Emergence of New Delhi metallo-β-lactamase type 1-producing Enterobacteriaceae and non-Enterobacteriaceae: global case detection and bacterial surveillance

Evolutionary trends of carbapenem-resistant and susceptible Acinetobacter baumannii isolates in a major tertiary care setting from North India

Emergence of carbapenem-resistant A. baumannii (CRAB) is a global, ongoing healthcare concern. CRAB is among the topmost priority pathogens, with various studies focusing on its global population structure and resistant allelic profiles. However, carbapenem-susceptible A. baumannii (CSAB) isolates are often overlooked due to their sensitivity to beta-lactams, which can provide important insights into origin of CRAB lineages and isolates. In the present study, we report genomic investigation of CRAB and CSAB coexisting in Indian hospital setting. MLST based population structure and phylogenomics suggest they mainly follow distinct evolutionary routes forming two phylogroups. PG-I exclusively for a successful clone (ST2) of CRAB and PG-II comprises diversified CSAB isolates except PG3373, which is CRAB. Additionally, there are few CRAB isolates not belonging to PG-I and sharing clonal relationship with CSAB isolates indicating role of genome plasticity towards extensive drug resistance in the nosocomial environment. Further, genealogical analysis depicts prominent role of recombination in emergence and evolution of a major CRAB lineage. Further, CRAB isolates are enriched in resistomes as compared to CSAB isolates, which were encoded on the genomic island. Such comparative genomic insights will aid in our understanding and localized management of rapidly evolving pandrug resistant nosocomial pathogens.

Carbapenem resistance in Enterobacterales from agricultural, environmental and clinical origins: South Africa in a global context

Carbapenem agents are regarded as last-resort antibiotics, however, bacterial resistance towards carbapenems has been reported in both clinical and agricultural settings worldwide. Carbapenem resistance, defined as the resistance of a bacteria towards one or more carbapenem drugs, can be mediated in either of, or a combination of, three mechanisms-although, the mechanism mediated through the production of carbapenemases (β-lactamases that are able to enzymatically degrade carbapenems) is of most significance. Of particular concern is the occurrence of carbapenemase producing Enterobacterales (CPE), with literature describing a dramatic increase in resistance globally. In South Africa, increases of carbapenemase activity occurring in Enterobacter species, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa have recently been reported. CPE can also be found in agricultural environments, as global studies have documented numerous instances of CPE presence in various animals such as pigs, cattle, seafood, horses and dogs. However, most reports of CPE occurrence in agricultural settings come from Northern America, Europe and some parts of Asia, where more extensive research has been conducted to understand the CPE phenomenon. In comparison to clinical data, there are limited studies investigating the spread of CPE in agricultural settings in Africa, highlighting the importance of monitoring CPE in livestock environments and the food chain. Further research is necessary to uncover the true extent of CPE dissemination in South Africa. This review will discuss the phenomenon of bacterial antibiotic resistance (ABR), the applications of the carbapenem drug and the occurrence of carbapenem resistance globally.

The roles of bedside nurses in Japan in antimicrobial stewardship

BACKGROUND

In the United States and the United Kingdom, the roles of nurses in antimicrobial stewardship (AS) have been described in guidelines. However, in Japan, no previous studies have clarified nurses' recognition of the role of AS. Moreover, how the AS roles were implemented among nurses in Japan has not been fully clarified. The objectives of this study were to determine the perceptions of infection control nurses (ICNs) in Japan regarding the AS role of nurses and the extent of nurses' practice.

METHODS

A questionnaire survey of ICNs was conducted.

RESULTS

Four hundred responses (response rate, 30.8%) were analyzed. Some of the items that have already gained consensus as the AS role of nurses were not recognized as the AS role of nurses by ICNs or had low implementation rates in Japan. Meanwhile, both recognition and implementation rates were high for the 5 types of care proposed.

DISCUSSION

The reason the ICNs agreed that these 5 types of care are AS roles for nurses is that they know that such care can prevent infection and thereby obviate the need for antimicrobial administration. However, whether nurses themselves understand that these are roles for nurses in AS is unclear. To promote AS in Japan, communicating the fact that nurses already contribute to AS, strengthening nurse education, and improving staffing are desirable.

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.

An Alliance of Carbapenem-Resistant Klebsiella pneumoniae with Precise Capsular Serotypes and Clinical Determinants: A Disquietude in Hospital Setting

Carbapenemase-resistant Klebsiella pneumoniae (CRKP) is a genuine burden for physicians and researchers. We aimed at carbapenemase resistance and its relation with capsular serotyping in K. pneumoniae and studied some clinical determinants, which may influence the clinical infections. Initially, 61 K. pneumoniae isolates obtained from various clinical specimens were confirmed at the molecular level and then antimicrobial susceptibility test was performed followed by capsular serotyping performed by multiplex PCR. All isolates were subjected to the detection of carbapenemase genes including blaKPC, blaNDM-1, blaOXA-48, blaVIM, and blaIMP. Clinical and demographic data of all patients were reviewed including age, gender, underlying diseases, and the treatment obtained. Multidrug-resistance was a predominant feature in 77% K. pneumoniae strains. Presence of extended-spectrum beta-lactamase was detected phenotypically in 59% K. pneumoniae strains. Carbapenem resistance was noticed phenotypically in 24.6% isolates. blaOXA-48 and blaNDM-1 were the most frequent carbapenemase genes. blaNDM-1 positive isolates correlated with gentamicin, amikacin, imipenem, and meropenem resistance ( $p<0.05$ ). The nosocomial isolates mostly harbored blaOXA-48 gene ( $p<0.02$ ). Amongst all the K. pneumoniae isolates, 59% isolates could be typed and serotype K54 had the highest prevalence followed by K20 and K5. Correlation between the carbapenemase genes, serotype and type of infection showed that blaOXA-48 positive strains had a significant association with K20 serotype and urinary tract infections ( $p=0.2$ ) while, K20 serotype and blaKPC positive strains were significantly associated with wound infections (K20, $p=0.3$ and blaKPC, and $p=0.4$ ). Mucoid phenotype was not found related to presence of specific carbapenemase genes or serotypes except serotype K20 ( $p<0.001$ ). Patients with monotherapy had treatment failure in comparison to the combination therapy for blaKPC-associated infections. In conclusion, the present investigation exhibited the significant association between K20 serotype with blaOXA-48. The predominance of K54 reveals the possibility of endemicity in our hospital setting. K. pneumoniae isolated from wound specimens significantly harbors K20 serotype and blaKPC gene. Comprehensive clinical information and the distribution of antibiotic resistance genes, and serotypes may play important roles in the treatment process.

