Klebsiella pneumoniae Carbapenemase Producers in South Korea between 2013 and 2015

Differential mucosal tropism and dissemination of classical and hypervirulent Klebsiella pneumoniae infection

Klebsiella pneumoniae (Kp) infection is an important healthcare concern. The ST258 classical (c)Kp strain is dominant in hospital-acquired infections in North America and Europe, while ST23 hypervirulent (hv)Kp prevails in community-acquired infections in Asia. This study aimed to develop symptomatic mucosal infection models in mice that mirror natural infections in humans to gain a deeper understanding of Kp mucosal pathogenesis. We showed that cKp replicates in the nasal cavity instead of the lungs, and this early infection event is crucial for the establishment of chronic colonization in the cecum and colon. In contrast, hvKp replicates directly in the lungs to lethal bacterial load, and early infection of esophagus supported downstream transient colonization in the ileum and cecum. Here, we have developed an in vivo model that illuminates how differences in Kp tropism are responsible for virulence and disease phenotype in cKp and hvKp, providing the basis for further mechanistic study.

Phytochemical profiling, in vitro analysis for anti-inflammatory, immunomodulatory activities, structural elucidation and in silico evaluation of potential selective COX-2 and TNF-α inhibitor from Hydrilla verticillata (L.f.) Royle

Hydrilla verticillata (L.f.) Royle is a perennial aquatic plant, which exhibits nutritional as well as therapeutic properties. The present study has been carried out to evaluate anti-inflammatory and immunomodulatory activities along with in silico evaluation of potential selective COX-2 and TNF-α inhibitors from methanolic extract of H. verticillata (L.f.) Royle. The potential therapeutic compounds have been identified by high-resolution GC-MS analysis. Its capacity to inhibit inflammatory responses using lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophage cells has been explored. The anti-inflammatory properties of the plant extract were investigated by inhibiting inducible nitric oxide (NO) synthase and reduced NO generation driven by LPS on stimulated RAW 264.7 macrophage cells. Further investigation for the underlying molecular mechanism of the anti-inflammatory activity of plant extract has been carried out by molecular docking and molecular dynamics simulation approaches with COX-2 and TNF-α inhibitors ability against the most potent phytocompound phytol from the plant extract. To evaluate whether the extract causes any toxicity, the cytotoxicity test has been carried out with the Human embryonic kidney cell line (Hek-293), Mouse fibroblast (L929), human mesenchyme stem cells (hMSCs) and human breast epithelial cell line (MCF-10a). Ultimately, our findings suggest that the plant extract have great potential to reduce inflammation without causing any toxicity to normal cell.Communicated by Ramaswamy H. Sarma.

Ehretia Species Phytoconstituents as Potential Lead Compounds against Klebsiella pneumoniae Carbapenemase: A Computational Approach

The evolution of antibiotic-resistant carbapenemase has negatively impacted the management of critical healthcare-associated infections. K. pneumoniae carbapenemase-2- (KPC-2-) expressing bacteria have developed resistance to conventional therapeutic options, including those used as a last resort for life-threatening diseases. In this study, Ehretia species phytoconstituents were screened for their potential to inhibit KPC-2 protein using in silico approaches. Molecular docking was used to identify strong KPC-2 protein binding phytoconstituents retrieved from the literature. The best-docked conformation of the ligands was selected based on their glide energy and binding interactions. To determine their binding free energies, these hit compounds were subjected to molecular mechanics with generalized born and surface area (MM-GBSA) in the PRIME module. Pharmacological assessments of the ligands were performed to evaluate their drug-likeness. Molecular dynamic (MD) simulations were used to analyze the conformational stability of the selected druglike compounds within the active site of the KPC-2 protein. Overall, a total of 69 phytoconstituents were compiled from the literature. Fourteen of these compounds exhibited a stronger binding affinity for the protein target than the reference drugs. Four of these top hit compounds, DB09, DB12, DB28, and DB66, revealed the highest efficacy in terms of drug-likeness properties. The MD simulation established that among the druglike compounds, DB66 attained stable conformations after 150 ns simulation in the active site of the protein. We concluded that DB66 from Ehretia species could play a significant role in therapeutic efforts against KPC-2-expressing bacteria.

An IncN-ST7 epidemic plasmid mediates the dissemination of carbapenem-resistant Klebsiella pneumoniae in a neonatal intensive care unit in China over 10 years

OBJECTIVES

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has widely disseminated globally, but its epidemiological characterization and clinical significance in paediatric patients are not well understood. In this study, we aimed to trace the dissemination dynamics of CRKP in the neonatal intensive care unit (NICU) of a tertiary hospital over a 10-y period.

METHODS

We collected 67 non-duplicate K. pneumoniae species complex isolates from the NICU with patient metadata during 2009-2018. Antimicrobial susceptibility was determined by the agar or broth microdilution method. Risk factors for CRKP-positive patients were identified by univariate and multivariate analysis. Genetic characterization was dissected by whole-genome sequencing. Plasmid transmissibility, stability, and fitness were assessed.

