Bla New Delhi Metallo-β-lactamase-1 Research Articles

Wide distribution of Escherichia coli carrying IncF plasmids containing bla NDM-5 and rmtB resistance genes from hospitalized patients in England.

Introduction. The New Delhi metallo-β-lactamase (NDM) variant NDM-5 was first described in 2011 in an isolate of Escherichia coli. We noted that a high proportion of isolates of E. coli positive for bla NDM carbapenemase genes submitted to the UK Health Security Agency (formerly Public Health England) between 2019 and mid-2021 carried the bla NDM-5 allele, with many co-harbouring rmtB, rendering them highly resistant to aminoglycosides as well as to most β-lactams.Hypothesis/Gap Statement. This observation suggested that a common plasmid may be circulating.Aim. To compare these isolates and describe the plasmids carrying these resistance elements.Methodology. All isolates were sequenced on an Illumina platform, with five also subjected to long-read nanopore sequencing to provide complete assemblies. The locations of bla NDM-5, rmtB and other associated genetic elements were identified. Susceptibility testing to a wide range of antibiotics was carried out on representative isolates.Results. The 34 isolates co-harbouring bla NDM-5 and rmtB were from 14 hospital groups and six different regions across England and consisted of 11 distinct sequence types. All carried IncF plasmids. Assembly of the NDM plasmids in five isolates revealed that they carried rmtB and bla NDM-5 in an IncF conjugative plasmid ranging in size from 85.5 to 161 kb. All carried a highly conserved region, previously described in E. coli plasmid pHC105-NDM, that included bla TEM-1B and rmtB followed by sequence bounded by two IS26 elements containing ΔISAba125, bla NDM-5, ble, trpF and tat followed by ISCR1 and an integron with sul1, aadA2 and dfrA12 cassettes. This arrangement has been described in isolates from other countries and continents, suggesting that such plasmids are widely distributed, at least in E. coli, with similar plasmids also found in Klebsiella pneumoniae. Tested isolates were resistant to most antibiotics except colistin, fosfomycin and tigecycline.Conclusion. These observations suggest that conjugative plasmids carrying a highly conserved resistance gene segment have become widespread in England and elsewhere. This study highlights the value of routine whole-genome sequencing in identifying genetic elements responsible for resistance dissemination.

In Vitro Efficacy of Biocompatible Zinc Ion Chelating Molecules as Metallo-β-Lactamase Inhibitor among NDM Producing Escherichia coli.

Objective This article assesses the effectiveness of captopril, tetracycline, and ciprofloxacin as metallo-β-lactamase (MBL) inhibitors against New Delhi metallo-β-lactamase (NDM)-producing Escherichia coli. Materials and Methods Twenty-four well-characterized carbapenem-resistant E. coli isolates which produced NDM ( n = 21) and Oxa-48-like enzymes ( n = 3) were used to assess the inhibitors. The positive control organism was designed by cloning the NDM gene into pET-24a plasmid and transforming it into expression vector E. coli BL21. All the proposed inhibitors were assessed for their interaction with MBLs using checkerboard minimum inhibitory concentration (MIC) assay with imipenem and meropenem. The fractional inhibitory concentration (FIC) index was calculated to assess the activity of molecules. Results The E. coli BL21 (DE3) pET-24a- bla NDM showed carbapenem resistance upon isopropyl β-D-1-thiogalactopyranoside induction and had MIC of 32 µg/mL for both imipenem and meropenem. For the test isolates, ∑FIC values of imipenem and meropenem with ethylenediaminetetraacetic acid (EDTA) ranged from 0.039 to 0.266 and 0.023 to 0.156, respectively. At a 256 µg/mL concentration, captopril had ∑FIC index value for imipenem and meropenem as 0.133 to 0.375 and 0.133 to 0.188, respectively. The tetracycline and ciprofloxacin in combination with meropenem/imipenem showed indifferent results. Conclusion Among the three molecules tested, captopril had MBL inhibitory activity, but the concentration required for inhibition was beyond the therapeutic safety levels. Ciprofloxacin and tetracycline had weak or no MBL inhibitory activity. Checkerboard MIC of EDTA with carbapenem antibiotic and control organism with NDM enzyme production helped us create a reference system for comparing and assessing the results of potential MBL inhibitors in future.