Occurrence of New Delhi Metallo-Beta-Lactamase 1 Producing Enterococcus Species in Oghara Water Nexus: An Emerging Environmental Implications of Resistance Dynamics

Various members of the enteric bacteria in recent times are evolving diverse survival mechanisms for antibiotic therapy resulting in failure of treatment in infection and disease cases. The Enterococcus species are potential strains implicated in gastrointestinal tract infection and are recently evolving in the resistance mechanism. The study evaluates the occurrence of New Delhi Metallo-beta-lactamase 1 (NDM-1) amongst Enterococcus species using the phenotypic and genomic characterization of environmental strains in the Oghara water nexus. Presumptive isolates of Enterococcus species were retrieved from various sampled water sources and confirmed using polymerase chain reaction (PCR). Antibiotic susceptibility testing was conducted on confirmed isolates using Kirby-Bauer disk diffusion methods. The result reveals 63 genus isolates confirmed Enterococcus species, of which 42 (67%) were Enterococcus faecium, 15 (23%) were Enterococcus faecalis, and 6 (10%) were other Enterococcus species. Fourteen among the E. faecalis isolates show resistance to Ertapenem-EDTA, while 17 (44.8%) of the E. faecium show resistance to Ertapenem-EDTA to presumptively reveal their NDM-1 phenotype. The PCR detection of the NDM-1 gene further confirmed 23 (36.5%) isolates as positive genotypes amongst the isolates that previously showed presumptive NDM-1 phenotype. It was also observed that 10 (15.9%) of Enterococcus faecium members harbored the NDM-1 genotype, whereas 8 (12.7%) members of the Enterococcus faecalis harbored the NDM-1 genotype. The observation of such resistance determinants necessitates a call for the adroit application of relevant therapeutics in the management of related infections and an environmental health caution to prevent the spread of such resistance potential enteric bacteria pathogens.

Infections Due to Acinetobacter baumannii-calcoaceticus Complex: Escalation of Antimicrobial Resistance and Evolving Treatment Options

Bacteria within the genus Acinetobacter (principally A. baumannii-calcoaceticus complex [ABC]) are gram-negative coccobacilli that most often cause infections in nosocomial settings. Community-acquired infections are rare, but may occur in patients with comorbidities, advanced age, diabetes mellitus, chronic lung or renal disease, malignancy, or impaired immunity. Most common sites of infections include blood stream, skin/soft-tissue/surgical wounds, ventilator-associated pneumonia, orthopaedic or neurosurgical procedures, and urinary tract. Acinetobacter species are intrinsically resistant to multiple antimicrobials, and have a remarkable ability to acquire new resistance determinants via plasmids, transposons, integrons, and resistance islands. Since the 1990s, antimicrobial resistance (AMR) has escalated dramatically among ABC. Global spread of multidrug-resistant (MDR)-ABC strains reflects dissemination of a few clones between hospitals, geographic regions, and continents; excessive antibiotic use amplifies this spread. Many isolates are resistant to all antimicrobials except colistimethate sodium and tetracyclines (minocycline or tigecycline); some infections are untreatable with existing antimicrobial agents. AMR poses a serious threat to effectively treat or prevent ABC infections. Strategies to curtail environmental colonization with MDR-ABC require aggressive infection-control efforts and cohorting of infected patients. Thoughtful antibiotic strategies are essential to limit the spread of MDR-ABC. Optimal therapy will likely require combination antimicrobial therapy with existing antibiotics as well as development of novel antibiotic classes.

Co-occurrence of Carbapenemase-encoding Genes Among Klebsiella pneumoniae Clinical Isolates: Positive Relationship of bla NDM and bla SIM with Imipenem Resistance

Background: Carbapenem-resistant Klebsiella pneumoniae (CR-KP), known as a significant public health threat, is the most common causative agent of nosocomial and community-acquired infections. Objectives: This study aimed to evaluate resistance to carbapenems and determine the prevalence of carbapenemase genes and multilocus sequence typing (MLST) of K. pneumoniae clinical isolates. Methods: One-hundred K. pneumoniae isolates were evaluated. The minimum inhibitory concentrations (MIC) of imipenem and meropenem were assessed by the broth microdilution method. Multiplex-polymerase chain reaction (PCR) was applied to detect 11 carbapenemase-encoding genes belonging to different classes. The alleles and sequence types (ST) of three isolates were identified by MLST. Results: The MIC of carbapenems for the isolates ranged from 0.062 to 32 µg/mL. Overall, resistance rates to imipenem and meropenem were reported 11% and 34%, respectively. The bla IMP gene was the most abundant (78.4%), followed by bla OXA-48 (48.6%), bla GIM (27%), bla KPC (27%), bla SIM (21.6%), bla BIC (21.6%), bla NDM (16.2%), bla AIM (16.2%), bla VIM (16.2%), bla DIM (8.1%), and bla SPM (8.1%). The co-existence of carbapenemase genes was observed in 81.8% of the isolates. A positive relationship was found between the presence of bla NDM and bla SIM and resistance to imipenem. Multilocus sequence typing results showed three different sequence types, including ST14, ST5188, and ST1861. Conclusions: This study revealed a high prevalence of CR-KP isolates that suggests a high risk of horizontal gene transfer and potential to spread resistance among other strains. Since STs are reported for the first time in Iran, they can be considered as emerging strains.

A Sarcina bacterium linked to lethal disease in sanctuary chimpanzees in Sierra Leone

Human and animal infections with bacteria of the genus Sarcina (family Clostridiaceae) are associated with gastric dilation and emphysematous gastritis. However, the potential roles of sarcinae as commensals or pathogens remain unclear. Here, we investigate a lethal disease of unknown etiology that affects sanctuary chimpanzees (Pan troglodytes verus) in Sierra Leone. The disease, which we have named "epizootic neurologic and gastroenteric syndrome" (ENGS), is characterized by neurologic and gastrointestinal signs and results in death of the animals, even after medical treatment. Using a case-control study design, we show that ENGS is strongly associated with Sarcina infection. The microorganism is distinct from Sarcina ventriculi and other known members of its genus, based on bacterial morphology and growth characteristics. Whole-genome sequencing confirms this distinction and reveals the presence of genetic features that may account for the unusual virulence of the bacterium. Therefore, we propose that this organism be considered the representative of a new species, named "Candidatus Sarcina troglodytae". Our results suggest that a heretofore unrecognized complex of related sarcinae likely exists, some of which may be highly virulent. However, the potential role of "Ca. S. troglodytae" in the etiology of ENGS, alone or in combination with other factors, remains a topic for future research.

