEs/ICEs showed that they shared similar conserved backbone regions, respectively. Comprehensive annotation revealed that bla _RSA-1 was carried by the gene cassette of a novel integron In2148 on Tn7413a, and bla _NDM-1 was captured by an insertion sequence ISCR14-like on the ICE of 211703. We speculated that mobile genetic elements (MGEs) such as ICE and IME facilitated the spread of resistance genes such as bla _RSA-1 and bla _NDM-1.

Discussion

In conclusion, this study provides an overall understanding of the genomic characterization of clinically isolated A. caviae 211703, and an in-depth discussion of multiple acquisition methods of drug resistance genes in Aeromonas. To the best of our knowledge, this is the first report of A. caviae carrying bla _RSA-1 even both bla _RSA-1 and bla _NDM-1, and this is the first bacterium carrying bla _RSA-1 isolated from the clinical setting.

PHT427 as an effective New Delhi metallo-β-lactamase-1 (NDM-1) inhibitor restored the susceptibility of meropenem against Enterobacteriaceae producing NDM-1

Introduction

With the increasingly serious problem of bacterial drug resistance caused by NDM-1, it is an important strategy to find effective inhibitors to assist β-lactam antibiotic treatment against NDM-1 resistant bacteria. In this study, PHT427 (4-dodecyl-N-1,3,4-thiadiazol-2-yl-benzenesulfonamide) was identified as a novel NDM-1 inhibitor and restored the susceptibility of meropenem against Enterobacteriaceae producing NDM-1.

Methods

We used a high throughput screening model to find NDM-1 inhibitor in the library of small molecular compounds. The interaction between the hit compound PHT427 and NDM-1 was analyzed by fluorescence quenching, surface plasmon resonance (SPR) assay, and molecular docking analysis. The efficacy of the compound in combination with meropenem was evaluated by determining the FICIs of Escherichia coli BL21(DE3)/pET30a(+)-bla _NDM-1 and Klebsiella pneumoniae clinical strain C1928 (producing NDM-1). In addition, the mechanism of the inhibitory effect of PHT427 on NDM-1 was studied by site mutation, SPR, and zinc supplementation assays.

Results

PHT427 was identified as an inhibitor of NDM-1. It could significantly inhibit the activity of NDM-1 with an IC₅₀ of 1.42 μmol/L, and restored the susceptibility of meropenem against E. coli BL21(DE3)/pET30a(+)-bla _NDM-1 and K. pneumoniae clinical strain C1928 (producing NDM-1) in vitro. The mechanism study indicated that PHT427 could act on the zinc ions at the active site of NDM-1 and the catalytic key amino acid residues simultaneously. The mutation of Asn220 and Gln123 abolished the affinity of NDM-1 by PHT427 via SPR assay.

Discussion

This is the first report that PHT427 is a promising lead compound against carbapenem-resistant bacteria and it merits chemical optimization for drug development.

A Nationwide Plasmidome Surveillance in Thailand Reveals a Limited Variety of New Delhi Metallo-β-Lactamase-Producing Carbapenem-Resistant Enterobacteriaceae Clones and Spreading Plasmids

Despite frequent identification of plasmids carrying carbapenemase genes, the transfer of plasmids carrying carbapenemase genes is not well recognized in clinical settings because of technical limitations. To investigate the detailed mechanisms of the spread of carbapenem-resistant Enterobacteriaceae (CRE), we performed multifaceted genomic surveillance of CRE isolates in Thailand and analyzed their plasmidome. We analyzed 371 Enterobacteriaceae isolates carrying bla_NDM-1 and 114 Enterobacteriaceae isolates carrying bla_NDM-5 obtained from clinical samples of 473 patients in 11 representative hospitals located in six provinces in Thailand between 2012 and 2017. The complete structures of plasmids carrying bla_NDM and chromosomal phylogeny were determined by combining Southern blotting hybridization analysis and our previously performed whole-genome short-read sequencing data. Dissemination of the bla_NDM-5 gene among the Enterobacteriaceae isolates in Thailand was mainly owing to the nationwide clonal spread of Escherichia coli ST410 and regional clonal spreads of Escherichia coli ST361 and ST405. Analysis of bla_NDM-1-carrying isolates revealed nationwide dissemination of two specific plasmids and nationwide clonal dissemination of Klebsiella pneumoniae ST16 accompanied with regional disseminations of three distinctive K. pneumoniae clones (ST231, ST14, and ST147) with different plasmids. Dissemination of CRE carrying bla_NDM in Thailand is mainly based on nationwide clonal expansions of E. coli ST410 carrying bla_NDM-5 and K. pneumoniae ST16 carrying bla_NDM-1, nationwide dissemination of two distinctive plasmids carrying bla_NDM-1, and accumulation of clonal expansions in regional areas. Although the overuse of antibiotics can promote CRE dissemination, the limited variety of transmitters highlights the importance of preventing horizontal dissemination among patients.