Transmission of Carbapenem Resistance Between Human and Animal NDM-Positive Escherichia coli Strains

Although carbapenem use is prohibited in animals in China, carbapenem-resistant Escherichia coli (CREC), especially New Delhi metallo-β-lactamase (NDM)-producing strains, are widely prevalent in food-producing animals. At present, the impact of livestock-associated CREC strains on human populations at the national level is unknown. Here, we conduct a retrospective cross-sectional study to investigate the prevalence of CREC from clinical settings across 22 Chinese provinces or municipalities and analyze anthropogenic factors associated with their presence. We also ascertain the bla NDM and bla KPC abundance among pig and chicken farms and present a detailed genomic framework for CREC of animal and human origin. Overall, 631/29 799 (2.1%) clinical Escherichia coli ( E. coli ) isolates were identified as CREC. Multivariable analysis revealed that being male, an age below 1, an age between 13 and 18, provinces with greater chicken production, and provinces with higher pig production were associated with higher odds of CREC infection. In general, 73.8% ( n = 45/61) of pig farms and 62.2% ( n = 28/45) of chicken farms had a bla NDM abundance of 1 × 10 −5 to 1 × 10 −3 and 1 × 10 −3 to 1 × 10 −2 , respectively. Among all the Chinese NDM-positive E. coli ( n = 463) available at the National Center for Biotechnology Information (NCBI), the genomic analysis revealed that bla NDM-5 and IncX3 were the predominant carbapenemase gene-plasmid combination, while a highly homogeneous relationship between NDM-positive isolates from humans and animals was demonstrated at the plasmid and core genome levels. All the findings suggest frequent CREC transmission between humans and animals, indicating that further discussions on the use of antibiotics in animals and humans are needed, both in China and across the globe.

Carbapenemase investigation with rapid phenotypic test (RESIST-4 O.K.N.V) and comparison with PCR in carbapenem-resistant Enterobacterales strains.

RESİST-4 O.K.N.V. assay is a lateral immunochromatocraphic test for the identification of oxacillinase (OXA)-48-like, Klebsiella pneumoniae carbapenemase (KPC), New Delhi metallo-β-lactamase (NDM), and Verona integron-encoded metallo-β-lactamase (VIM) producing strains. It was aimed to evaluate the performance of the RESIST-4 O.K.N.V. test and to compare it with the reference method polymerase chain reaction (PCR). Also, the objective was to determine the distribution of carbapenemase types of CRE strains isolated in our hospital. Between January 2016-October 2019, 187 strains isolated from clinical samples were included in this study. Bacterial identification was done using MALDI-TOF MS. Antibiotic susceptibility tests were studied with the VITEK-2 automated system. Meropenem minimum inhibitory concentrations (MICs) were determined by the gradient test. All strains were studied with the RESIST-4 O.K.N.V. test and then the strains were selected for the PCR test. bla OXA-48, bla NDM, bla KPC, and bla VIM were investigated with PCR. K. pneumoniae NCTC® 13438 (KWIKSTIKTM, Microbiologics®, USA) was used as the positive control, E. coli ATTC® 25922 TM (Microbiologics®, USA) and three carbapenem-sensitive clinical isolates were also used as the negative control. Meropenem MIC50 and MIC90 values were determined to be >32 mg/L. With PCR bla OXA-48, bla NDM, bla KPC and bla VIM were detected in 79, 63, 20, and 4 strains, respectively. bla OXA-48 and bla NDM were found together in 51 of the isolates. bla OXA-48, bla NDM, bla KPC, and bla VIM were not detected in two strains with carbapenem resistance in susceptibility tests. The sensitivity of the immunochromatographic test was 100% for OXA-48, KPC, and VIM but 84.1% for NDM. Specificity was determined as 100% for OXA-48, NDM, KPC, and VIM. RESIST-4 O.K.N.V. test showed high sensitivity and specificity in detecting OXA-48, KPC, NDM, and VIM type carbapenemases. However, it should be kept in mind that there may be false-negative results related to NDM.