Genetic Features Leading to Reduced Susceptibility to Aztreonam-Avibactam among Metallo-β-Lactamase-Producing Escherichia coli Isolates

Metallo-β-lactamase (MBL)-producing Escherichia coli isolates resistant to the newly developed β-lactam/β-lactamase inhibitor drug combination aztreonam-avibactam (ATM-AVI) have been reported. Here, we analyzed a series of 118 clinical MBL-producing E. coli isolates of various geographical origins for susceptibility to ATM-AVI. The nature of the PBP3 protein sequence and the occurrence of bla _CMY genes for susceptibility to ATM-AVI were investigated. We showed here that elevated MICs of ATM-AVI among MBL-producing E. coli isolates resulted from a combination of different features, including modification of PBP3 protein sequence through specific amino acid insertions and production of CMY-type enzymes, particularly, CMY-42. We showed here that those insertions identified in the PBP3 sequence are not considered the unique basis of resistance to ATM-AVI, but they significantly contribute to it.

Potential Inhibitors Against NDM-1 Type Metallo-β-Lactamases: An Overview

A new member of the class metallo-β-lactamase (MBL), New Delhi metallo-beta-lactamase 1 (NDM-1) has emerged recently as a leading threat to the treatment of infections that have spread in all major Gram-negative pathogens. The enzyme inactivates antibiotics of the carbapenem family, which are a mainstay for the treatment of antibiotic-resistant bacterial infections. This review provides information about NDM-1 spatial structure, potential features of the active site, and its mechanism of action. It also enlists the inhibitors/compounds/drugs against NDM-1 in various development phases. Understanding their mode of inhibition and the structure-activity relationship would be beneficial for development, synthesis, and even increasing biological efficacy of inhibitors, making them more promising drug candidates.

Hypervirulence and carbapenem resistance: two distinct evolutionary directions that led high-risk Klebsiella pneumoniae clones to epidemic success

Introduction: Over the past few decades, Klebsiella pneumoniae has become a significant threat to public health and is now listed as an ESKAPE pathogen. Evolving with versatile capabilities, K. pneumoniae is a population composed of genetically and phenotypically diverse bacteria. However, epidemic K. pneumoniae are restricted to specific clonal lineages. The clonal group CG23 comprises hypervirulent K. pneumoniae displaying limited resistance to antimicrobials and is frequently associated with the community-acquired invasive syndrome. On the other hand, CG258 is another clonal group of K. pneumoniae that has evolved resistance to carbapenems, primarily by acquiring the carbapenemase-encoding genes through nosocomial carriage. Areas covered: With a focus on the high-risk K. pneumoniae clonal lineages CG23 and CG258, we review recent advances including the newly discovered lineage-specific genomic features, and the molecular basis of K. pneumoniae-associated epidemiology, antimicrobial resistance, and hypervirulence. Expert opinion: Both CG23 and CG258 can establish reservoirs in susceptible individuals. Empirical antimicrobial regimens that are prescribed for immediate treatments frequently create selective pressures that favor the high-risk lineages to develop into prominent colonizers. This dilemma reinforces the need for effective therapies that require rapid and accurate diagnosis of epidemic K. pneumoniae.

Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates

The emergence and spread of metallo-beta-lactamase–producing multidrug-resistant (MDR) Klebsiella pneumoniae is a serious public health threat, which is further complicated by the increased prevalence of colistin resistance. The link between antimicrobial resistance acquired by strains of Klebsiella and their unique metabolic capabilities has not been determined. Here, we reconstruct genome-scale metabolic models for 22 K. pneumoniae strains with various resistance profiles to different antibiotics, including two strains exhibiting colistin resistance isolated from Cairo, Egypt. We use the models to predict growth capabilities on 265 different sole carbon, nitrogen, sulfur, and phosphorus sources for all 22 strains. Alternate nitrogen source utilization of glutamate, arginine, histidine, and ethanolamine among others provided discriminatory power for identifying resistance to amikacin, tetracycline, and gentamicin. Thus, genome-scale model based predictions of growth capabilities on alternative substrates may lead to construction of classification trees that are indicative of antibiotic resistance in Klebsiella isolates.

Investigation of the prevalence of genes conferring resistance to carbapenems in Pseudomonas aeruginosa isolates from burn patients

Background and aim: Currently, the rate of hospital-acquired infections due to drug-resistant Pseudomonas aeruginosa strains shows an increasing trend and remains one of the principal reasons for mortalilty in burn patients. This study aimed to investigate the prevalence of genes conferring resistance to carbapenems in P. aeruginosa isolates from burn patients. Methods: A total of 50 P. aeruginosa isolates were tested for antibiotic susceptibility and presence of multidrug-resistant (MDR) and extensively drug resistant (XDR) isolates, using phenotypic tests. Screening for genes conferring resistance to carbapenems was investigated by multiplex PCR method. Results: Susceptibility testing demonstrated the highest resistance against amikacin, ceftazidime (n=44/88% each), and gentamicin (84%), while colistin sulfate was the most effective antibiotic. The rate of MDR and XDR isolates was revealed as 50% and 40% respectively. We detected the following carbapenemase genes: blaNDM (32%), followed by blaOXA-48 (18%), and blaBIC-1 (14%). This study revealed a high antibiotic resistance in P. aeruginosa isolates with a total of 40% and 50% MDR and XDR isolates respectively, and 70% carbapenem resistance. The prevalence of carbapenem conferring genes tested among carbapenem-resistant isolates was demonstrated as 65.7%. Conclusion: Due to the prevalence of P. aeroginosa strains carrying blaOXA-48 and blaNDM genes in our hospital, more attention and implementation of effective control measures against nosocomial infection are recommended.