Multidrug-Resistant Acinetobacter: Detection of ESBL, MBL, bla NDM-1 Genotype, and Biofilm Formation at a Tertiary Care Hospital in Eastern Nepal

BACKGROUND

The Acinetobacter species is an important hospital-acquired pathogen. The rapid development of resistance to multiple drugs and the ability to form biofilm make these bacteria more adaptable to survive in healthcare facilities, thus posing a challenge to their effective management.

OBJECTIVE

This study aimed to characterize clinical isolates of Acinetobacter spp and to study their antimicrobial susceptibility patterns and ability to form biofilm. Resistant Acinetobacter was further analyzed for the detection of extended-spectrum β-lactamases (ESBLs), metallo β-lactamases (MBLs), carbapenemase production, and presence of blaNDM-1 gene.

MATERIALS AND METHODS

A total of 324 Acinetobacter species were isolated from various clinical specimens which were submitted to the Department of Microbiology, B.P. Koirala Institute of Health Sciences, Dharan, Nepal, and were studied for antibiotic susceptibility testing, detection of ESBL and MBL production, and formerly biofilm formation was performed by standard microbiological methods. PCR was carried out to determine the presence of the blaNDM-1 gene.

RESULTS

The predominant Acinetobacter species isolated was A calcoaceticus-baumannii Complex (Acb complex) 167 (51.5%). Among those, all A. species 128 (40%) were multidrug resistant (MDR). In which 13 (4.0%) were ESBL producers, 70 (61.9%) were MBL, and 12 (10.6%) were carbapenemases producers. The blaNDM1 gene was present in 33 isolates. Thirty-seven percent (121/324) of isolates formed biofilm. The majority of A. species were resistant to cefotaxime 73.8% (239) and cefepime 74.4% (241). A significant proportion of biofilm producers were MDR (p < 0.001).

CONCLUSION

Drug-resistant Acinetobacter formed a substantial proportion of this hospital's samples with a large presence of the bla NDM-1 gene. A matter of great concern is the association of multidrug-resistant phenotype with biofilm formation. This situation warranted stringent surveillance and adherence to infection prevention and control practices.

Carbapenemase-producing Enterobacterales and vancomycin-resistant Enterococcus faecium carriage in patients who have traveled in foreign countries: A single center 5-year prospective study

BACKGROUND

Numerous patients carrying carbapenemase-producing Enterobacterales (CPE) and/or vancomycin-resistant Enterococcus faecium (VRE) in France have previously travelled abroad. The risk of spreading CPE/VRE by patients who have stayed abroad without hospitalization is underexplored. This prompted us to screen and isolate all patients who travelled abroad in the previous 12 months upon admission to our hospital. Our aim was to evaluate the efficiency of this CPE/VRE-related risk policy.

METHODS

From 2014 to 2018, patients who had travelled abroad in the previous year before their admission underwent microbiological screening and were pre-emptively isolated. Contact precautions were verified and CPE/VRE cross-transmission events investigated.

RESULTS

Among 1,780 screened patients, 59 (3.3%) were colonized with CPE and/or VRE, of whom 17 (29.3%) were not hospitalized abroad. Nine generated 18 readmissions. No episodes of CPE/VRE cross-transmission were related to patients with a stay abroad without hospitalization, whereas 2 patients hospitalized abroad generated one episode each, despite implementation of contact precautions reaching values from 73.6% to 87.5%.

DISCUSSION

Throughout 17 admissions and 18 readmissions, patients who stayed abroad without hospitalization represented a true risk of spreading CPE/VRE, without generating cross-transmission.

CONCLUSIONS

Our strategy of CPE/VRE-related risk policy is successful.

The Molecular Characterization of Nosocomial Carbapenem-Resistant Klebsiella pneumoniae Co-Harboring blaNDM and blaOXA-48 in Jeddah