RESULTS

Thirty-four of 67 isolates (50.75%) were identified as CRKP. Premature rupture of membranes, gestational age, and invasive procedures are independent risk factors for CRKP-positive patients. The annual isolation rate of CRKP varied between 0% and 88.9%, and multiple clonal replacements were observed during the study period, which could be largely due to the division of the NICU. All but one CRKP produced IMP-4 carbapenemase, which was encoded by an IncN-ST7 epidemic plasmid, suggesting that the IncN-ST7 plasmid mediated the CRKP dissemination in the NICU over 10 y. The same plasmid was found in several CRKP isolates from adult patients, of which two ST17 isolates from the neurosurgery department shared a high homology with the ST17 isolates from the NICU, indicating possible cross-departmental transmission.

CONCLUSION

Our study highlights the urgent need for infection control measures targeting high-risk plasmids like IncN-ST7.

Intensive Care Unit Sluice Room Sinks as Reservoirs and Sources of Potential Transmission of Carbapenem-Resistant Bacteria in a South African Tertiary Care Hospital

Purpose

Carbapenem-resistant bacteria (CRB) pose a major health risk to patients in intensive care units (ICU) across African hospitals. There are hardly any data about the role of hospital sinks as reservoirs of CRB in resource-poor African settings. Furthermore, the specific within-sink location of the highest concentration of pathogens and the role of splash back as a transmission mechanism remains poorly clarified.

Methods

We swabbed ICU sluice room sinks in a tertiary hospital in Cape Town, South Africa. Swabs were taken from four different parts of the sluice room sinks (tap-opening, trap, below the trap, and u-bend). Dilutions were prepared and plated on carbapenem-infused agar. Colonies were identified and drug resistance profiles were determined using a biochemical analyser. To evaluate the potential transmission from the sink, similar plates were placed at fixed distances from the sink when the tap was turned on and off.

Results

CRB were isolated from the trap, water interface below the trap, and the u-bend (the latter harboured the highest density of CRB species). Five CRB, resistant to at least 7 antibiotic classes, were isolated including Pseudomonas, Klebsiella, Citrobacter, Serratia, and Providencia. CRB could be cultured from droplets that fell on agar-containing plates placed at a varying distance from the trap.

Conclusion

There is a higher density of CRB in the u-bend of ICU sluice room sinks which can act as a potential source of transmission. The data inform targeted CRB transmission-interruption strategies in resource-poor settings.

Characteristics of Environmental Klebsiella pneumoniae and Klebsiella oxytoca Bacteriophages and Their Therapeutic Applications

In recent years, multidrug-resistant (MDR) strains of Klebsiella pneumoniae have spread globally, being responsible for the occurrence and severity of nosocomial infections. The NDM-1-kp, VIM-1 carbapenemase-producing isolates as well as extended-spectrum beta lactamase-producing (ESBL) isolates along with Klebsiella oxytoca strains have become emerging pathogens. Due to the growing problem of antibiotic resistance, bacteriophage therapy may be a potential alternative to combat such multidrug-resistant Klebsiella strains. Here, we present the results of a long-term study on the isolation and biology of bacteriophages active against K. pneumoniae, as well as K. oxytoca strains. We evaluated biological properties, morphology, host specificity, lytic spectrum and sensitivity of these phages to chemical agents along with their life cycle parameters such as adsorption, latent period, and burst size. Phages designated by us, vB_KpnM-52N (Kpn52N) and VB_KpnM-53N (Kpn53N), demonstrated relatively broad lytic spectra among tested Klebsiella strains, high burst size, adsorption rates and stability, which makes them promising candidates for therapeutic purposes. We also examined selected Klebsiella phages from our historical collection. Notably, one phage isolated nearly 60 years ago was successfully used in purulent cerebrospinal meningitis in a new-born and has maintained lytic activity to this day. Genomic sequences of selected phages were determined and analyzed. The phages of the sequenced genomes belong to the Slopekvirus and Jiaodavirus genus, a group of phages related to T4 at the family level. They share several features of T4 making them suitable for antibacterial therapies: the obligatorily lytic lifestyle, a lack of homologs of known virulence or antibiotic resistance genes, and a battery of enzymes degrading host DNA at infection.