Distribution of clinically relevant antibiotic resistance genes in Lake Tai, China

Lake Tai is China's third largest freshwater lake and an important water resource for agriculture, industrial sectors, and as drinking water for several large cities. In this study, the occurrence of five antibiotic resistance genes (sul1, bla_TEM, bla_NDM-1, bla_CTX-M-32, mcr-1) was investigated in water and sediment samples collected from Lake Tai. Antibiotic resistances are currently increasing, posing a significant threat to public health. The sulfonamide resistance gene sul1 was highly abundant in all analyzed water and sediment samples. In addition, the two β-lactamase genes bla_TEMand bla_NDM-1 - encoding clinically relevant antibiotic resistances - were detected in 67.1 and 7.3% of the water samples and in 70.7 and 15.4% of the sediment samples. The third β-lactamase gene, bla_CTX-M-32, was only detected in water samples (13.4%), while the colistin resistance gene mcr-1 was not detected in any of the samples. No significant variations between different sampling sites or time points could be observed. The investigation of drinking water treatment at Lake Tai, using lake water as influent, showed a significant reduction of the antibiotic resistance genes through the treatment process. Microbial source tracking showed only low fecal contamination by humans, ruminants, and pigs, indicating the relevance of other sources such as fish farms. Overall, our results provide important insights into the occurrence and abundance of antibiotic resistance genes in the Lake Tai water system and their elimination via drinking water treatment.

Draft Genome Sequences of Four Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates, Including Two Colistin-Resistant Strains, from Cairo, Egypt

The emergence and spread of metallo-beta-lactamase-producing multidrug-resistant Klebsiella pneumoniae are a serious public health threat. Here, we report the draft genome sequences of four K. pneumoniae strains isolated from Cairo, Egypt, including two panresistant colistin-resistant strains. Genome annotation indicated a number of virulence and resistance genes agreeing with observed phenotypes.

Vancomycin Analogue Restores Meropenem Activity against NDM-1 Gram-Negative Pathogens

New Delhi metallo-β-lactamase-1 (NDM-1) is the major contributor to the emergence of carbapenem resistance in Gram-negative pathogens (GNPs) and has caused many clinically available β-lactam antibiotics to become obsolete. A clinically approved inhibitor of metallo-β-lactamase (MBL) that could restore the activity of carbapenems against resistant GNPs has not yet been found, making NDM-1 a serious threat to human health. Here, we have rationally developed an inhibitor for the NDM-1 enzyme, which has the ability to penetrate the outer membrane of GNPs and inactivate the enzyme by depleting the metal ion (Zn²⁺) from the active site. The inhibitor reinstated the activity of meropenem against NDM-1 producing clinical isolates of GNPs like Klebsiella pneumoniae and Escherichia coli. Further, the inhibitor efficiently restored meropenem activity against NDM-1 producing K. pneumoniae in a murine sepsis infection model. These findings demonstrate that a combination of the present inhibitor and meropenem has high potential to be translated clinically to combat carbapenem-resistant GNPs.

Prevalence of carbapenemase-producing organisms at the Kidney Center of Rawalpindi (Pakistan) and evaluation of an advanced molecular microarray-based carbapenemase assay

AIM

A DNA microarray-based assay for the detection of antimicrobial resistance (AMR) genes was used to study carbapenemase-producing organisms at the Kidney Center of Rawalpindi, Pakistan.

METHODS

The evaluation of this assay was performed using 97 reference strains with confirmed AMR genes. Testing of 7857 clinical samples identified 425 Gram-negative bacteria out of which 82 appeared carbapenem resistant. These isolates were analyzed using VITEK-2 for phenotyping and the described AMR assay for genotyping.

RESULTS

The most prevalent carbapenemase gene was blaNDM and in 12 isolates we detected two carbapenemase genes (e.g., blaNDM/blaOXA-48).

CONCLUSION

Our prevalence data from Pakistan show that - as in other parts of the world - carbapenemase-producing organisms with different underlying resistance mechanisms are emerging, and this warrants intensified and constant surveillance.

Hydrolysis of cephalexin and meropenem by New Delhi metallo-β-lactamase: the substrate protonation mechanism is drug dependent

Emergence of antibiotic resistance due to New Delhi metallo-β-lactamase (NDM-1) bacterial enzymes is of great concern due to their ability to hydrolyze a wide range of antibiotics. There are ongoing efforts to obtain the atomistic details of the hydrolysis mechanism in order to develop inhibitors for NDM-1. In particular, it remains elusive how drug molecules of different families of antibiotics are hydrolyzed by NDM-1 in an efficient manner. Here we report the detailed molecular mechanism of NDM-1 catalyzed hydrolysis of cephalexin, a cephalosporin family drug, and meropenem, a carbapenem family drug. This study employs molecular dynamics (MD) simulations using hybrid quantum mechanical/molecular mechanical (QM/MM) methods at the density functional theory (DFT) level, based on which reaction pathways and the associated free energies are obtained. We find that the mechanism and the free energy barrier for the ring-opening step are the same for both the drug molecules, while the subsequent protonation step differs. In particular, we observe that the mechanism of the protonation step depends on the R2 group of the drug molecule. Our simulations show that allylic carbon protonation occurs in the case of the cephalexin drug molecule where Lys211 is the proton donor, and the proton transfer occurs via a water chain formed (only) at the ring-opened intermediate structure. Based on the free energy profiles, the overall kinetics of drug hydrolysis is discussed. Finally, we show that the proposed mechanisms and free energy profiles could explain various experimental observations.

Indistinguishable NDM-producing Escherichia coli isolated from recreational waters, sewage, and a clinical specimen in Ireland, 2016 to 2017

In this study, New Delhi metallo-beta-lactamase (NDM)-producing Enterobacteriaceae were identified in Irish recreational waters and sewage. Indistinguishable NDM-producing Escherichia coli by pulsed-field gel electrophoresis were isolated from sewage, a fresh water stream and a human source. NDM-producing Klebsiella pneumoniae isolated from sewage and seawater in the same area were closely related to each other and to a human isolate. This raises concerns regarding the potential for sewage discharges to contribute to the spread of carbapenemase-producing Enterobacteriaceae.

