Identification and characterization of the first Escherichia coli strain carrying NDM-1 gene in China

First Detection of mcr-9 in a Multidrug-Resistant Escherichia coli of Animal Origin in Italy Is Not Related to Colistin Usage on a Pig Farm

The emergence of colistin resistance raises growing concerns because of its use as a last-resort antimicrobial for the treatment of severe gram-negative bacterial infections in humans. Plasmid-borne mobile colistin resistance genes (mcr) are particularly worrisome due to their high propensity to spread. An mcr-9-positive Escherichia coli was isolated from a piglet in Italy, representing the first isolation of this gene from an E. coli of animal origin in the country. Whole genome sequencing (WGS) revealed that mcr-9 was borne by an IncHI2 plasmid carrying several other resistance genes. The strain was indeed phenotypically resistant to six different antimicrobial classes, including 3rd and 4th generation cephalosporins. Despite the presence of mcr-9, the isolate was susceptible to colistin, probably because of a genetic background unfavourable to mcr-9 expression. The lack of colistin resistance, coupled with the fact that the farm of origin had not used colistin in years, suggests that mcr-9 in such a multidrug-resistant strain can be maintained thanks to the co-selection of neighbouring resistance genes, following usage of different antimicrobials. Our findings highlight how a comprehensive approach, integrating phenotypical testing, targeted PCR, WGS-based techniques, and information on antimicrobial usage is crucial to shed light on antimicrobial resistance.

High Genetic Diversity and Antimicrobial Resistance in Escherichia coli Highlight Arapaima gigas (Pisces: Arapaimidae) as a Reservoir of Quinolone-Resistant Strains in Brazilian Amazon Rivers

The increasing prevalence of multi-drug resistant (MDR) Escherichia coli in distinct ecological niches, comprising water sources and food-producing animals, such as fish species, has been widely reported. In the present study, quinolone-resistant E. coli isolates from Arapirama gigas, a major fish species in the Brazilian Amazon rivers and fish farms, were characterized regarding their antimicrobial susceptibility, virulence, and genetic diversity. A total of forty (40) specimens of A. gigas, including 20 farmed and 20 wild fish, were included. Thirty-four quinolone-resistant E. coli isolates were phenotypically tested by broth microdilution, while resistance and virulence genes were detected by PCR. Molecular epidemiology and genetic relatedness were analyzed by MLST and PFGE typing. The majority of isolates were classified as MDR and detected harboring bla_CTX-M, qnrA and qnrB genes. Enterotoxigenic E. coli pathotype (ETEC) isolates were presented in low prevalence among farmed animals. MLST and PFGE genotyping revealed a wide genetic background, including the detection of internationally spread clones. The obtained data point out A. gigas as a reservoir in Brazilian Amazon aquatic ecosystems and warns of the interference of AMR strains in wildlife and environmental matrices.

Corrigendum: First Report of Coexistence of bla SFO-1 and bla NDM-1 β-Lactamase Genes as Well as Colistin Resistance Gene mcr-9 in a Transferrable Plasmid of a Clinical Isolate of Enterobacter hormaechei

[This corrects the article DOI: 10.3389/fmicb.2021.676113.].

Coexistence of aminoglycoside resistance genes in CTX-M-producing isolates of Klebsiella pneumoniae in Bushehr province, Iran

Background and Objectives:

Increasing the rate of extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae has given rise to a major healthcare issue in clinical settings over the past few years. Treatment of these strains is hardly effective since the plasmid encoding ESBL may also carry other resistance genes including aminoglycosides. The current study aimed to evaluate the prevalence of ESBL-producing K. pneumoniae and investigate the coexistence of Cefoxitamase-Munich (bla_CTX-M) with aminoglycoside-modifying enzyme (AME) genes, aac(3)IIa as well as aac(6′)Ib, in CTX-M-producing K. pneumoniae isolated from patients in Bushehr province, Iran.

Materials and Methods:

A total of 212 K. pneumoniae isolates were collected and confirmed using polymerase chain reaction (PCR) of the malate dehydrogenase gene. Isolates were screened for production of ESBL. Phenotypic confirmatory test was performed using combined disk test. The genes encoding CTX-M groups and AME genes, aac(3)IIa and aac(6′)Ib, were investigated by PCR.

Results:

The ESBL phenotype was detected in 56 (26.4%) K. pneumoniae isolates. Moreover, 83.9% of ESBL-producing isolates carried the genes for CTX-M type β-lactamases, which were distributed into the two genetic groups of CTX-M-1 (97.8%)- and CTX-M-2 (2.1%)-related enzymes. Notably, among K. pneumoniae isolates containing the bla_CTX-M gene, 68.08% of isolates harbored AME genes. In addition, the coexistence of bla_CTX-M with aac(3)-IIa and aac(6′)-Ib was observed in 46.8% of CTX-M-producing K. pneumoniae isolates.

Conclusion:

This study provides evidence of a high prevalence of AME genes in CTX-M-producing K. pneumoniae isolates; therefore, in the initial empirical treatment of infections caused by ESBL-KP in regions with such antibiotic resistance patterns, aminoglycoside combination therapy should be undertaken carefully.