Comparison of Virulence between Two Main Clones (ST11 and ST307) of Klebsiella pneumoniae Isolates from South Korea

In this study, we investigate the characteristics of two main clones of carbapenemase-producing Klebsiella pneumoniae isolates from South Korea, ST11 and ST307, including carbapenem-susceptible isolates. Antibiotic susceptibility, serotype or wzi allelic type, the presence of virulence genes, and virulence with respect to serum resistance and macrophage internalization were determined for ST11 and ST307 isolates. ST11 isolates had a wide range of characteristics, including serotype and virulence, compared with those of homogeneous ST307 isolates. The wzi14 or K14 type had higher virulence than that of other serotypes among the ST11 isolates, and the homogeneous ST307 isolates showed similar virulence level as that of the wzi14-type ST11 isolates. Our data suggest that it is necessary to monitor not only the introduction and spread of a specific clone, but also its detailed serotype.

Association of Carbapenemase-Producing Enterobacterales Detected in Stream and Clinical Samples

Background

The spread of carbapenem-resistant Enterobacterales (CRE) strains has caused treatment failure and is a worldwide threat to public health. However, there are limited reports on the prevalence of carbapenemase-producing Enterobacterales (CPE) in aquatic environments and its association with clinical isolates. This study aimed to investigate the prevalence of CPE in a stream environment and its genetic relationship with clinical isolates in Korea.

Methods

A total of 4,582 water samples were collected from 94 streams. Multiplex PCR and sequencing were used to detect and identify six carbapenemase genes. Multi-locus sequence typing (MLST) was performed to investigate the genetic relatedness between the environmental strains and clinical isolates.

Results

A total of 133 CRE strains were isolated from the streams. Klebsiella pneumoniae was the most common CRE (45.9%), followed by Enterobacter cloacae complex (29.3%), Escherichia coli (13.5%), Raoultella ornithinolytica (5.3%), and Citrobacter freundii (2.3%). Ninety (67.7%) isolates carried carbapenemase genes. K. pneumoniae carbapenemase-2 (36.7%) and New Delhi metallo-β-lactamase-5 (32.2%) were the common carbapenemases detected. Sequence type (ST)307 and ST11 K. pneumoniae strains harboring the bla_KPC-2 gene were the most prevalent in stream and patient samples.

Conclusion

CPE was highly prevalent in streams and closely related to the isolates obtained from patients. Therefore, continuous monitoring of stream environments is required to control the spread of carbapenem resistance.

Whole genome sequencing of Klebsiella pneumoniae clinical isolates sequence type 627 isolated from Egyptian patients

Klebsiella pneumoniae is considered a threat to public health especially due to multidrug resistance emergence. It is largely oligoclonal based on multi-locus sequence typing (MLST); in Egypt, ST 627 was recently detected. Despites the global dissemination of this ST, there is still paucity of information about it. Herein, we used 4 K. pneumoniae ST627 for whole genome sequencing utilizing an Illumina MiSeq platform. Genome sequences were examined for resistance and virulence determinants, capsular types, plasmids, insertion sequences, phage regions, and Clustered Regularly Interspaced Palindromic Repeats (CRISPR) regions using bioinformatic analysis. The molecular characterization revealed 15 and 65 antimicrobial resistance and virulence genes, respectively. Resistance genes such as tet(D), aph(3’’)-Ib, aph(6)-Id, blaTEM-234, fosA, and fosA6; were mainly responsible for tetracycline, aminoglycoside, and fosfomycin resistance; respectively. The capsular typing revealed that the four strains are KL-24 and O1v1. One plasmid was found in all samples known as pC17KP0052-1 and another plasmid with accession no. NZ_CP032191.1 was found only in K90. IncFIB(K) and IncFII(K) are two replicons found in all samples, while ColRNAI replicon was found only in K90. Entero P88, Salmon SEN5, and Klebsi phiKO2 intact phage regions were identified. All samples harbored CRISPR arrays including CRISPR1 and CRISPR2. Our results shed light on critical tasks of mobile genetic elements in ST 627 in antibiotic resistance spreading.

Genetic Characterization of Carbapenem-Resistant Klebsiella spp. from Municipal and Slaughterhouse Wastewater

Currently, human and veterinary medicine are threatened worldwide by an increasing resistance to carbapenems, particularly present in opportunistic Enterobacterales pathogens (e.g., Klebsiella spp.). However, there is a lack of comprehensive and comparable data on their occurrence in wastewater, as well as on the phenotypic and genotypic characteristics for various countries including Germany. Thus, this study aims to characterize carbapenem-resistant Klebsiella spp. isolated from municipal wastewater treatment plants (mWWTPs) and their receiving water bodies, as well as from wastewater and process waters from poultry and pig slaughterhouses. After isolation using selective media and determination of carbapenem (i.e., ertapenem) resistance using broth microdilution to apply epidemiological breakpoints, the selected isolates (n = 30) were subjected to WGS. The vast majority of the isolates (80.0%) originated from the mWWTPs and their receiving water bodies. In addition to ertapenem, Klebsiella spp. isolates exhibited resistance to meropenem (40.0%) and imipenem (16.7%), as well as to piperacillin-tazobactam (50.0%) and ceftolozan-tazobactam (50.0%). A high diversity of antibiotic-resistance genes (n = 68), in particular those encoding β-lactamases, was revealed. However, with the exception of bla_GES-5-like, no acquired carbapenemase-resistance genes were detected. Virulence factors such as siderophores (e.g., enterobactin) and fimbriae type 1 were present in almost all isolates. A wide genetic diversity was indicated by assigning 66.7% of the isolates to 12 different sequence types (STs), including clinically relevant ones (e.g., ST16, ST252, ST219, ST268, ST307, ST789, ST873, and ST2459). Our study provides information on the occurrence of carbapenem-resistant, ESBL-producing Klebsiella spp., which is of clinical importance in wastewater and surface water in Germany. These findings indicate their possible dissemination in the environment and the potential risk of colonization and/or infection of humans, livestock and wildlife associated with exposure to contaminated water sources.