Semi-rational screening of the inhibitors and β-lactam antibiotics against the New Delhi metallo-β-lactamase 1 (NDM-1) producing E. coli

Bacteria containing bla NDM-1 gene are a growing threat to almost all clinically β-lactam antibiotics. Especially, the New Delhi metallo-β-lactamase (NDM-1) has become a potential public survival risk. In this study, a novel and efficient strategy for inhibitors and β-lactam antibiotics screening using recombinant New Delhi metallo-beta-lactamase (NDM-1) was developed. First, the gene of bla NDM-1 were identified and cloned from multi-drug resistance of Acinetobacter baumannii isolate; by the means of protein expression and purification, recombinant NDM-1 activity was up to 68.5 U ml-1, and high purity NDM-1 protein with activity of 347.4 U mg-1 was obtained. Finally, for NDM-1, the inhibitors (aspergillomarasmine A (AMA) and EDTA) with high affinity (HI) and the β-lactam antibiotics (imipenem) with low affinity (LA) were screened out. Surprisingly, the inhibition of the NDM-1 was enhanced by the use of inhibitor combinations (AMA-EDTA (1 : 2)), where the IC50 of AMA-EDTA was reduced by 88% and 95%, respectively, comparing to the AMA and EDTA alone. More interesting, AMA-EDTA could restore the activity of imipenem when tested against NDM-1 expressing strains (E. coli and Acinetobacter baumannii), with a working time of 120 min and 330 min, respectively. This method is expected to be used in high-throughput screening, drug redesign (including new inhibitors and drugs) and "old drug new use".

Multiple Antibiotic-Resistant, Extended Spectrum-β-Lactamase (ESBL)-Producing Enterobacteria in Fresh Seafood

Members of the family Enterobacteriaceae include several human pathogens that can be acquired through contaminated food and water. In this study, the incidence of extended spectrum β-lactamase (ESBL)-producing enterobacteria was investigated in fresh seafood sold in retail markets. The ESBL-positive phenotype was detected in 169 (78.60%) isolates, with Escherichia coli being the predominant species (53), followed by Klebsiella oxytoca (27), and K. pneumoniae (23). More than 90% of the isolates were resistant to third generation cephalosporins, cefotaxime, ceftazidime, and cefpodoxime. Sixty-five percent of the isolates were resistant to the monobactam drug aztreonam, 40.82% to ertapenem, and 31.36% to meropenem. Resistance to at least five antibiotics was observed in 38.46% of the isolates. Polymerase Chain Reaction (PCR) analysis of ESBL-encoding genes detected bla_CTX, bla_SHV, and bla_TEM genes in 76.92%, 63.3%, and 44.37% of the isolates, respectively. Multiple ESBL genes were detected in majority of the isolates. The recently discovered New Delhi metallo-β-lactamase gene (bla_NDM-1) was detected in two ESBL⁺ isolates. Our study shows that secondary contamination of fresh seafood with enteric bacteria resistant to multiple antibiotics may implicate seafood as a potential carrier of antibiotic resistant bacteria and emphasizes an urgent need to prevent environmental contamination and dissemination of such bacteria.

Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307

Klebsiella pneumoniae is a major human pathogen responsible for high morbidity and mortality rates. The emergence and spread of strains resistant to multiple antimicrobial agents and documented large nosocomial outbreaks are especially concerning. To develop new therapeutic strategies for K. pneumoniae, it is imperative to understand the population genomic structure of strains causing human infections. To address this knowledge gap, we sequenced the genomes of 1,777 extended-spectrum beta-lactamase-producing K. pneumoniae strains cultured from patients in the 2,000-bed Houston Methodist Hospital system between September 2011 and May 2015, representing a comprehensive, population-based strain sample. Strains of largely uncharacterized clonal group 307 (CG307) caused more infections than those of well-studied epidemic CG258. Strains varied markedly in gene content and had an extensive array of small and very large plasmids, often containing antimicrobial resistance genes. Some patients with multiple strains cultured over time were infected with genetically distinct clones. We identified 15 strains expressing the New Delhi metallo-beta-lactamase 1 (NDM-1) enzyme that confers broad resistance to nearly all beta-lactam antibiotics. Transcriptome sequencing analysis of 10 phylogenetically diverse strains showed that the global transcriptome of each strain was unique and highly variable. Experimental mouse infection provided new information about immunological parameters of host-pathogen interaction. We exploited the large data set to develop whole-genome sequence-based classifiers that accurately predict clinical antimicrobial resistance for 12 of the 16 antibiotics tested. We conclude that analysis of large, comprehensive, population-based strain samples can assist understanding of the molecular diversity of these organisms and contribute to enhanced translational research.IMPORTANCEKlebsiella pneumoniae causes human infections that are increasingly difficult to treat because many strains are resistant to multiple antibiotics. Clonal group 258 (CG258) organisms have caused outbreaks in health care settings worldwide. Using a comprehensive population-based sample of extended-spectrum beta-lactamase (ESBL)-producing K. pneumoniae strains, we show that a relatively uncommon clonal type, CG307, caused the plurality of ESBL-producing K. pneumoniae infections in our patients. We discovered that CG307 strains have been abundant in Houston for many years. As assessed by experimental mouse infection, CG307 strains were as virulent as pandemic CG258 strains. Our results may portend the emergence of an especially successful clonal group of antibiotic-resistant K. pneumoniae.

Implications of direct amplification for measuring antimicrobial resistance using point-of-care devices

Antimicrobial resistance (AMR) is recognized as a global threat to human health. Rapid detection and characterization of AMR is a critical component of most antibiotic stewardship programs. Methods based on amplification of nucleic acids for detection of AMR are generally faster than culture-based approaches but they still require several hours to more than a day due to the need for transporting the sample to a centralized laboratory, processing of sample, and sometimes DNA purification and concentration. Nucleic acids-based point-of-care (POC) devices are capable of rapidly diagnosing antibiotic-resistant infections which may help in making timely and correct treatment decisions. However, for most POC platforms, sample processing for nucleic acids extraction and purification is also generally required prior to amplification. Direct amplification, an emerging possibility for a number of polymerases, has the potential to eliminate these steps without significantly impacting diagnostic performance. This review summarizes direct amplification methods and their implication for rapid measurement of AMR. Future research directions that may further strengthen the possibility of integrating direct amplification methods with POC devices are also summarized.