First Report of Coexistence of bla SFO-1 and bla NDM-1 β-Lactamase Genes as Well as Colistin Resistance Gene mcr-9 in a Transferrable Plasmid of a Clinical Isolate of Enterobacter hormaechei

Many antimicrobial resistance genes usually located on transferable plasmids are responsible for multiple antimicrobial resistance among multidrug-resistant (MDR) Gram-negative bacteria. The aim of this study is to characterize a carbapenemase-producing Enterobacter hormaechei 1575 isolate from the blood sample in a tertiary hospital in Wuhan, Hubei Province, China. Antimicrobial susceptibility test showed that 1575 was an MDR isolate. The whole genome sequencing (WGS) and comparative genomics were used to deeply analyze the molecular information of the 1575 and to explore the location and structure of antibiotic resistance genes. The three key resistance genes (bla_SFO–1, bla_NDM–1, and mcr-9) were verified by PCR, and the amplicons were subsequently sequenced. Moreover, the conjugation assay was also performed to determine the transferability of those resistance genes. Plasmid files were determined by the S1 nuclease pulsed-field gel electrophoresis (S1-PFGE). WGS revealed that p1575-1 plasmid was a conjugative plasmid that possessed the rare coexistence of bla_SFO–1, bla_NDM–1, and mcr-9 genes and complete conjugative systems. And p1575-1 belonged to the plasmid incompatibility group IncHI2 and multilocus sequence typing ST102. Meanwhile, the pMLST type of p1575-1 was IncHI2-ST1. Conjugation assay proved that the MDR p1575-1 plasmid could be transferred to other recipients. S1-PFGE confirmed the location of plasmid with molecular weight of 342,447 bp. All these three resistant genes were flanked by various mobile elements, indicating that the bla_SFO–1, bla_NDM–1, and mcr-9 could be transferred not only by the p1575-1 plasmid but also by these mobile elements. Taken together, we report for the first time the coexistence of bla_SFO–1, bla_NDM–1, and mcr-9 on a transferable plasmid in a MDR clinical isolate E. hormaechei, which indicates the possibility of horizontal transfer of antibiotic resistance genes.

Molecular Characterization of KPC-2-Producing Enterobacter cloacae Complex Isolates from Cali, Colombia

The Enterobacter cloacae complex is an emerging opportunistic pathogen whose increased resistance to carbapenems is considered a public health problem. This is due to the loss of efficacy of beta-lactam antibiotics, which are used as the first treatment option in the management of infections caused by Gram-negative bacteria. The objective of this study was to perform the molecular characterization of 28 isolates of the E. cloacae complex resistant to cephalosporins and carbapenems isolated between 2011 and 2018 from five hospitals located in the municipality of Santiago de Cali, Colombia. Molecular detection of bla_KPC, bla_VIM, bla_NDM and bla_OXA-48-like genes was performed on these isolates and the genetic relationship between the isolates was assessed using multilocus sequence typing (MLST). Forty-three percent of the isolates carried the bla_KPC-2 gene variant. MLST showed high genetic diversity among isolates, the most frequent being the sequence type ST510 with a frequency of 50%. The identification of the genes involved in carbapenem resistance and dispersing genotypes is an important step toward the development of effective prevention and epidemiological surveillance strategies in Colombian hospitals.

Population genomics and antimicrobial resistance dynamics of Escherichia coli in wastewater and river environments

Aquatic environments are key niches for the emergence, evolution and dissemination of antimicrobial resistance. However, the population diversity and the genetic elements that drive the dynamics of resistant bacteria in different aquatic environments are still largely unknown. The aim of this study was to understand the population genomics and evolutionary events of Escherichia coli resistant to clinically important antibiotics including aminoglycosides, in anthropogenic and natural water ecosystems. Here we show that less different E. coli sequence types (STs) are identified in wastewater than in rivers, albeit more resistant to antibiotics, and with significantly more plasmids/cell (6.36 vs 3.72). However, the genomic diversity within E. coli STs in both aquatic environments is similar. Wastewater environments favor the selection of conserved chromosomal structures associated with diverse flexible plasmids, unraveling promiscuous interplasmidic resistance genes flux. On the contrary, the key driver for river E. coli adaptation is a mutable chromosome along with few plasmid types shared between diverse STs harboring a limited resistance gene content.

Emergence of High Level Carbapenem and Extensively Drug Resistant Escherichia coli ST746 Producing NDM-5 in Influent of Wastewater Treatment Plant, Seoul, South Korea

High level carbapenem and extensively drug resistant (XDR) Escherichia coli strain N7, which produces a variant of New Delhi metallo-β-lactamase (NDM-5), was isolated from the influent of the Jungnang wastewater treatment plant located on Han River, Seoul, South Korea. Phenotypic and genotypic resistances to carbapenem were tested using agar and broth dilution methods, and polymerase chain reaction. Whole-genome sequencing was performed to characterize the genetic structure of strain N7. E. coli strain N7, which harbors the bla NDM-5 gene, showed high level of carbapenem resistance at concentrations of doripenem (512 mg/L) and meropenem (256 mg/L), and XDR to 15 antibiotics. Based on the genomic sequence analysis, two plasmids, a hybrid IncHI2/N-type and an IncX3 type, were present. The former contains a cluster (bla NDM-5-ble MBL -trpF-dsbD) bracketed by multi-insertional sequences, IS3000, ISAba125, IS5, and IS26. The latter carries the following resistance genes: bla CTX-14, aac(3)-IV, aadA1, aadA2, aph(3')-Ia, aph(4)-Ia, sul1, sul2, sul3, dfrA12, fosA3, oqxA, oqxB, mph(A), and floR, and cmlA1. The chromosome, contig3, and contig5 also carry bla CTX-64 and mdf(A), tet(A), and erm(B), tet(M) and aadA22, respectively. Strain N7 also harbors virulence factors such as fimH, flu, ecpABCDE, sfmA, hlyE, and gadA. This study demonstrates the emergence of high level carbapenem resistant XDR E. coli strain N7 containing bla NDM-5 in aquatic environment, Seoul, South Korea. Due to the presence of mobile genetic elements, this strain could horizontally transfer resistance genes, including bla NDM-5 to environmental bacteria. Thus, it is necessary to conduct continuous surveillance for carbapenem resistance in various aquatic environments.