Disinfection and mechanism of super-resistant Acinetobacter sp. and the plasmid-encoded antibiotic resistance gene blaNDM-1 by UV/peroxymonosulfate

• UV/PMS could efficiently inactivate ARB and control the risk of photoreactivation. • bla NDM-1 was greater resistance to UV/PMS than bla OXA-58 in the same plasmid. • ARGs base pairs number and length were responsible for ARGs removal. • 1 O 2 plays an important role on the plasmid-encoded ARGs removal in UV/PMS. The super-resistant bacteria that produce the New Delhi metallo-β-lactamase 1 (NDM-1) enzyme are becoming a conceivably major worldwide clinical issue with serious consequences. Studying the disinfection and mechanism of super-resistant bacteria and their antibiotic resistance genes (ARGs) is crucial for controlling their spread in the water environment. In this study, the disinfection of the super-resistant bacterium Acinetobacter sp. CS-2 and its transferable ARGs (plasmid-encoded bla NDM-1 and bla OXA-58 ) by ultraviolet radiation (UV), peroxymonosulfate (PMS), and ultraviolet/peroxymonosulfate (UV/PMS) exposure were investigated. UV/PMS could completely inactivate CS-2 and control the photoreactivation risk, while bacteria that underwent UV and PMS treatment had survival ratios of 0.22% and 0.28%, respectively. The removal efficiencies of bla NDM-1 and bla OXA-58 ranged from 3.64 to 4.05 log, and the advantage of UV/PMS treatment on ARGs damage was further identified by gel electrophoresis analysis. The removal efficiency of bla NDM-1 was lower than that of bla OXA-58 , which was attributed to the low number of adjacent 5′-TT-3′ harbored by bla NDM-1 . The removal rate constants of the ARGs by UV treatment were significantly correlated with the number of adjacent base pairs (e.g., 5′-TT-3′, 5′-CT-3′, 5′-TC-3′ and 5′-CC-3′) and length, with R -values ranging from 0.9044 to 0.9512. Singlet oxygen ( 1 O 2 ) played a vital role in the reduction of bla NDM-1 and bla OXA-58 in the UV/PMS treatment. UV/PMS showed high removal efficiency under natural pH conditions and in the presence of various aqueous ions (e.g., Cl − , SO 4 2− and HCO 3 − ). Overall, this study provides new understandings and theoretical support for the risk control of super-resistant bacteria and plasmid-encoded ARGs.

Emergence of a multidrug-resistant plasmid encoding bla NDM-1, bla OXA-420 and armA in a clinical isolate of Acinetobacter variabilis in Japan

Acinetobacter variabilis (formerly genospecies 15 sensu Tjernberg and Ursing) has been isolated from humans and animals and was proposed to be a novel species in 2015. A multidrug-resistant A. variabilis isolate, RYU24, was obtained in 2012 from an inpatient in Okinawa, Japan, with no record of overseas travel. The isolate was resistant to carbapenems, aminoglycosides and ciprofloxacin, with minimum inhibitory concentrations (MICs) of 32 µg ml-1 for imipenem and meropenem; > 1024 µg ml-1 for amikacin, arbekacin, gentamicin and tobramycin; and 8 µg ml-1 for ciprofloxacin. The isolate was found to harbour a 68-kbp plasmid carrying bla NDM-1, which encodes New Delhi metallo-β-lactamase-1 (NDM-1); bla OXA-420, which encodes an OXA-58-like carbapenemase and; armA, which encodes ArmA 16S rRNA methylase conferring pan-aminoglycoside resistance. To our knowledge, this is the first report of a plasmid harbouring the three major drug-resistance genes, bla NDM-1, bla OXA-420 and armA.

Determination of incompatibility group plasmids and copy number of the bla NDM-1 gene in carbapenem-resistant Klebsiella pneumoniae strains recovered from different hospitals in Kerman, Iran.