NDM-5-producing carbapenem-resistant Klebsiella pneumoniae of sequence type 789 emerged as a threat for neonates: a multi-center genome-based study

Klebsiella pneumoniae is a major human pathogen and carbapenems are the main agents of choice to treat severe K. pneumoniae infections but carbapenem-resistant K. pneumoniae (CRKP) has emerged as a major global problem. Novel high-risk CRKP lineages are continuously emerging but those associated with neonatal infections are understudied. In this study, we identified a common CRKP lineage carrying bla_NDM-5 carbapenemase-encoding gene belonging to sequence type 789 (ST789) based on analyses of genome sequences of 28 isolates including 27 clinical isolates from neonates and one from sink recovered in 2019 from multiple hospitals in Chengdu, southwest China. Isolates of this lineage caused various infections (pneumonia, bloodstream infection, and urinary tract infection) in neonates and had circulated in and been transmitted between neonatal ICUs of multiple local hospitals for several years. Its emergency was likely due to clonal expansion after acquiring a bla_NDM-5-carrying self-transmissible IncX3 plasmid. Genome clock analysis dated the emergence of this lineage in December 2016 (95% confidence intervals, January 2015 to December 2017). The above findings highlight that CRKP lineages in neonates and adults may be different. This ST789 bla_NDM-5-carrying CRKP lineage represents a new, emerging, threat for neonates and warrants rigorous monitoring.

Prevalence and antimicrobial resistance of Klebsiella species isolated from clinically ill companion animals

Background

Klebsiella spp. is an important conditional pathogen in humans and animals. However, due to the indiscriminate use of antibiotics, the incidence of antimicrobial resistance has increased.

Objectives

The purpose of this study was to investigate antimicrobial resistance in strains of Klebsiella strains and the phylogenetic relatedness of extended-spectrum cephalosporin (ESC)-resistance among Klebsiella strains isolated from clinically ill companion animals.

Methods

A total of 336 clinical specimens were collected from animal hospitals. Identification of Klebsiella species, determination of minimum inhibitory concentrations, detection of ESC resistance genes, polymerase chain reaction-based replicon typing of plasmids by conjugation, and multilocus sequence typing were performed.

Results

Forty-three Klebsiella strains were isolated and, subsequently, 28 were identified as K. pneumoniae, 11 as K. oxytoca, and 4 as K. aerogenes. Eleven strains were isolated from feces, followed by 10 from ear, 7 from the nasal cavity, 6 from urine, 5 from genitals, and 4 from skin. Klebsiella isolates showed more than 40% resistance to penicillin, cephalosporin, fluoroquinolone, and aminoglycoside. ESCresistance genes, CTX-M groups (CTX-M-3, CTX-M-15, and CTX-M-65), and AmpC (CMY-2 and DHA-1) were most common in the K. pneumoniae strains. Some K. pneumoniae carrying CTX-M or AmpC were transferred via IncFII plasmids. Two sequence types, ST709 and ST307, from K. pneumoniae were most common.

Conclusions

In conclusion, this is the first report on the prevalence, ESCresistance genotypes, and sequence types of Klebsiella strains isolated from clinically ill companion animals. The combination of infectious diseases and antimicrobial resistance by Klebsiella in companion animals suggest that, in clinical veterinary, antibiotic selection should be made carefully and in conjunction with the disease diagnosis.

Two Distinct Genotypes of KPC-2-Producing Klebsiella pneumoniae Isolates from South Korea

In this study, we investigated the characteristics of KPC-2-producing Klebsiella pneumoniae (KP-Kp) isolates from a hospital in South Korea. Among the 37 KP-Kp isolates, two main clones were identified-ST11 and ST307. ST11 isolates showed higher minimum inhibitory concentrations for carbapenems than ST307 isolates. All ST307 isolates were resistant to gentamicin and trimethoprim-sulfamethoxazole, but ST11 isolates were not. However, most tigecycline-resistant or colistin-resistant isolates belonged to ST11. The two KP-Kp clones showed different combinations of wzi and K serotypes. Plasmids from ST11 KP-Kp isolates exhibited diverse incompatibility types. Serum resistance and macrophage infection assays indicated that ST11 may be more virulent than ST307. The changes in the main clones of KP-Kp isolates over time as well as the different characteristics of these clones, including virulence, suggest the need for their continuous monitoring.