Gram Negative Extended Spectrum Beta-Lactamase Producing Bacteria Prevalence in Jouf Region Tertiary Care Hospital, Saudi Arabia

Extended Spectrum beta lactamase producing pathogens are reported in many clinical samples and pose an emerging threat health. To find the prevalence of ESBL producing Enterobactriacea pathogens isolated from inpatients (Medical and Surgical Wards; Hospital stay > 72 h) admitted to Prince, Mutib, Hospital Sakaka, Jouf. A total of 1043 Enterobactriacea were isolated during April 2015 to October 2016 study period. Vitek -2 compact (biomeriux Leon, France) was used for identification and antimicrobial sensitivity (AST) test. A Total of 115/1043 (11.02%) ESBL producing pathogens were isolated from urine 15.07% (n=242), sputum 13.6 % (n=220), wound 10.8% (n=287) and blood 5.4 % (n=294). Klebsiella pneumonia is most dominant followed by E coli and Proteus miribilis. Cephamycins and carbapenems were found most effective (100% sensitivity) against the pathogens isolated. The aminoglycosides, beta lactams and Fluroquinolnes class of antibiotics, microorganisms have gained the resistance of 20%, 22.7%, 40-70% respectively. The infection control measures should be taken seriously and making of effective use of antibiotics is need of hour.

Genetics of Acquired Antibiotic Resistance Genes in Proteus spp

Proteus spp. are commensal Enterobacterales of the human digestive tract. At the same time, P. mirabilis is commonly involved in urinary tract infections (UTI). P. mirabilis is naturally resistant to several antibiotics including colistin and shows reduced susceptibility to imipenem. However higher levels of resistance to imipenem commonly occur in P. mirabilis isolates consecutively to the loss of porins, reduced expression of penicillin binding proteins (PBPs) PBP1a, PBP2, or acquisition of several antibiotic resistance genes, including carbapenemase genes. In addition, resistance to non-β-lactams is also frequently reported including molecules used for treating UTI infections (e.g., fluoroquinolones, nitrofurans). Emergence and spread of multidrug resistant P. mirabilis isolates, including those producing ESBLs, AmpC cephalosporinases and carbapenemases, are being more and more frequently reported. This review covers Proteus spp. with a focus on the different genetic mechanisms involved in the acquisition of resistance genes to multiple antibiotic classes turning P. mirabilis into a dreadful pandrug resistant bacteria and resulting in difficult to treat infections.

Bogotá River anthropogenic contamination alters microbial communities and promotes spread of antibiotic resistance genes

The increase in antibiotic resistant bacteria has raised global concern regarding the future effectiveness of antibiotics. Human activities that influence microbial communities and environmental resistomes can generate additional risks to human health. In this work, we characterized aquatic microbial communities and their resistomes in samples collected at three sites along the Bogotá River and from wastewaters at three city hospitals, and investigated community profiles and antibiotic resistance genes (ARGs) as a function of anthropogenic contamination. The presence of antibiotics and other commonly used drugs increased in locations highly impacted by human activities, while the diverse microbial communities varied among sites and sampling times, separating upstream river samples from more contaminated hospital and river samples. Clinically relevant antibiotic resistant pathogens and ARGs were more abundant in contaminated water samples. Tracking of resistant determinants to upstream river waters and city sources suggested that human activities foster the spread of ARGs, some of which were co-localized with mobile genetic elements in assembled metagenomic contigs. Human contamination of this water ecosystem changed both community structure and environmental resistomes that can pose a risk to human health.

Fecal carriage and molecular epidemiology of carbapenem-resistant Enterobacteriaceae from outpatient children in Shanghai

Background

Fecal colonization with carbapenem-resistant Enterobacteriaceae (CRE) is a risk factor for bacterial translocation resulting in subsequent endogenous infections. The purpose of this study is to investigate the prevalence of CRE strains colonization in stool samples of outpatient in a tertiary pediatric hospital of Shanghai, China.

Methods

In a retrospective study, fecal samples were consecutively obtained from patients in 2016 and screening test for CRE was conducted by using home-made MacConkey agar. Antimicrobial susceptibility was determined by the broth microdilution method and β-lactamases were characterized by polymerase chain reaction (PCR) assays and DNA sequencing. Multilocus sequence typing (MLST) was performed for the genetic relationships of the isolates.

Results

A total of 880 fecal samples were included for this screening test and 32 CRE strains were identified in 32 non-duplicate fecal samples from 32 children (1.3 ± 1.5 years), with a carriage rate of 3.6%. These strains mainly distributed in Klebsiella pnuemoniae (37.5%) and Escherichia coli (37.5%). All CRE strains showed high resistance to most of the routinely used antibiotics (> 90%) except for polymyxin B and tigecycline. The bla_NDM gene was the major carbapenemase gene harbored by gastrointestinal CRE strains, followed by bla_KPC-2, bla_IMP-26, and bla_IMP-4. Other β-Lactamase genes including bla_CTX-M, bla_SHV, bla_TEM-1, and bla_DHA-1 were also detected. MLST analysis revealed that various sequence types (STs) were detected in these strains, with ST11 and ST37 being more prevalent in K.pneumoniae and ST101 in E.coli.

Conclusions

This study revealed the prevalence of CRE fecal carriage in children from outpatient and urgent implementation of infection control measure should be conducted to limit the spread of CRE strains.