Introduction. New Delhi metallo-β-lactamase (NDM)-producing Klebsiella pneumoniae has become a serious global health concern.Hypothesis/Gap Statement. Due to the high genetic diversity among NDM-positive K. pneumoniae, we need further surveillance and studies to better understand the relationships between them. In addition, the coexistence of several plasmid replicon types in NDM-positive K. pneumoniae may affect the copy number of bla NDM, the MIC level to antibiotics, as well as increasing the chance of horizontal gene transfer.Aim. The aim of this study was to determine incompatible plasmid groups and copy numbers of bla NDM, and to investigate the genetic relationship of 37 NDM-positive K. pneumoniae in Kerman, Iran.Methodology. The bla NDM-1 gene was detected and confirmed by PCR-sequencing. The plasmid replicon types were determined by PCR-based replicon typing (PBRT) and the copy number of bla NDM-1 was determined by quantitaive real time-PCR (qPCR). Random amplified polymorphic DNA (RAPD)-PCR typing was used to detect genetic relationships between the strains.Results. In this study, 10 different replicon types, including Frep [n=25 (67.5 %)], FIIAs [n=11 (29.7 %)], FIA [n=5 (13.5 %)], FIB [n=3 (8.1 %)], I1-Iγ [n=2 (5.4 %)], L/M [n=7 (18.9 %)], A/C [n=7 (18.9 %)], Y [n=3 (8.1 %)], P [n=1 (2.7 %)] and FIC [n=1 (2.7 %)] were reported. The copy numbers of the bla NDM-1 gene varied from 30.00 to 5.0×106 and no statistically significant correlation was observed between a rise of the MIC to imipenem and the copy numbers of bla NDM-1 (P>0.05). According to RAPD typing results, 35 strains were divided into five clusters, while two strains were non-typeable.Conclusion. The spread of NDM-1-producing K. pneumoniae strains that carry several plasmid replicon types increases the chance of horizontal transfer of antibiotic resistance genes in hospital settings. In this study, 10 different replicon types were identified. We could not find any relationship between the increase of MIC levels to imipenem and the copy numbers of bla NDM-1. Therefore, due to the identification of different replicon types in this study, the type and genetic characteristics of bla NDM-1-carrying plasmids, and other factors such as antibiotic selective pressure, probably affect the copy number of bla NDM-1 and change the MIC level to imipenem.

Emergence of Almost Identical F36:A-:B32 Plasmids Carryingbla NDM-5andqepAinEscherichia colifrom Both Pakistan and Canada.

The New Delhi Metallo-β-lactamase (NDM) producing Enterobacteriaceae is spreading worldwide. Although the blaNDM gene has been identified in animal associated Enterobacteriaceae isolates in many countries, little is known about its occurrence in animal products in Pakistan. In this study, 13 Escherichia coli isolates were collected from chicken meat samples in Pakistan. Two isolates, 15978 and C4109, exhibited reduced susceptibility (MIC ≥1 μg/mL) to imipenem, and carried blaNDM-5 and blaNDM-7 gene, respectively. Whole-genome sequencing and Oxford Nanopore MinION sequencing revealed that 15978 and C4109 belonged to ST156 and ST167, respectively. blaNDM-7 was carried by an IncX3 plasmid that has disseminated worldwide, whereas blaNDM-5 was located on an F36: A-: B32 plasmid, which shared high identity with two plasmids carried by E. coli isolates from other countries (one from a patient in Canada). To the best of our knowledge, this is the first report characterizing blaNDM-carrying plasmids from chicken meat samples in Pakistan. The dissemination of almost identical blaNDM-5-bearing F36:A-:B32 and blaNDM-7-bearing IncX3 plasmids in different countries highlights the importance of international trade and travel in the spread of antimicrobial resistance strains and plasmids worldwide.

Occurrence of Highly Conjugative IncX3 Epidemic Plasmid Carrying bla NDM in Enterobacteriaceae Isolates in Geographically Widespread Areas.