Multidrug-resistant mcr-1 gene-positive Klebsiella pneumoniae ST307 causing urinary tract infection in a cat

RESUMO

The Klebsiella pneumoniae (K. pneumoniae) bacterium is responsible for many opportunistic infections such as sepsis, and a multidrug-resistant (MDR) clone sequence type (ST) 307 has recently begun to spread. The objective of this study was to report the first occurrence of this virulent genotype, which was found in the context of a urinary infection in a domestic feline in Brazil. The K. pneumoniae isolate was identified from the urine of a 6-month-old male crossbreed cat using 16S rRNA sequencing. It was then subjected to antimicrobial susceptibility testing, followed by multilocus sequence typing analysis, and PCR detection of virulence and resistance genes. The antimicrobial susceptibility profile demonstrated that the isolate was MDR and associated with the presence of the colistin resistance gene (mcr-1). Genotyping allowed us to classify the isolate as K. pneumoniae ST307 with the presence of wabG, uge, and entB genes. MDR K. pneumoniae is important in human and veterinary medicine because it causes many types of infections. Clonal propagation of virulent or MDR genotypes such as K. pneumoniae ST307 is a global concern. This report of ST307 isolation from a urine sample in a domestic feline is the first in Brazil.

Handwashing Sink Contamination and Carbapenem-resistant Klebsiella Infection in the Intensive Care Unit: A Prospective Multicenter Study

BACKGROUND

Handwashing sinks can become contaminated by carbapenem-resistant Klebsiella (CRK), including carbapenem-resistant Klebsiella pneumoniae (CRKP) and carbapenem-resistant Klebsiella oxytoca (CRKO), but whether they are major sources of CRK infections remains unknown.

METHODS

We performed a prospective multicenter study in 16 intensive care units (ICUs) (9 general and 7 neonatal) at 11 hospitals. All sinks at these locations were sampled to screen CRK. All CRK clinical isolates recovered between 2 weeks before and 3 months after sampling in ICUs with CRK-positive sinks or other participating ICUs at the same hospital were collected. Whole-genome sequencing of all isolates was performed. Isolates of the same sequence type (ST) were assigned to clones by calling single-nucleotide polymorphisms.

RESULTS

Among 158 sinks sampled, 6 CRKP and 6 CRKO were recovered from 12 sinks in 7 ICUs, corresponding to a 7.6% CRK contamination rate. Twenty-eight clinical isolates were collected, and all were CRKP. The 34 CRKP isolates belonged to 7 STs, including ST789 (n = 14, all had blaNDM-5); ST11 (n = 12, 5 belonged to KL64 and 7 to KL47, all had blaKPC-2); ST709 (n = 4, all had blaNDM-5); and ST16, ST20, ST1027, and ST2407 (n = 1 each). One particular ST789 clone caused an outbreak and contaminated a sink. ST11_KL47 sink isolates were likely the source of a cluster of clinical isolates. Two ST11_KL64 isolates belonged to a common clone but were from 2 hospitals.

CONCLUSIONS

Contaminated sinks were not the major source of CRK in our local settings. ST789 blaNDM-5-carrying CRKP might represent an emerging lineage causing neonatal infections.

Mobile Carbapenemase Genes in Pseudomonas aeruginosa

Carbapenem-resistant Pseudomonas aeruginosa is one of the major concerns in clinical settings impelling a great challenge to antimicrobial therapy for patients with infections caused by the pathogen. While membrane permeability, together with derepression of the intrinsic beta-lactamase gene, is the global prevailing mechanism of carbapenem resistance in P. aeruginosa, the acquired genes for carbapenemases need special attention because horizontal gene transfer through mobile genetic elements, such as integrons, transposons, plasmids, and integrative and conjugative elements, could accelerate the dissemination of the carbapenem-resistant P. aeruginosa. This review aimed to illustrate epidemiologically the carbapenem resistance in P. aeruginosa, including the resistance rates worldwide and the carbapenemase-encoding genes along with the mobile genetic elements responsible for the horizontal dissemination of the drug resistance determinants. Moreover, the modular mobile elements including the carbapenemase-encoding gene, also known as the P. aeruginosa resistance islands, are scrutinized mostly for their structures.

Vertical and horizontal dissemination of an IncC plasmid harbouring rmtB 16S rRNA methylase gene, conferring resistance to plazomicin, among invasive ST258 and ST16 KPC-producing Klebsiella pneumoniae

OBJECTIVES

Carbapenem resistance in Klebsiella pneumoniae is a major clinical challenge. Aminoglycosides remain an important asset in the current therapeutic arsenal to treat these infections. We examined aminoglycoside resistance phenotypes and genomics in a collection of 100 invasive KPC-producing K. pneumoniae isolates sequentially collected in a Brazilian tertiary hospital between 2014 and 2016.