Dissemination of genetically diverse NDM-1, -5, -7 producing-Gram-negative pathogens isolated from pediatric patients in Pakistan

Aim: To determine the prevalence of New Delhi metallo-β-lactamase (NDM)-producing Gram-negative pathogens isolated from children's samples. Materials & methods: Carbapenem-resistant clinical isolates (n = 117) were confirmed by VITEK^® 2 compact system, matrix-assisted laser desorption ionization-time of flight and multilocus sequence typing. MIC (μg/ml) of various antibiotics was determined by VITEK 2 compact system. Molecular characterization of the isolates was performed by PCR, DNA sequencing, PFGE and DNA hybridization. Results: Out of 117 carbapenemase producers, 37 (31.6%) and 29 (24.7%) were Klebsiella pneumoniae and Acinetobacter baumannii, respectively. 72 (61.5%) isolates were NDM positive and among these 60, 9 and 3 were NDM-1, -5 and -7, respectively. Majority of the NDM-producing K. pneumoniae belonged to ST11 and ST273 while most of the Escherichia coli belonged to ST405 and ST101. bla_NDM were mainly located on 150kb plasmids. MIC displayed high resistance against β-lactams drugs including carbapenems, and the most sensitive drugs were tigecycline and colistin. Conclusion: Dissemination of bla_NDM-producing pathogens, particularly in children clinical settings, is a matter of great public health concern.

B1-Metallo-β-Lactamases: Where Do We Stand?

Metallo-β-Lactamases (MBLs) are class Bβ-lactamases that hydrolyze almost all clinically-availableβ-lactam antibiotics. MBLs feature the distinctive αβ/βα sandwich fold of the metallo-hydrolase/oxidoreductase superfamily and possess a shallow active-site groove containing one or two divalent zinc ions, flanked by flexible loops. According to sequence identity and zinc ion dependence, MBLs are classified into three subclasses (B1, B2 and B3), of which the B1 subclass enzymes have emerged as the most clinically significant. Differences among the active site architectures, the nature of zinc ligands, and the catalytic mechanisms have limited the development of a common inhibitor. In this review, we will describe the molecular epidemiology and structural studies of the most prominent representatives of class B1 MBLs (NDM-1, IMP-1 and VIM-2) and describe the implications for inhibitor design to counter this growing clinical threat.

First Report of Complete Sequence of a blaNDM-13-Harboring Plasmid from an Escherichia coli ST5138 Clinical Isolate

Since the first report of bla_NDM-1, 16 bla_NDM variants have been identified among Gram-negative bacteria worldwide. Recently, a novel bla_NDM variant, bla_NDM-13, was identified in the chromosome of an ST101 Escherichia coli isolate from Nepal. Here we first reported plasmid-mediated bla_NDM-13 in a carbapenem-resistant E. coli ST5138 clinical isolate associated with hospital-acquired urinary tract infection from China. bla_NDM-13 and bla_SHV-12 coexisted on the a ~54 Kb self-transferable plasmid. Compared with NDM-1, NDM-13, NDM-3, and NDM-4 had two amino acid substitutions (D95N and M154L), one amino acid substitution (D95N) and one amino acid substitutions (M154L), respectively. Complete plasmid sequencing showed that bla_NDM-13-harboring plasmid (pNDM13-DC33) was highly similar to the bla_NDM-1-harboring IncX3 plasmid pNDM-HN380, a common bla_NDM-harboring vector circulating in China. In accordance with the structure of pNDM-HN380, pNDM13-DC33 consists of a 33-kb backbone encoding plasmid replication (repB), stability partitioning, and transfer (tra, trb, and pil) functions, and a 21-kb antimicrobial resistance region with high GC content between umuD and mpr genes. In conclusion, the present study is the first report of a plasmid-encoded bla_NDM-13 and the complete sequence of a bla_NDM-13-harboring plasmid (pNDM13-DC33). bla_NDM-13 maybe originate from bla_NDM-1 located on a pNDM-HN380-like plasmid by sequential mutations.

NDM-producing Enterobacteriaceae in a Chinese hospital, 2014-2015: identification of NDM-producing Citrobacterwerkmanii and acquisition of blaNDM-1-carrying plasmid in vivo in a clinical Escherichia coli isolate

New Delhi metallo-β-lactamase (NDM)-producing Enterobacteriaceae (NPE) shows prevalence in China. Little is known about the mechanisms related to the spread of NPE. Recently, a total of 51 non-duplicated NPE isolates were collected from a tertiary-care hospital in China and analysed for genetic relatedness by PFGE, antimicrobial susceptibility by Etest and sequence type by multilocus sequence typing. S1-PFGE and Southern blot analysis or PCR amplification were used for plasmid profiling. Between 2014 and 2015, 22 Escherichia coli, 10 Klebsiella pneumoniae, 9 Enterobacter cloacae, 2 Enterobacter aerogenes, 3 Providencia rettgeri, 1 Klebsiella oxytoca, 1 Proteus mirabilis, 1 Citrobacter freundii, 1 Citrobacterwerkmanii and 1 Raoultella planticola were identified as NPE. Results of PFGE and multilocus sequence typing showed that most strains were genetically unrelated. Among the 45 blaNDM-carrying plasmids, there were 25 IncX3 plasmids with a size of about 30 to 50 kb, one 100 kb IncX3 plasmid, 11 IncA/C plasmids with a size range from 70 to 300 kb, six 90 to 120 kb IncB/O plasmids, one IncN plasmid with a size of 100 kb and one 140 kb IncFrep plasmid. An NDM-1-producing isolate of C. werkmanii was identified, which had not been reported previously. An Escherichia coli strain was found acquiring a blaNDM-1-carrying IncFrep plasmid in vivo during infection. In conclusion, an NDM-1-producing isolate of C. werkmanii was identified. An Escherichia coli strain acquired a blaNDM-1-carrying plasmid in vivo. IncX3 and IncA/C plasmids with various sizes might have emerged as the main platforms mediating the spread of the blaNDM genes in China.