Carbapenem-resistant Klebsiella pneumoniae (CRKP)-associated infections have become a major concern and life-threatening worldwide. Understanding the epidemiology of CRKP using a reliable molecular technology can help to develop an effective infection control policies. In the western region of Saudi Arabia, there are no sufficient data on the prevalence of CRKP and its carbapenem-resistant determinants. Therefore, this study aimed to determine the molecular epidemiology of CRKP and identify the most common carbapenemase genes. In the current study, a total of 191 CRKP isolates were collected and obtained from clinical specimens of patients at King Fahad Armed Forces Hospital (KFAFH), Jeddah, Saudi Arabia. All isolates that were resistant or intermediately susceptible to either of the carbapenem antimicrobials (imipenem, meropenem, or ertapenem) were included. All CRKP showed resistance to ceftazidime, cefepime, and piperacillin/tazobactam, whereas low (14%) and moderate (37.7%) levels of resistance were reported against tigecycline and colistin, respectively. The most common carbapenemase genes identified were blaOXA-48 (n = 157 [82.2%]), followed by blaNDM in 27 (14%) isolates. The blaVIM and blaKPC were reported in only one isolate each and no blaIMP producers were detected among all tested isolates. The high prevalence of OXA-48 among K. pneumoniae isolates reported in the current study may reflect that OXA-48 has become an endemic in Saudi Arabian hospitals. The second major finding was that the identification of CRKP co-harbors both blaNDM and blaOXA-48, and such isolates can be threating for healthcare societies (patients and healthcare workers) due to their high level of resistance to carbapenems. These results suggest that the use of molecular diagnostic methods and proper surveillance programs are required to monitor and control the spread of all multidrug-resistant (MDR) bacteria, including CRKP. Therefore, further research is recommended to expand the study and further analyze the genotyping of the most common clones of CRKP in other hospitals in the western regions of Saudi Arabia.

NDM-1 Zn1-binding residue His116 plays critical roles in antibiotic hydrolysis

Bacteria expressing NDM-1 have been labeled as superbugs because it confers upon them resistance to a broad range of β-lactam antibiotics. The enzyme has a di‑zinc active centre, with the Zn2 site extensively studied. The roles of active-site Zn1 ligand residues are, however, still not fully understood. We carried out structure-function studies using the mutants, H116A, H116N, and H116Q. Zinc content analysis showed that Zn1 binding was weakened by 40 to 60% in the H116 mutants. The enzymatic-activity studies showed that the lower hydrolysis rates were mainly caused by their weaker substrate binding. The catalytic efficiency (k_cat/K_m) of the mutants followed the order: WT > > H116Q (decreased by 4-20 fold) > H116A (decreased by 20-700 fold) ≥ H116N (decreased by 6-800 fold). The maximum effect was observed on H116N against penicillin G, whereas ampicillin was not hydrolyzed at all. The fold-increase of K_m values, which informs the weakening of substrate binding, were: H116A by 5-45 fold; H116N by 6-100 fold; H116Q by 2-10 fold. Molecular dynamics simulations suggested that the Zn1 site mutations affected the positions of Zn2 and the bridging hydroxide, by 0.8 to 1.2 Å, with the largest changes of ~1.5 Å observed on Zn2 ligand C221. A native hydrogen bond between H118 and D236 was disrupted in the H116N and H116Q mutants, which led to increased flexibility of loop 10. Consequently, residue N233 was no longer maintained at an optimal position for substrate binding. H116 connected loop 7 across Zn1 to loop 10, thereby contributed to the overall integrity. This work revealed that the H116-Zn1 interaction plays a critical role in defining the substrate-binding site. From these results, it can be inferred that inhibition strategies targeting the zinc ions may be a new direction for drug development.

Myrtenol Inhibits Biofilm Formation and Virulence in the Drug-Resistant Acinetobacter baumannii: Insights into the Molecular Mechanisms

Background

blaNDM-1-producing Acinetobacter baumannii (BP-AB) remains a critical problem in nosocomial infections, because of its resistance mediated by the biofilm formation and virulence factors. No studies have confirmed myrtenol’s efficacy in inhibiting the biofilm formation and virulence associated with biofilm of BP-AB.

Methods

The tested concentrations of myrtenol were wild type (A), 50 μg/mL (B), 100 μg/mL (C), 200 μg/mL (D), 250 μg/mL (E), and 300 μg/mL (F).

Results

The BP-AB biofilm inhibition was significantly higher in the D, E, and F groups than in the A, B, and C groups. Myrtenol significantly reduced the air-liquid interface ring formation in glass tubes. It also effectively inhibited the attachment of BP-AB strains on polystyrene surfaces as shown by crystal violet staining. Microscopy showed a significant reduction in biofilm formation with dispersed BP-AB strains. The confocal laser scanning microscopy analysis showed a significant reduction in the biofilm’s biomass, covered surface area, and thickness. The scanning electron microscopy analysis revealed significantly fewer BP-AB aggregates on the coverslip surface. In the CompStat analysis, the biofilm’s biomass, maximum thickness, and surface-to-volume ratio were significantly reduced. The qPCR analysis revealed a significant down-regulation of bfmR, bap, csuA/B, and ompA expression, which positively correlated with the biofilm’s biomass, maximum thickness, and surface-to-volume ratio in BP-AB strains. Myrtenol significantly improved the susceptibility of BP-AB to the antibiotics amikacin, piperacillin/tazobactam, cefoperazone/sulbactam, and ceftazidime.