METHODS

Aminoglycoside susceptibility testing was performed. We used a combined long-read (MinION) and short-read (Illumina) whole-genome sequencing strategy to provide a genomic picture of aminoglycoside resistance genes, with particular emphasis on 16S rRNA methyltransferases and related plasmids.

RESULTS

68% of the strains were resistant to gentamicin and 42% to amikacin, with 35% resistant to both of these commonly used aminoglycosides. We identified the 16S rRNA methyltransferase gene rmtB in 30% of these isolates: 97% (29/30) belonged to sequence type 258 (ST258) and a single isolate to the emergent ST16 clone. In ST258 and ST16 the rmtB gene was located on large IncC plasmids of 177 kb and 174 kb, respectively, highly similar to a plasmid previously identified in Proteus mirabilis in the same hospital. Moreover, 99% of the isolates remained susceptible to the veterinary-approved drug apramycin, currently under clinical development for human medicine.

CONCLUSION

Such findings in geographically and temporally related isolates suggest a combination of vertical clonal spread as well as horizontal interspecies and intraspecies plasmid transfer. This broad rmtB dissemination in an endemic setting for KPC-producing clones is worrisome since it provides resistance to most clinically available aminoglycosides, including the novel aminoglycoside-modifying enzyme-resistant plazomicin.

Molecular and Epidemiological Characteristics of Carbapenemase-Producing Klebsiella pneumoniae Clinical Isolates in Japan

Carbapenems serve as a last resort for the clinical treatment of multidrug-resistant infections. Therefore, the rapid spread of carbapenemase-producing strains represents a serious public health threat, further limiting antibiotic choices. The current findings of hypervirulent carbapenemase-producing Klebsiella pneumoniae clinical isolates in Japan demonstrate the potential broad spread and transfer of these genes, necessitating close surveillance.

Carbapenemase-producing Enterobacteriaceae represent a serious public health threat worldwide. Carbapenemase genes, harbored on a transferable plasmid, have been isolated globally with distinct geographical features. Klebsiella pneumoniae, included in Enterobacteriaceae, also produces carbapenemase and often shows hypervirulence. Overlapping carbapenem resistance and hypervirulence in K. pneumoniae have been reported, but such strains have not yet been found in Japan. Here, we screened 104 carbapenemase-producing K. pneumoniae isolates collected from 37 hospitals and outpatient clinics in Japan between September 2014 and July 2015. PCR and DNA sequencing demonstrated IMP-1 in 21 isolates and IMP-6 in 83 isolates, 77 of which coharbored CTX-M-2. Most of the isolates showed low MICs toward imipenem and meropenem but high MICs toward penicillin and cephalosporins. Conjugation experiments with an Escherichia coli J53 recipient showed that most of the plasmids in IMP-6 producers were transferable, whereas only one-half of the plasmids in IMP-1 producers were transferable. PCR-based replicon typing and multiplex PCR identified five isolates belonging to the CG258 non-tonB79 cluster and no isolate belonging to the CG258-tonB79 cluster or sequence type 307 (ST307). Four K1-ST23 isolates, 10 K2-ST65 isolates, and 7 K2-ST86 isolates were detected that harbored virulence genes. The resistance genes in 85 isolates were transferable, but the virulence genes were not transferred. These results demonstrate the acquisition of IMP-type carbapenemase genes and CTX-M-type genes among hypervirulence isolates in Japan, warranting further attention and countermeasures. In this study, we have determined the molecular characteristics and epidemiology of IMP-6 producers that coharbored various CTX-M genes in Japan.

IMPORTANCE Carbapenems serve as a last resort for the clinical treatment of multidrug-resistant infections. Therefore, the rapid spread of carbapenemase-producing strains represents a serious public health threat, further limiting antibiotic choices. The current findings of hypervirulent carbapenemase-producing Klebsiella pneumoniae clinical isolates in Japan demonstrate the potential broad spread and transfer of these genes, necessitating close surveillance.