Phenotypic Detection of Metallo-Beta-Lactamases in Carbapenem Resistant Acinetobacter baumannii Isolated from Pediatric Patients in Pakistan

Multidrug resistant A. baumannii has emerged as an important and problematic human pathogen as it is the causative agent of several types of infections especially in neonates and immunocompromised patients because they have least capacity to fight against infections. Carbapenems are used as last resort antibiotics for treating these infections but currently resistance against carbapenems due to MBL production is on the rise. The objective of this study was to determine the frequency of antibiotic resistance in A. baumannii and also to compare the efficacy of combined disk test and double disk synergy test for detection of metallo-beta-lactamases. A total of 112 A. baumannii were identified from various clinical samples and antibiotic susceptibility profile was determined by Kirby-Bauer Disk Diffusion method. Out of 112, 66 (58.9%) isolates were resistant to both imipenem and meropenem (OXOID). These resistant isolates were tested for carbapenemase production, and 55 (83.3%) were carbapenemase producers by Modified Hodge Test. These isolates were further tested for MBL production by combined disk test and double disk synergy test. Out of 66, 49 isolates were positive by both methods, CDT and DDST, and only one isolate was detected as negative (with kappa value = 0.038). All MBL producing strains showed remarkable resistance to cephalosporins, fluoroquinolones, aminoglycosides, and piperacillin/tazobactam (OXOID). The antibiotic resistance was very high in A. baumannii which were isolated from children in Pakistan specially attending a nephrology unit.

First Characterization of CTX-M-15-Producing Escherichia coli Strains Belonging to Sequence Type (ST) 410, ST224, and ST1284 from Commercial Swine in South America

We report for the first time the isolation of CTX-M-15-producingEscherichia colistrains belonging to sequence type (ST) 410, ST224, and ST1284 in commercial swine in Brazil. TheblaCTX-M-15gene was located on F-::A9::B1 and C1::A9::B1 IncF-type plasmids, surrounded by a new genetic context comprising the IS26insertion sequence truncated with the ISEcp1element upstream ofblaCTX-M-15 These results reveal that commercial swine have become a new reservoir of CTX-M-15-producing bacteria in South America.

New Delhi Metallo-β-Lactamase-Mediated Carbapenem Resistance: Origin, Diagnosis, Treatment and Public Health Concern

Objective:

To review the origin, diagnosis, treatment and public health concern of New Delhi metallo-β-lactamase (NDM)-producing bacteria.

Data Sources:

We searched database for studies published in English. The database of PubMed from 2007 to 2015 was used to conduct a search using the keyword term “NDM and Acinetobacter or Enterobacteriaceae or Pseudomonas aeruginosa.”

Study Selection:

We collected data including the relevant articles on international transmission, testing methods and treatment strategies of NDM-positive bacteria. Worldwide NDM cases were reviewed based on 22 case reports.

Results:

The first documented case of infection caused by bacteria producing NDM-1 occurred in India, in 2008. Since then, 13 blaNDM variants have been reported. The rise of NDM is not only due to its high rate of genetic transfer among unrelated bacterial species, but also to human factors such as travel, sanitation and food production and preparation. With limited treatment options, scientists try to improve available therapies and create new ones.

Conclusions:

In order to slow down the spread of these NDM-positive bacteria, a series of measures must be implemented. The creation and transmission of blaNDM are potentially global health issues, which are not issues for one country or one medical community, but for global priorities in general and for individual wound care practitioners specifically.

Escherichia coli of sequence type 3835 carrying bla NDM-1, bla CTX-M-15, bla CMY-42 and bla SHV-12

New Delhi metallo-β-lactamase (NDM) represents a serious challenge for treatment and public health. A carbapenem-resistant Escherichia coli clinical strain WCHEC13-8 was subjected to antimicrobial susceptibility tests, whole genome sequencing and conjugation experiments. It was resistant to imipenem (MIC, >256 μg/ml) and meropenem (MIC, 128 μg/ml) and belonged to ST3835. bla NDM-1 was the only carbapenemase gene detected. Strain WCHEC13-8 also had a plasmid-borne AmpC gene (bla CMY-42) and two extended-spectrum β-lactamase genes (bla CTX-M-15 and bla SHV-12). bla NDM-1 and bla SHV-12 were carried by a 54-kb IncX3 self-transmissible plasmid, which is identical to plasmid pNDM-HF727 from Enterobacter cloacae. bla CMY-42 was carried by a 64-kb IncI1 plasmid and bla CTX-M-15 was located on a 141-kb plasmid with multiple F replicons (replicon type: F36:A4:B1). bla CMY-42 was in a complicated context and the mobilisation of bla CMY-42 was due to the transposition of ISEcp1 by misidentifying its right-end boundary. Genetic context of bla NDM-1 in strain WCHEC13-8 was closely related to those on IncX3 plasmids in various Enterobacteriaceae species in China. In conclusion, a multidrug-resistant ST3835 E. coli clinical strain carrying bla NDM-1, bla CTX-M-15, bla CMY-42 and bla SHV-12 was identified. IncX3 plasmids may be making a significant contribution to the dissemination of bla NDM among Enterobacteriaceae in China.

Acinetobacter calcoaceticus from a fatal case of pneumonia harboring bla(NDM-1) on a widely distributed plasmid

BACKGROUND

We have recovered one bla(NDM-1)-harboring bacterial strain, designated as XM1570, from a sputum sample obtained from a fatal case of pneumonia in China.

METHODS

Biochemical profiling, 16S rRNA sequencing and antimicrobial susceptibility testing were performed. Conjugation experiments were conducted to determine transmissibility of resistance. Pulsed-field gel electrophoresis and whole genome sequencing were performed to identify strain-specific features.