The emergence of New Delhi metallo-β-lactamase (NDM) in common enterobacterial species is a major concern for healthcare. Early reports have revealed that the spread of NDM involved diverse and heterogeneous plasmids. Recently, the involvement of a rare, IncX3 subtype plasmid has been increasingly recognized. Here, we studied the prevalence of IncX plasmid subtypes in 198 carbapenem-resistant Enterobacteriaceae, originating from a territory-wide active surveillance in Hong Kong in 2016. The complete sequences and biological features of the blaNDM-carrying plasmids were investigated. A total of 62 NDM-type, 21 OXA-48 type, 14 IMP-type, 8 KPC-type, 4 IMI-type producers, and 89 non-carbapenemase-producers were tested for presence of IncX subtypes. IncX3 (n = 60) was the most common subtype, followed by IncX4 (n = 6) and IncX1 (n = 2). The prevalence of IncX3 subtype in isolates producing NDM, other carbapenemase types and non-carbapenemase producers were 75.8, 21.3, and 3.4%, respectively (P < 0.001). An IncX3 plasmid (size ∼50 kb) was confirmed to carry blaNDM in 47 isolates of different enterobacterial species. Thirteen IncX3 plasmids originating from six healthcare regions in Hong Kong were completely sequenced. The results showed that the IncX3 plasmids carrying blaNDM share a high degree of sequence identity with a previously reported plasmid, pNDM-HN380 (GenBank accession JX104760), over the backbone and genetic load regions. A blast search further revealed the occurrence of identical or nearly identical IncX3 plasmids carrying blaNDM in other part of China, Korea, Myanmar, India, Oman, Kuwait, Italy, and Canada. Two IncX3 carrying blaNDM were investigated further. Conjugation experiments demonstrated that the IncX3 plasmids could be efficiently transferred to multiple enterobacterial species at frequencies that are comparable or higher than the epidemic IncFII plasmid carrying blaCTX-M (pHK01). In addition, efficient transfer of the NDM plasmids occurred over a range of temperatures. In conclusion, this study demonstrated the important role played by IncX3 in the dissemination of NDM and the occurrence of pNDM-HN380-like plasmids in geographically widespread areas. The high mobility of IncX3 plasmid across different enterobacterial species highlights the ability of this plasmid replicon to be an important vehicle in worldwide dissemination of NDM.

New Delhi metallo-β-lactamase-1: structure, inhibitors and detection of producers.

Since its discovery in 2008, New Delhi metallo-β-lactamase-1 (NDM-1)-producing Enterobacteriaceae have disseminated globally, facilitated predominantly by gut colonization and the spread of plasmids carrying the bla NDM-1 gene. With few effective antibiotics against NDM-1 producers, and resistance developing to those which remain, there is an urgent need to develop new treatments. To date, most drug design in this area has been focused on developing an NDM-1 inhibitor and has been aided by the wealth of structural and mechanistic information available from high resolution x-ray crystallography and molecular modeling. This review aims to summarize current knowledge regarding the detection of NDM-1 producers, the mechanism of action of NDM-1 and to highlight recent attempts toward the development of clinically useful inhibitors.

Epidemiological characteristics of blaNDM-1 in Enterobacteriaceae and the Acinetobacter calcoaceticus-Acinetobacter baumannii complex in China from 2011 to 2012.

ObjectivesThe study aimed to investigate the prevalence and epidemiological characteristics of bla NDM-1 (encoding New Delhi metallo-β-lactamase 1) in Enterobacteriaceae and the Acinetobacter calcoaceticus-Acinetobacter baumannii complex (ABC) in China from July 2011 to June 2012.MethodsPCR was used to screen for the presence of bla NDM-1 in all organisms studied. For bla NDM-1-positive strains, 16S rRNA analysis and Analytical Profile Index (API) strips were used to identify the bacterial genus and species. The ABCs were reconfirmed by PCR detection of bla OXA-51-like. Antibiotic susceptibilities of the bacteria were assessed by determining minimum inhibitory concentration (MIC) of them using two-fold agar dilution test, as recommended by the Clinical and Laboratory Standards Institute (CLSI). Molecular typing was performed using pulsed-field gel electrophoresis (PFGE). S1 nuclease-pulsed-field gel electrophoresis (S1-PFGE) and Southern blot hybridization were conducted to ascertain the gene location of bla NDM-1. Conjugation experiments were conducted to determine the transmission of bla NDM-1-positive strains.ResultsAmong 2,170 Enterobacteriaceae and 600 ABCs, seven Enterobacteriaceae strains and two A. calcoaceticus isolates from five different cities carried the bla NDM-1 gene. The seven Enterobacteriaceae strains comprised four Klebsiella pneumoniae, one Enterobacter cloacae, one Enterobacter aerogen and one Citrobacter freundii. All seven were non-susceptible to imipenem, meropenem or ertapenem. Two A. calcoaceticus species were resistant to imipenem and meropenem. Three K. pneumoniae showed the same PFGE profiles. The bla NDM-1 genes of eight strains were localized on plasmids, while one was chromosomal.ConclusionsCompared with previous reports, the numbers and species containing the bla NDM-1 in Enterobacteriaceae have significantly increased in China. Most of them are able to disseminate the gene, which is cause for concern. Consecutive surveillance should be implemented and should also focus on the dissemination of bla NDM-1 among gram-negative clinical isolates.