A Novel KPC Variant KPC-55 in Klebsiella pneumoniae ST307 of Reinforced Meropenem-Hydrolyzing Activity

A novel Klebsiella pneumoniae carbapenemase (KPC) variant, KPC-55, produced by a K. pneumoniae ST307 strain was characterized. K. pneumoniae strain BS407 was recovered from an active surveillance rectal swab of a patient newly admitted to a general hospital in Busan, South Korea. Carbapenemase production was confirmed by the modified Hodge test, and the MICs of β-lactams were determined by the broth microdilution method. The whole genome was sequenced. Cloning and expression of the bla_KPC–55 gene in Escherichia coli and MIC determination were performed. The enzyme KPC-55 was used for kinetic assays against β-lactams and compared with the KPC-2 enzyme. The new allele of the bla_KPC gene had a T794A alteration compared to the bla_KPC–2 gene, resulting in the amino acid substitution Y264N in the middle of the β9-sheet. Compared to the KPC-2-producing strain, the KPC-55-producing strain exhibited a lower level of resistance to most β-lactam drugs tested, however, the KPC-55 enzyme catalyzed aztreonam and meropenem at an increased efficiency compared to the catalytic activity of KPC-2. KPC subtypes could have varied phenotypes due to alterations in amino acid sequences, and such an unexpected resistance phenotype emphasizes the importance of detailed characterizations for the carbapenemase-producing Enterobacterales.

Beneficial Chromosomal Integration of the Genes for CTX-M Extended-Spectrum β-Lactamase in Klebsiella pneumoniae for Stable Propagation

Dominant F-type plasmids harboring the gene have been pointed out to be responsible for the dissemination of the CTX-M extended-spectrum-β-lactamase (ESBL)-producing K. pneumoniae. Recently, the emergence of K. pneumoniae isolates with the bla_CTX-M gene in their chromosomes has been reported occasionally worldwide. Such a chromosomal location of the resistance gene could be beneficial for stable propagation, as was the Acinetobacter baumannii ST191 harboring chromosomal bla_OXA-23 that is endemic to South Korea. Through the present study, particular clones were identified as having built-in resistance genes in their chromosomes, and the chromosomal integration events were tracked by assessing their genomes. The cefotaxime-resistant K. pneumoniae clones of this study were particularized as results of the fastidiousness for plasmids to acquire the bla_CTX-M gene for securing the diversity and of the chromosomal addiction of the bla_CTX-M gene for ensuring propagation.

The acquired CTX-M-type extended-spectrum-β-lactamase (ESBL)-producing Enterobacterales are of great concern in clinical settings because they limit therapeutic options for patients infected by the pathogens. An intriguing clonality of CTX-M ESBL-producing Klebsiella pneumoniae blood isolates was observed from a national cohort study, and comparative genomics were assessed for the 115 K. pneumoniae blood isolates carrying the bla_CTX-M gene. The plasmid preference of particular clones of a sequence type (ST) was assessed by liquid mating. A quarter of the bla_CTX-M gene-carrying K. pneumoniae blood isolates harbor the gene in their chromosome, and most of those with the built-in bla_CTX-M gene belonged either to ST307 or ST48. Notably, all 16 K. pneumoniae ST48 isolates harbored two copies of the bla_CTX-M-15 gene in the chromosome. The chromosomal integration of the bla_CTX-M-15 gene was mostly derived from the ISEcp1-targeting 5-bp AT-rich locus in the chromosome. The IS26-mediated chromosomal integration occurred when the upstream ISEcp1 from the bla_CTX-M gene was truncated, targeting the anchor IS26 copy in the chromosome. Higher transfer efficiency of the bla_CTX-M-15 gene-carrying FIA:R plasmid was observed in ST17 than that of the bla_CTX-M-14 gene-carrying FIB:FII plasmid. The transfer efficiency of the plasmid differed by isolate among the ST307 members. The K. pneumoniae clones ST307 and ST48 harboring the bla_CTX-M-15 gene in the chromosome were able to disseminate stably in clinical settings regardless of the environmental pressure, and the current population of K. pneumoniae blood isolates was constructed. Further follow-up is needed for the epidemiology of this antimicrobial resistance.

IMPORTANCE Dominant F-type plasmids harboring the gene have been pointed out to be responsible for the dissemination of the CTX-M extended-spectrum-β-lactamase (ESBL)-producing K. pneumoniae. Recently, the emergence of K. pneumoniae isolates with the bla_CTX-M gene in their chromosomes has been reported occasionally worldwide. Such a chromosomal location of the resistance gene could be beneficial for stable propagation, as was the Acinetobacter baumannii ST191 harboring chromosomal bla_OXA-23 that is endemic to South Korea. Through the present study, particular clones were identified as having built-in resistance genes in their chromosomes, and the chromosomal integration events were tracked by assessing their genomes. The cefotaxime-resistant K. pneumoniae clones of this study were particularized as results of the fastidiousness for plasmids to acquire the bla_CTX-M gene for securing the diversity and of the chromosomal addiction of the bla_CTX-M gene for ensuring propagation.