RESULTS

The isolate XM1570 was identified as Acinetobacter calcoaceticus. Whole genome sequencing identified two plasmids, pXM1 and pXM2. Comparative analysis showed >99% similarity between XM1570 and A. calcoaceticus PHEA-2. Plasmid pXM1 carried the carbapenemase gene bla(NDM-1) and displayed high homology with previously described plasmids isolated from different Acinetobacter spp., which were collected from human or livestock distributed in China and worldwide. The bla(NDM-1) gene was located on this conjugative plasmid in a transposon-like region flanked by two copies of the insertion sequence ISAba125; and resistance to all tested β-lactams was observed. Transferability of resistance from pXM1 to the transconjugants was identified. Plasmid pXM2 had an insertion sequence ISAba125 and a -35 region of the bla NDM-1 gene promoter but the bla NDM-1 gene was not present. A chromosomally located carbapenemase-encoding gene bla OXA-75 was detected; however, this gene was interrupted by an insertion sequence ISAba22 belonging to IS3 family.

CONCLUSIONS

Location of bla(NDM-1) on different self-transmissible plasmids could facilitate geographically broad dissemination and host range expansion of the bla(NDM-1) gene via horizontal gene transfer. Our findings of this normally environmental species A. calcoaceticus XM1570 further underline the significant clinical challenge and the essential need for surveillance including molecular methods and plasmid analyses.

NDM-1-producing Enterobacteriaceae in a teaching hospital in Shanghai, China: IncX3-type plasmids may contribute to the dissemination of blaNDM-1

OBJECTIVES

To provide the epidemiological dissemination and the genetic characteristics of bla(NDM-1) in a teaching hospital in Shanghai, China.

METHODS

Here, the carbapenemase genes of 114 CRE isolates were evaluated by polymerase chain reaction (PCR). Clonal relatedness was assessed by pulsed-field gel electrophoresis (PFGE). Conjugation experiments and Southern blot hybridization were performed to determine the transferability of plasmids. Then plasmids were completely sequenced by the shotgun method.

RESULTS

Two Klebsiella pneumoniae strains (RJA1227 and RJF866) and one Raoultella planticola strain (RJA274) were identified as NDM-1 positive. The two K. pneumoniae isolates belonged to ST11 and exhibited highly similar PFGE patterns. Shotgun sequencing showed that plasmid pRJF866 (ca. 110 kb) contained genes associated with the IncFII-FIB group and was highly similar to plasmid pKOX_NDM1. RJA274 (ca. 50 kb) harbored bla(NDM-1) on an IncX3 plasmid, which was nearly identical to plasmid pNDM-HN380 except that part of the ISAba125 element is missing.

CONCLUSION

This is the first report of NDM-1-positive Enterobacteriaceae from Shanghai, China. IncX3 plasmids, reported in various species in the United Arab Emirates and China, may contribute to the dissemination of bla(NDM-1.). More attention should be devoted to monitoring the dissemination of the NDM-1 gene due to its potential horizontal transfer via mobile genetic elements.

Carbapenemase-producing Gram-negative bacteria: current epidemics, antimicrobial susceptibility and treatment options

ABSTRACT 

Carbapenemases, with versatile hydrolytic capacity against β-lactams, are now an important cause of resistance of Gram-negative bacteria. The genes encoding for the acquired carbapenemases are associated with a high potential for dissemination. In addition, infections due to Gram-negative bacteria with acquired carbapenemase production would lead to high clinical mortality rates. Of the acquired carbapenemases, Klebsiella pneumoniae carbapenemase (Ambler class A), Verona integron-encoded metallo-β-lactamase (Ambler class B), New Delhi metallo-β-lactamase (Ambler class B) and many OXA enzymes (OXA-23-like, OXA-24-like, OXA-48-like, OXA-58-like, class D) are considered to be responsible for the worldwide resistance epidemics. As compared with monotherapy with colistin or tigecycline, combination therapy has been shown to effectively lower case-fatality rates. However, development of new antibiotics is crucial in the present pandrug-resistant era.

Ebselen as a potent covalent inhibitor of New Delhi metallo-β-lactamase (NDM-1)

We identified a potent NDM-1 inhibitor that formed a S–Se bond with the Cys²²¹ residue at the active site, thereby exhibiting a new inhibition mechanism with broad spectrum inhibitory potential.

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

Objectives

The 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.

Methods

PCR 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.

Results

Among 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.

Conclusions

Compared 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.

First report in China of Enterobacteriaceae clinical isolates coharboring blaNDM-1 and blaIMP-4 drug resistance genes

AIMS

To describe the identification of two carbapenem-resistant, NDM-1 and IMP-4, carbapenemases coproducing Enterobacteriaceae isolates recovered from hospitalized patients in China. Both Klebsiella pneumoniae clinical isolates (Kpn922 and Kpn9599) were resistant to meropenem and imipenem and were subjected to additional antibiotic susceptibility testing. Polymerase chain reaction (PCR) and sequence analyses were used to characterize bacterial carbapenemase resistance genes, extended-spectrum β-lactamases, plasmid-mediated AmpC enzymes, quinolone resistance, and 16s RNA methylase. Genetic relatedness was determined using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Plasmids were analyzed by S1-PFGE and Southern blot.

RESULTS

PCR analyses revealed that the Kpn922 isolate carried blaNDM-1, blaIMP-4, blaTEM-1, and blaSHV-1 genes, while Kpn9599 carried blaNDM-1, blaIMP-4, blaTEM-1, and blaSHV-12 genes. MLST determined that the two isolates were ST1043 and ST571 sequence types. Southern blot analyses revealed that metallo-β-lactamase genes were plasmid borne in both isolates. Plasmids ∼300 kb simultaneously carried blaNDM-1 and blaIMP-4.