Conclusion

Myrtenol attenuates the BP-AB biofilm formation and virulence by suppressing the expression of bfmR, bap, csuA/B, and ompA.

Emergence of a Salmonella Rissen ST469 clinical isolate carrying blaNDM-13 in China

New Delhi metallo-β-lactamase-13 (NDM-13) is an NDM variant that was first identified in 2015 and has not been detected in Salmonella species prior to this study. Here we describe the first identification of a Salmonella Rissen strain SR33 carrying bla_NDM-13. The aim of this study was to molecularly characterize SR33’s antimicrobial resistance and virulence features as well as investigate the genetic environment of bla_NDM-13. The Salmonella Rissen SR33 strain was isolated from a patient with fever and diarrhea. SR33 belonged to ST469, and it was found to be multidrug-resistant (MDR) and to carry many virulence genes. Phylogenetic analysis showed that SR33 shared a close relationship with most of the Chinese S. Rissen ST469 strains. bla_NDM-13 was located in a transmissible IncI1 plasmid pNDM13-SR33. Sequence analysis of bla_NDM-13-positive genomes downloaded from GenBank revealed that a genetic context (ΔISAba125-bla_NDM-13-ble_MBL-trpF) and a hybrid promoter (consisting of −35 sequences provided by ISAba125 and −10 sequences) were conserved. ISAba125 was truncated by IS1294 in three plasmids carrying bla_NDM-13, including pNDM13-SR33. To our knowledge, this is the first report of bla_NDM-13 carried by Salmonella. The emergence of bla_NDM-13 in a clinical MDR S. Rissen ST469 strain highlights the critical need for monitoring and controlling the dissemination of bla_NDM-13. bla_NDM-13 carried by a transmissible IncI1 plasmid may result in an increased risk of bla_NDM-13 transmission. IS1294 may be involved in the movement of bla_NDM-13.

Structural insights into the design of reversible fluorescent probes for metallo-β-lactamases NDM-1, VIM-2, and IMP-1

Metallo-β-lactamases (MBLs) are enzymes that are capable of hydrolyzing most β-lactam antibiotics and all clinically relevant carbapenems. We developed a library of reversible fluorescent turn-on probes that are designed to directly bind to the dizinc active site of these enzymes and can be used to study their dynamic metalation state and enzyme-inhibitor interactions. Structure-function relationships with regards to inhibitory strength and fluorescence turn-on response were evaluated for three representative MBLs.

Clinical data from studies involving novel antibiotics to treat multidrug-resistant Gram-negative bacterial infections

Multidrug-resistant (MDR) Gram-negative bacteria (GNB) are a critical threat to healthcare worldwide, worsening outcomes and increasing mortality among infected patients. Carbapenemase- and extended-spectrum β-lactamase-producing Enterobacterales, as well as carbapenemase-producing Pseudomonas and Acinetobacter spp., are common MDR pathogens. To address this threat, new antibiotics and combinations have been developed. Clinical trial findings support several combinations, notably ceftazidime-avibactam (CZA, a cephalosporin-β-lactamase inhibitor combination) which is effective in treating complicated urinary tract infections (cUTI), complicated intra-abdominal infections and hospital-acquired and ventilator-associated pneumonia caused by GNBs. Other clinically effective combinations include meropenem-vaborbactam (MVB), ceftolozane-tazobactam (C/T) and imipenem- relebactam (I-R). Cefiderocol is a recent siderophore β-lactam antibiotic that is useful against cUTIs caused by carbapenem-resistant Enterobacterales (CRE) and is stable against many β-lactamases. CRE are a genetically heterogeneous group that vary in different world regions and are a substantial cause of infections, among which Klebsiella pneumoniae are the most common. Susceptible CRE infections can be treated with fluoroquinolones, aminoglycosides or fosfomycin, but alternatives include CZA, MVB, I-R, cefiderocol, tigecycline and eravacycline. MDR Acinetobacter baumannii and Pseudomonas aeruginosa are increasingly common pathogens producing a range of different carbapenemases, and infections are challenging to treat, often requiring novel antibiotics or combinations. Currently, no single agent can treat all MDR-GNB infections, but new β-lactam-β-lactamase inhibitor combinations are often effective for different infection sites, and, when used appropriately, have the potential to improve outcomes. This article reviews clinical studies investigating novel β-lactam approaches for treatment of MDR-GNB infections.