Emergence of NDM-producing non-baumannii Acinetobacter spp. isolated from China

One hundred and thirty-six bla OXA-51-negative strains were identified from 1,067 Acinetobacter calcoaceticus-A. baumannii complex (ACB complex) isolates, which were collected during October 2010 to March 2013 from 15 general hospitals in 10 cities throughout Zhejiang Province, China. Seven of the 136 bla OXA-51-negative ACB complex isolates were New Delhi metallo-β-lactamase-1 (NDM-1)-positive, among which three were identified as A. nosocomialis and four were identified as A. pittii strains using 16S-23S rRNA gene intergenic spacer (ITS) sequencing and partial RNA polymerase β-subunit (rpoB) sequencing. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) analysis showed that the seven NDM-positive isolates belonged to three clonal strains with three novel sequence types (STs). Polymerase chain reaction (PCR) assays and DNA sequence analysis of the carbapenemase and other β-lactamase genes indicated that all the isolates harbored the bla NDM-1 gene, and that only one strain of A. nosocomialis isolates harbored both bla NDM-1 and bla OXA-23. All of them were positive for bla ADC, from which three novel bla ADC genes (designated as bla ADC-69, bla ADC-70, and bla ADC-71) were detected for the first time. The presence of ISAba125 upstream of bla NDM-1 was identified through genetic environment analysis. Carbapenem resistance can be transferred from A. nosocomialis and A. pittii to Escherichia coli EC600 by the conjugation experiment. Plasmid analysis, DNA hybridization, and extraction experiments indicated that bla NDM-1 was located on a plasmid of approximately 50 kb. In conclusion, we characterized the dissemination of NDM-1-positive A. pittii strains in Zhejiang Province, China, and reported the NDM-producing A. nosocomialis for the first time.

Higher Isolation of NDM-1 Producing Acinetobacter baumannii from the Sewage of the Hospitals in Beijing

Multidrug resistant microbes present in the environment are a potential public health risk. In this study, we investigate the presence of New Delhi metallo-β-lactamase 1 (NDM-1) producing bacteria in the 99 water samples in Beijing City, including river water, treated drinking water, raw water samples from the pools and sewage from 4 comprehensive hospitals. For the bla NDM-1 positive isolate, antimicrobial susceptibility testing was further analyzed, and Pulsed Field Gel Electrophoresis (PFGE) was performed to determine the genetic relationship among the NDM-1 producing isolates from sewage and human, as well as the clinical strains without NDM-1. The results indicate that there was a higher isolation of NDM-1 producing Acinetobacter baumannii from the sewage of the hospitals, while no NDM-1 producing isolates were recovered from samples obtained from the river, drinking, or fishpond water. Surprisingly, these isolates were markedly different from the clinical isolates in drug resistance and pulsed field gel electrophoresis profiles, suggesting different evolutionary relationships. Our results showed that the hospital sewage may be one of the diffusion reservoirs of NDM-1 producing bacteria.

Global spread of antibiotic resistance: the example of New Delhi metallo-β-lactamase (NDM)-mediated carbapenem resistance

The rapidity with which new types of antibiotic resistance can disseminate globally following their initial emergence or recognition is exemplified by the novel carbapenemase New Delhi metallo-β-lactamase (NDM). The first documented case of infection caused by bacteria producing NDM occurred in 2008, although retrospective analyses of stored cultures have identified the gene encoding this enzyme (blaNDM) in Enterobacteriaceae isolated in 2006. Since its first description, NDM carbapenemase has been reported from 40 countries worldwide, encompassing all continents except South America and Antarctica. The spread of NDM has a complex epidemiology involving the spread of a variety of species of NDM-positive bacteria and the inter-strain, inter-species and inter-genus transmission of diverse plasmids containing blaNDM, with the latter mechanism having played a more prominent role to date. The spread of NDM illustrates that antibiotic resistance is a public health problem that transcends national borders and will require international cooperation between health authorities if it is to be controlled.