CONCLUSIONS

Coexistence of blaNDM-1 and blaIMP-4 in these clinical isolates may herald the emergence of a new pattern of drug resistance. Surveillance of carbapenemases, particularly metallo-β-lactamases, in Enterobacteriaceae is urgently needed to control and prevent the spread of these resistance determinants in China.

Increasing resistance rate to carbapenem among blood culture isolates of Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa in a university-affiliated hospital in China, 2004-2011

The objective of this study is to investigate the profile of antimicrobial resistance of Gram-negative bacteria in blood cultures from 2004-2011. Pathogens from positive blood cultures were subcultured, and identified in the First Affiliated Hospital of Nanjing Medical University from January 2004 to December 2011. The antibiotic resistance pattern was analyzed by WHONET 5.4. A total of 1224 cases of Gram-negative bacterial isolates were documented, accounting for 38.6% of the total pathogens isolated from positive blood cultures in the 8-year period. The isolation rates of Klebsiella pneumoniae and Acinetobacter baumannii increased nearly three times over the same time span. Most Gram-negative bacteria isolates, except the isolates of Pseudomonas aeruginosa, showed a significantly increased resistance rate to cephalosporins (in particular third/fourth generation cephalosporins). Noteworthy, the antimicrobial resistance of K. pneumoniae, A. baumannii and P. aeruginosa isolates to carbapenem (imipenem and meropenem) was significantly increased and the resistant rate to carbapenem was >80.0% in A. baumannii in 2011. The results from PCR detection for carbapenemases were as follows: 82.8% (24/29) isolates of K. pneumoniae carried the kpc-2 gene; only three metallo-beta-lactamase-positive P. aeruginosa isolates were detected; and 93.1% (67/72) A. baumannii isolates were blaOXA-23 positive. The antimicrobial resistance rate of Gram-negative bacteria isolated from blood cultures significantly increased from 2004 to 2011, with significant resistance to the third/fourth generation cephalosporins and carbapenem.

High incidence and endemic spread of NDM-1-positive Enterobacteriaceae in Henan Province, China

The emergence and spread of New Delhi metallo-β-lactamase 1 (NDM-1)-producing carbapenem-resistant Enterobacteriaceae (CRE) present an urgent threat to human health. In China, the bla(NDM-1 gene has been reported mostly in Acinetobacter spp. but is rarely found in Enterobacteriaceae. Here, we report a high incidence and endemic spread of NDM-1-producing CRE in Henan Province in China. Sixteen (33.3%) of the 48 CRE isolates obtained from patients during June 2011 to July 2012 were positive for bla(NDM-1), and the gene was found to be carried on plasmids of various sizes (∼ 55 to ∼ 360 kb). These plasmids were readily transferrable to recipient Escherichia coli by conjugation, conferred resistance to multiple antibiotics, and belonged to multiple replicon types. The bla(NDM-1)-positive CRE isolates were genetically diverse, and six new multilocus sequence typing (MLST) sequence types were linked to the carriage of NDM-1. Five of the isolates were classified as extensively drug-resistant (XDR) isolates, four of which also carried the fosA3 gene conferring resistance to fosfomycin, an alternative drug for treating infections by CRE. In each bla(NDM-1)-positive CRE isolate, the bla(NDM-1) gene was downstream of an intact ISAba125 element and upstream of the bleMBL gene. Furthermore, gene environment analysis suggested the possible transmission of bla(NDM-1)-containing sequences from Acinetobacter spp. to Klebsiella pneumoniae and Klebsiella oxytoca. These findings reveal the emergence and active transmission of NDM-1-positive CRE in China and underscore the need for heightened measures to control their further spread.

Genotypic characteristics of multidrug-resistant Escherichia coli isolates associated with urinary tract infections

Escherichia coli is an important pathogen involved in community-acquired urinary tract infections (CA-UTIs). In this study, we analyzed the prevalence of frequently occurring genes and the distribution of integrons in 51 multidrug-resistant (MDR) E. coli isolates associated with CA-UTIs. The clonality of these strains was investigated by phylogrouping, multi-locus sequence typing, and pulsed-field gel electrophoresis (PFGE). All these strains were found to produce two or more resistance determinants, ceftazidime-hydrolyzing CTX-M-type extended-spectrum β-lactamases (ESBLs) and plasmid-mediated quinolone resistance determinants were the most prevalent (92.2% and 51.0%, respectively). A sulfhydryl variable-61-producing E. coli strain was identified for the first time in China. The prevalence of class 1 integrons was 54.9%, class 2 integrons were detected in three isolates but no isolate contained a class 3 integron. Phylogenetic group D was the dominant, observed in 70.6% of the isolates. PFGE analysis revealed a high level of diversity. Twenty-four distinctive sequence types (STs) including four major STs (ST648, ST224, ST38, and ST405) were identified. To our knowledge, this is the first report on the characterization of MDR E. coli isolates associated with CA-UTIs in China; our results suggest that an MDR D-ST648 clone producing CTX-M-ESBLs has emerged as a major clone in the community setting.