Carbapenem-Resistant Acinetobacter baumannii and Enterobacteriaceae in South and Southeast Asia

Carbapenem-resistant Gram-negative bacteria, in particular the Acinetobacter baumannii-calcoaceticus complex and Enterobacteriaceae, are escalating global public health threats. We review the epidemiology and prevalence of these carbapenem-resistant Gram-negative bacteria among countries in South and Southeast Asia, where the rates of resistance are some of the highest in the world. These countries house more than a third of the world's population, and several are also major medical tourism destinations. There are significant data gaps, and the almost universal lack of comprehensive surveillance programs that include molecular epidemiologic testing has made it difficult to understand the origins and extent of the problem in depth. A complex combination of factors such as inappropriate prescription of antibiotics, overstretched health systems, and international travel (including the phenomenon of medical tourism) probably led to the rapid rise and spread of these bacteria in hospitals in South and Southeast Asia. In India, Pakistan, and Vietnam, carbapenem-resistant Enterobacteriaceae have also been found in the environment and community, likely as a consequence of poor environmental hygiene and sanitation. Considerable political will and effort, including from countries outside these regions, are vital in order to reduce the prevalence of such bacteria in South and Southeast Asia and prevent their global spread.

Carbapenem-Resistant Acinetobacter baumannii and Enterobacteriaceae in South and Southeast Asia

Carbapenem-resistant Gram-negative bacteria, in particular the Acinetobacter baumannii-calcoaceticus complex and Enterobacteriaceae, are escalating global public health threats. We review the epidemiology and prevalence of these carbapenem-resistant Gram-negative bacteria among countries in South and Southeast Asia, where the rates of resistance are some of the highest in the world. These countries house more than a third of the world's population, and several are also major medical tourism destinations. There are significant data gaps, and the almost universal lack of comprehensive surveillance programs that include molecular epidemiologic testing has made it difficult to understand the origins and extent of the problem in depth. A complex combination of factors such as inappropriate prescription of antibiotics, overstretched health systems, and international travel (including the phenomenon of medical tourism) probably led to the rapid rise and spread of these bacteria in hospitals in South and Southeast Asia. In India, Pakistan, and Vietnam, carbapenem-resistant Enterobacteriaceae have also been found in the environment and community, likely as a consequence of poor environmental hygiene and sanitation. Considerable political will and effort, including from countries outside these regions, are vital in order to reduce the prevalence of such bacteria in South and Southeast Asia and prevent their global spread.

Detection of Antibiotic Resistance Genes in Source and Drinking Water Samples from a First Nations Community in Canada

Access to safe drinking water is now recognized as a human right by the United Nations. In developed countries like Canada, access to clean water is generally not a matter of concern. However, one in every five First Nations reserves is under a drinking water advisory, often due to unacceptable microbiological quality. In this study, we analyzed source and potable water from a First Nations community for the presence of coliform bacteria as well as various antibiotic resistance genes. Samples, including those from drinking water sources, were found to be positive for various antibiotic resistance genes, namely, ampC, tet(A), mecA, β-lactamase genes (SHV-type, TEM-type, CTX-M-type, OXA-1, and CMY-2-type), and carbapenemase genes (KPC, IMP, VIM, NDM, GES, and OXA-48 genes). Not surprisingly, substantial numbers of total coliforms, including Escherichia coli, were recovered from these samples, and this result was also confirmed using Illumina sequencing of the 16S rRNA gene. These findings deserve further attention, as the presence of coliforms and antibiotic resistance genes potentially puts the health of the community members at risk.

IMPORTANCE

In this study, we highlight the poor microbiological quality of drinking water in a First Nations community in Canada. We examined the coliform load as well as the presence of antibiotic resistance genes in these samples. This study examined the presence of antibiotic-resistant genes in drinking water samples from a First Nations Community in Canada. We believe that our findings are of considerable significance, since the issue of poor water quality in First Nations communities in Canada is often ignored, and our findings will help shed some light on this important issue.

Emergence of carbapenemase-producing urinary isolates at a tertiary care hospital in Dhaka, Bangladesh

OBJECTIVES

A growing incidence of pathogens producing carbapenemases has been observed in many countries including Bangladesh. The present study was carried out to determine the presence of carbapenemase producers among uropathogens.

MATERIALS AND METHODS

A total of 138 Gram-negative uropathogens were isolated and identified by conventional methods and were screened for carbapenemase production using imipenem discs. Phenotypic identification of carbapenemase production was done by the double disc synergy test, combined disc assay, and modified Hodge test. The minimum inhibitory concentration of imipenem was determined by the agar dilution method. Genes encoding blaNDM-1, blaIMP, blaVIM, blaKPC and blaOXA-48/blaOXA-181 were identified by polymerase chain reaction.

RESULTS

Twenty (14.49%) imipenem resistant strains were detected among 138 Gram-negative uro-pathogens. The most common isolates were Escherichia coli and Klebsiella spp. Among 20 imipenem resistant strains, 16 (80%) carbapenemase producers were detected by polymerase chain reaction, 13 (65%) by double disc synergy, 15 (75%) by combined disc assay, and seven (35%) by modified Hodge test. The blaNDM-1 gene was most prevalent (55%), followed by blaOXA-48/OXA-181, blaKPC (20%), blaVIM (15%), and blaIMP (10%). More than one carbapenemase gene was present in nine (45%) of the isolates. The minimum inhibitory concentration of imipenem of the carbapenemase producers ranged from ≥128 μg/mL to 4 μg/mL. Overall, carbapenemase encoding genes were detected in 11.6% (16/138) of the studied Gram-negative uropathogens. All (100%) of the carbapenemase-producing organisms were resistant to all tested antibiotics apart from colistin.

CONCLUSION

The study shows a significant rate of urinary isolates were carbapenemase producers, including a high prevalence of blaNDM-1, in Bangladesh.

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.

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.

Exploring the evidence base for national and regional policy interventions to combat resistance

The effectiveness of existing policies to control antimicrobial resistance is not yet fully understood. A strengthened evidence base is needed to inform effective policy interventions across countries with different income levels and the human health and animal sectors. We examine three policy domains-responsible use, surveillance, and infection prevention and control-and consider which will be the most effective at national and regional levels. Many complexities exist in the implementation of such policies across sectors and in varying political and regulatory environments. Therefore, we make recommendations for policy action, calling for comprehensive policy assessments, using standardised frameworks, of cost-effectiveness and generalisability. Such assessments are especially important in low-income and middle-income countries, and in the animal and environmental sectors. We also advocate a One Health approach that will enable the development of sensitive policies, accommodating the needs of each sector involved, and addressing concerns of specific countries and regions.