Prevalence of bla NDM, bla PER, bla VEB, bla IMP, and bla VIM Genes among Acinetobacter baumannii Isolated from Two Hospitals of Tehran, Iran

Background and Objectives. The aim of this study was to determine the frequency of bla NDM, bla PER, bla VEB, bla IMP, and bla VIM type genes among A. baumannii isolates from hospitalized patients in two hospitals in Tehran, Iran. Patients and Methods. Antibiotic susceptibility tests were performed by Kirby-Bauer disc diffusion and Broth microdilution methods. The frequency of MBL (metallo-beta-lactamase) and ESBL (extended-spectrum-beta-lactamase) producers was evaluated by CDDT. The β -lactamases genes were detected by PCR and sequencing methods. Results. The resistance of A. baumannii isolates against tested antibiotics was as follows: 103 (95.4%) to ceftazidime, 108 (100%) to cefotaxime, 105 (95.7%) to cefepime, 99 (91.7%) to imipenem, 99 (91.7%) to meropenem, 87 (80.6%) to amikacin, 105 (97.2%) to piperacillin, 100 (92.6%) to ciprofloxacin, 103 (95.4%) to piperacillin/tazobactam, 44 (40.7%) to gentamicin, 106 (98.1%) to ampicillin/sulbactam, 106 (98.1%) to co-trimoxazole, 87 (80.6%) to tetracycline, and 1 (1.8%) to colistin. Using combined disk diffusion test, 91 (84.2%) and 86 (86.86%) were ESBL and MBL producers, respectively. The prevalence of bla PER-1, bla VEB-1, bla IMP-1, and bla VIM-1 genes was 71 (78.03%), 36 (39.5%), 3 (3.48%), and 15 (17.44%), respectively. Conclusions. The prevalence of ESBLs and MBLs-producing A. baumannii strains detected in this study is a major concern and highlights the need of infection control measures.

Novel β-lactamase inhibitors: a therapeutic hope against the scourge of multidrug resistance

The increasing incidence and prevalence of multi-drug resistance (MDR) among contemporary Gram-negative bacteria represents a significant threat to human health. Since their discovery, β-lactam antibiotics have been a major component of the armamentarium against these serious pathogens. Unfortunately, a wide range of β-lactamase enzymes have emerged that are capable of inactivating these powerful drugs. In the past 30 years, a major advancement in the battle against microbes has been the development of β-lactamase inhibitors, which restore the efficacy of β-lactam antibiotics (e.g., ampicillin/sulbactam, amoxicillin/clavulanate, ticarcillin/clavulanate, and piperacillin/tazobactam). Unfortunately, many newly discovered β-lactamases are not inactivated by currently available inhibitors. Is there hope? For the first time in many years, we can anticipate the development and introduction into clinical practice of novel inhibitors. Although these inhibitors may still not be effective for all β-lactamases, their introduction is still welcome. This review focuses on the novel β-lactamase inhibitors that are closest to being introduced in the clinic.

First identification of coexistence of blaNDM-1 and blaCMY-42 among Escherichia coli ST167 clinical isolates

Background

Emergence of multidrug resistance in Enterobacteriaceae limits the selection of antimicrobials for treatment of infectious diseases. Identification of NDM-1 makes more difficulty in treating multidrug-resistant Enterobacteriaceae infections. Carbapenem-resistant Escherichia coli clinical isolates from a tertiary hospital in Wenzhou, east China, were investigated for NDM-1 production.

Results

The two tested isolates were negative for modified Hodge test, but positive for a double-disc synergy test used for detecting metallo-β-lactamase production. E. coli WZ33 and WZ51 exhibited discrepant-level resistance to most clinically frequent used antimicrobials, but still susceptible to trimethoprim/sulfamethoxazole, amikacin, fosfomycin, tigecycline and polymyxin B. E. coli WZ33 and WZ51 were positive for bla_NDM-1 determined by PCR and DNA sequencing. Other than bla_NDM-1, E. coli WZ33 also harbored bla_CTX-M-14 and bla_CMY-42, while E. coli WZ51 simultaneously harbored bla_SHV-12,bla_CTX-M-14 and bla_CMY-42. Carbapenem resistance for E. coli WZ51 and WZ33 could not be transferred to E. coli recipients through conjugation, but could be transferred to E. coli recipients by chemical transformation. The EcoR1-digested DNA pattern of plasmids from the transformant of E. coli WZ51 was different from that of E. coli WZ51. MLST showed that E. coli WZ33 and WZ51 belonged to an animal-associated clone (ST167).

Conclusion

The present study is the first report of bla_NDM-1 carriage in E. coli ST167 isolates and coexistence of bla_NDM-1 and bla_CMY-42 in same isolate. Systemic surveillance should focus on the dissemination of bla_NDM-1 among Enterobacteriaceae, especially E. coli ST167 clone associated with animal infection.

Characteristics of community-onset NDM-1-producing Klebsiella pneumoniae isolates

Multilocus sequence typing and in vitro antimicrobial susceptibility testing were performed for three community-onset New Delhi metallo-β-lactamase-1 (NDM-1)-producing Klebsiella pneumoniae isolates from Korea. The genetic structure surrounding the blaNDM-1 gene was determined in blaNDM-1-harbouring plasmids. Three NDM-1-producing K. pneumoniae isolates were found to belong to the same clone (sequence type 340). Each of these isolates showed the same genetic structure surrounding the blaNDM-1 gene. The genes blaNDM-1, bleMBL, trpF and dsbC were flanked by two intact insertion sequences, ISAba125 and IS26, which may promote horizontal gene transfer. The blaNDM-1-harbouring plasmids conferred antimicrobial resistance to carbapenems, cephalosporins, aminoglycosides and aztreonam in transconjugants. It can be speculated that either the entire blaNDM-1-harbouring plasmids or just the part of the plasmid containing the blaNDM-1 gene may have transferred between K. pneumoniae and Escherichia coli. Following the transfer, the isolate disseminated throughout Korea. This study suggests the need for monitoring the dissemination of NDM-1-producing isolates across countries or continents due to their potential transferability via ISAba125- and IS26-associated transposons.