Detection and characterization of carbapenemase-producing Enterobacteriaceae in wounded Syrian patients admitted to hospitals in northern Israel

Since 2013, four hospitals in northern Israel have been providing care for Syrian nationals, primarily those wounded in the ongoing civil war. We analyzed carbapenemase-producing Enterobacteriaceae (CPE) isolates obtained from these patients. Isolate identification was performed using the VITEK 2 system. Polymerase chain reaction (PCR) was performed for the presence of bla KPC, bla NDM, and bla OXA-48. Susceptibility testing and genotyping were performed on selected isolates. During the study period, 595 Syrian patients were hospitalized, most of them young men. Thirty-two confirmed CPE isolates were grown from cultures taken from 30 patients. All but five isolates were identified as Klebsiella pneumoniae and Escherichia coli. Nineteen isolates produced NDM and 13 produced OXA-48. Among a further 29 isolates tested, multilocus sequence typing (MLST) showed that ST278 and ST38 were the major sequence types among the NDM-producing K. pneumoniae and OXA-48-producing E. coli isolates, respectively. Most were resistant to all three carbapenems in use in Israel and to gentamicin, but susceptible to colistin and fosfomycin. The source for bacterial acquisition could not be determined; however, some patients admitted to different medical centers were found to carry the same sequence type. CPE containing bla NDM and bla OXA-48 were prevalent among Syrian wounded hospitalized patients in northern Israel. The finding of the same sequence type among patients at different medical centers implies a common, prehospital source for these patients. These findings have implications for public health throughout the region.

Genetic Characterization of Carbapenem-Resistant Enterobacteriaceae and the Spread of Carbapenem-Resistant Klebsiella pneumonia ST340 at a University Hospital in Thailand

Carbapenem-resistant Enterobacteriaceae (CRE) has increasingly spread worldwide in the past decade. The prevalence and characteristics of CRE in Thailand are unknown. In this study, we conducted a 2-year surveillance of CRE among 12,741 clinical isolates of Enterobacteriaceae at the largest university hospital in Thailand with molecular characterization of beta-lactamase (bla) genes, including carbapenemase genes. The CRE prevalence was 1.4%. bla_KPC-13 and bla_IMP-14a were the only carbapenemase genes detected among these CRE isolates. bla_KPC-13 gene was found in a single isolate of Escherichia coli, Enterobacter cloacae and Citrobacter freundii, and bla_IMP-14a was found in four isolates of Klebsiella pneumoniae. Carbapenem-resistant K. pneumoniae (CRKP) isolates were resistant to multiple carbapenems at a higher ratio than other CRE species, and thus were further characterized for resistance phenotypes, bla genotypes and molecular epidemiology. Most CRKP isolates harboured multiple bla genes, especially those related to extended-spectrum beta-lactamases. Seven CRKP isolates were resistant to all tested carbapenems, and showed decreased ompK35 and/or ompK36 porin gene expression. Molecular typing of CRKP based on pulsed-field gel electrophoresis (PFGE) demonstrated several unrelated clones. Multilocus sequence typing (MLST) was partially concordant with PFGE results and revealed that ST340, a member of drug-resistant K. pneumoniae clonal complex 258, was the most predominant clone, followed by ST48, ST11 and ST273. The novel ST1645 was identified from this study. ST340 has neither been shown to be predominated among CRKP from other studies, nor been reported in Thailand. Therefore, it emphases a critical concern to monitor and control the spread of CRKP.

Outbreak of NDM-1-producing Klebsiella pneumoniae causing neonatal infection in a teaching hospital in mainland China

The emergence and spread of bacteria carrying the bla(NDM-1) gene has become a worldwide concern. Here, we report eight cases of Klebsiella pneumoniae with bla(NDM-1) in the neonatal ward of a teaching hospital in mainland China. Multilocus sequence typing showed that seven isolates were clonally related and confirmed them as sequence type 17 (ST17). One isolate belonged to ST433. These findings suggest continuous spread of bla(NDM-1) in mainland China and emphasize the need for intensive surveillance and precautions.

Acquired metallo-β-lactamases and their genetic association with class 1 integrons and ISCR elements in Gram-negative bacteria

ABSTRACT 

Metallo-β-lactamases (MBLs) can hydrolyze almost all β-lactam antibiotics and are resistant to clinically available β-lactamase inhibitors. Numerous types of acquired MBLs have been identified, including IMP, VIM, NDM, SPM, GIM, SIM, DIM, KHM, TMB, FIM and AIM. IMPs and VIMs are the most frequent MBLs and disseminate in members of the family Enterobacteriaceae, Pseudomonas spp. and Acinetobacter spp. Acquired MBL genes are often embedded in integrons, and some are associated with insertion sequence (IS) elements. The class 1 integrons and IS common region (ISCR) elements are usually harbored in transposons and/or plasmids, forming so-called mobile vesicles for horizontal transfer of captured genes between bacteria. Here, we review the MBL superfamily identified in Gram-negative bacteria, with an emphasis on the phylogeny of acquired MBLs and their genetic association with class 1 integrons and IS common region elements.

"Roar" of blaNDM-1 and "silence" of blaOXA-58 co-exist in Acinetobacter pittii

Acinetobacter pittii 44551 was recovered from a patient with gout combined with tuberculosis and was found to harbor the carbapenemase genes bla_NDM-1 and bla_OXA-58 on two different plasmids pNDM-44551 and pOXA58-44551, respectively. pNDM-44551 displayed high self-transferability across multiple bacterial species, while pOXA58-44551 was likely co-transferable with pNDM-44551 into A. baumannii receipts. pNDM-44551 was a close variant of the previously characterized pNDM-BJ01, and the bla_NDM-1 gene cluster was arranged sequentially as orfA, ISAba14, aphA6, ISAba125, bla_NDM-1, ble_MBL, ΔtrpF, dsbC, tnpR, and zeta. pOXA58-44551 was a repAci9-containing plasmid, and bla_OXA-58 was embedded in a 372F-ISAba3-like-bla_OXA-58-ISAba3 structure. The mobile genetic platforms of bla_NDM-1 and bla_OXA-58 herein showed some differences from their previously characterized variants. The production of NDM-1 in strain 44551 contributed the majority to its high resistance to carbapenems, while the bla_OXA-58 stayed silent most likely due to the lack of an upstream promoter to drive its transcription. Increased surveillance of Acinetobacter co-harboring bla_NDM-1 (active) and bla_OXA-58 (either active or silent) is urgently needed.

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.

Characterization of Escherichia coli NDM isolates with decreased susceptibility to aztreonam/avibactam: role of a novel insertion in PBP3

OBJECTIVES

The spread of NDM-1 amongst Enterobacteriaceae has highlighted a significant threat to the clinical management of serious infections. The combination of aztreonam and avibactam, a non-β-lactam β-lactamase inhibitor, may provide a much-needed therapeutic alternative. This combination was potent against most NDM-containing Enterobacteriaceae, although activity was diminished against many Escherichia coli isolates. These E. coli isolates were characterized to elucidate the mechanism of decreased susceptibility to aztreonam/avibactam.

METHODS

MIC determinations were performed using broth microdilution, and whole-genome sequencing was performed to enable sequence-based analyses.

RESULTS

The decreased susceptibility was not due to avibactam being unable to inhibit the serine β-lactamases found in the E. coli isolates. Rather, it was manifested by a four-amino-acid insertion in PBP3. This same insertion was also found in non-NDM-containing E. coli that had reduced susceptibility to aztreonam/avibactam. Construction of an isogenic mutant confirmed that this insertion resulted in decreased susceptibility to aztreonam and several cephalosporins, but had no impact on carbapenem potency. Structural analysis suggests that this insertion will impact the accessibility of the β-lactam drugs to the transpeptidase pocket of PBP3.

CONCLUSIONS

The acquisition of β-lactamases is the predominant mechanism of β-lactam resistance in Enterobacteriaceae. We have demonstrated that small PBP3 changes will affect the susceptibility to a broad range of β-lactams. These changes were identified in multiple MLST lineages of E. coli, and were enriched in NDM-containing isolates. However, they were not present in other key species of Enterobacteriaceae despite significant conservation among the PBP3 proteins.

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.

Biochemical characterization of New Delhi metallo-β-lactamase variants reveals differences in protein stability

Objectives

Metallo-β-lactamase (MBL)-based resistance is a threat to the use of most β-lactam antibiotics. Multiple variants of the New Delhi MBL (NDM) have recently been reported. Previous reports indicate that the substitutions affect NDM activity despite being located outside the active site. This study compares the biochemical properties of seven clinically reported NDM variants.

Methods

NDM variants were generated by site-directed mutagenesis; recombinant proteins were purified to near homogeneity. Thermal stability and secondary structures of the variants were investigated using differential scanning fluorimetry and circular dichroism; kinetic parameters and MIC values were investigated for representative carbapenem, cephalosporin and penicillin substrates.

Results

The substitutions did not affect the overall folds of the NDM variants, within limits of detection; however, differences in thermal stabilities were observed. NDM-8 was the most stable variant with a melting temperature of 72°C compared with 60°C for NDM-1. In contrast to some previous studies, k_cat/K_M values were similar for carbapenem and penicillin substrates for NDM variants, but differences in kinetics were observed for cephalosporin substrates. Apparent substrate inhibition was observed with nitrocefin for variants containing the M154L substitution. In all cases, cefoxitin and ceftazidime were poorly hydrolysed with k_cat/K_M values <1 s⁻¹ μM⁻¹.

Conclusions

These results do not define major differences in the catalytic efficiencies of the studied NDM variants and carbapenem or penicillin substrates. Differences in the kinetics of cephalosporin hydrolysis were observed. The results do reveal that the clinically observed substitutions can make substantial differences in thermodynamic stability, suggesting that this may be a factor in MBL evolution.

Phenotypic and molecular characteristics of carbapenem-resistant Enterobacteriaceae in a health care system in Los Angeles, California, from 2011 to 2013

Carbapenem-resistant Enterobacteriaceae (CRE) are a concern for health care in the United States but remain relatively uncommon in California. We describe the phenotype, clonality, and carbapenemase-encoding genes present in CRE isolated from patients at a Californian tertiary health care system. CRE for this study were identified by evaluating the antibiograms of Enterobacteriaceae isolated in the UCLA Health System from 2011 to 2013 for isolates that were not susceptible to meropenem and/or imipenem. The identification of these isolates was subsequently confirmed by matrix-associated laser desorption ionization-time of flight, and broth microdilution tests were repeated to confirm the CRE phenotype. Real-time PCR for bla(KPC), bla(SME), bla(IMP), bla(NDM-1), bla(VIM), and bla(OXA-48) was performed. Clonality was assessed by repetitive sequence-based PCR (repPCR) and multilocus sequence typing (MLST). Of 15,839 nonduplicate clinical Enterobacteriaceae isolates, 115 (0.73%) met the study definition for CRE. This number increased from 0.5% (44/8165) in the first half of the study to 0.9% (71/7674) in the second (P = 0.004). The most common CRE species were Klebsiella pneumoniae, Enterobacter aerogenes, and Escherichia coli. A carbapenemase-encoding gene was found in 81.7% (94/115) of CRE and included bla(KPC) (78.3%), bla(NDM-1) (0.9%), and bla(SME) (2.6%). The majority of bla(KPC) genes were in K. pneumoniae isolates, which fell into 14 clonal groups on typing. bla(KPC) was identified in more than one species of CRE cultured from the same patient in four cases. Three bla(SME)-carrying Serratia marcescens isolates and one bla(NDM-1) carrying Providencia rettgeri isolate were detected. CRE are increasing in California, and carbapenemases, particularly KPC, are a common mechanism for carbapenem resistance in this region.

Genomic and transcriptomic analysis of NDM-1 Klebsiella pneumoniae in spaceflight reveal mechanisms underlying environmental adaptability

The emergence and rapid spread of New Delhi Metallo-beta-lactamase-1 (NDM-1)-producing Klebsiella pneumoniae strains has caused a great concern worldwide. To better understand the mechanisms underlying environmental adaptation of those highly drug-resistant K. pneumoniae strains, we took advantage of the China's Shenzhou 10 spacecraft mission to conduct comparative genomic and transcriptomic analysis of a NDM-1 K. pneumoniae strain (ATCC BAA-2146) being cultivated under different conditions. The samples were recovered from semisolid medium placed on the ground (D strain), in simulated space condition (M strain), or in Shenzhou 10 spacecraft (T strain) for analysis. Our data revealed multiple variations underlying pathogen adaptation into different environments in terms of changes in morphology, H₂O₂ tolerance and biofilm formation ability, genomic stability and regulation of metabolic pathways. Additionally, we found a few non-coding RNAs to be differentially regulated. The results are helpful for better understanding the adaptive mechanisms of drug-resistant bacterial pathogens.