Virulence evolution, molecular mechanisms of resistance and prevalence of ST11 carbapenem-resistant Klebsiella pneumoniae in China: A review over the last 10 years

Sequence type 11 (ST11) carbapenem-resistant Klebsiella pneumoniae (CRKP) has become the dominant clone in China. In this review, we trace the prevalence of ST11 CRKP in the China Antimicrobial Surveillance Network (CHINET), the key antimicrobial resistance mechanisms and virulence evolution. The recent emergence of ST11 carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) strains in China due to the acquisition of a pLVPK-like virulence plasmid, which may cause severe infections in relatively healthy individuals that are difficult to treat with current antibiotics, has attracted worldwide attention. There is a very close linkage among IncF plasmids, NTE_KPC and ST11 K. pneumoniae in China. Hybrid conjugative virulence plasmids are demonstrated to readily convert a ST11 CRKP strain to a CR-hvKP strain via conjugation. Understanding the molecular evolutionary mechanisms of resistance and virulence-bearing plasmids as well as the prevalence of ST11 CRKP in China allows improved tracking and control of such organisms.

Antimicrobial Resistance Caused by KPC-2 Encoded by Promiscuous Plasmids of the Klebsiella pneumoniae ST307 Strain

Background

A lineage of Klebsiella pneumoniae that produces carbapenemase-2 (KPC-2), sequence type (ST) 307, emerged in 2017. We analyzed the complete sequences of plasmids from KPC-2-producing K. pneumoniae (KPC-Kp) ST307, investigated the antimicrobial resistance conferred by this strain, and confirmed the horizontal interspecies transmission of KPC-carbapenemase-producing Enterobacteriaceae (CPE) characteristics among Enterobacteriaceae.

Methods

We performed antimicrobial susceptibility testing, PCR analysis, multilocus sequence typing, curing tests, and whole-genome sequencing to characterize plasmid-derived KPC-2-producing Enterobacteriaceae clinical isolates.

Results

Sequence analysis of KPC-Kp strain ST307 revealed novel plasmid-located virulence factors, including a gene cluster for glycogen synthesis. Three Enterobacteriaceae strains were identified in one patient: K. pneumoniae (CPKp1825), Klebsiella aerogenes (CPEa1826), and Escherichia coli (CPEc1827). The bla_KPC-2 gene from K. pneumoniae ST307 was horizontally transmitted between these strains. The plasmids could be transferred through conjugation, because all three strains of bacteria contained the type IV secretion system, pilus genes, and tra genes for conjugal transfer. The bla_KPC-2 gene was located on a truncated Tn4401 transposon. Plasmids containing the bla_KPC-2 gene could not be artificially removed; thus, the three strains could not be cured.

Conclusions

The ease of horizontal transfer of KPC-Kp ST307 carbapenem resistance has serious public health and epidemiological implications. This study provides a better understanding of the genetic characteristics that can contribute to the growth and spread of KPC-Kp ST307, and their association with antimicrobial resistance genes.

Risk of Bronchial Dehiscence in Lung Transplant Recipients With Carbapenemase-producing Klebsiella

BACKGROUND

Klebsiella pneumoniae is commonly isolated after lung transplantation. This study observed an increase in bronchial complications after an outbreak of Klebsiella pneumoniae carbapenemase-producing Klebsiella (KPC-KP).

METHODS

The study enrolled 173 patients who had undergone bilateral lung transplantation between 2012 and 2018 to examine the association between bronchial complications after lung transplantation and KPC-KP. The KPC-KP group was defined as patients whose isolates from sputum or bronchoalveolar lavage fluid were positive for KPC-KP. The presence of bronchial complications was defined as a positive finding on bronchoscopy in accordance with the criteria of the International Society for Heart and Lung Transplantation. Risk factors for bronchial complications were analyzed.

RESULTS

KPC-KP was identified in 29 patients (16.8%), and bronchial dehiscence was observed in 13 patients (7.5%). Smoking (odds ratio [OR], 5.690; 95% confidence interval [CI], 1.106- to 9.260; P = .037), the presence of KPC-KP (OR, 5.360; 95% CI, 1.380 to 20.810; P = .015), and bronchial necrosis (OR, 7.009; 95% CI, 1.811 to 27.124; P = .005) were associated with bronchial dehiscence in a multivariate logistic regression model.

CONCLUSIONS

The presence of KPC-KP in lung-transplant recipients significantly increased the risk of bronchial dehiscence, independent of bronchial necrosis. Thus, patients with KPC-KP require greater surveillance and follow-up bronchoscopy, irrespective of the presence or absence of bronchial necrosis or the overall patient condition.

Direct detection of intact Klebsiella pneumoniae carbapenemases produced by Enterobacterales using MALDI-TOF MS

Objectives

A MALDI-TOF MS-based identification method for KPC-producing Enterobacterales was developed.

Methods

The molecular mass of the intact KPC-2 polypeptide was estimated for blaKPC-2 transformants using MALDI Microflex and the exact mass was confirmed by LC and a high-resolution MS/MS system. A total of 1181 clinical Enterobacterales strains, including 369 KPC producers and 812 KPC non-producers, were used to set up the methodology and the results were compared with those from PCR analyses. For external validation, a total of 458 Enterobacterales clinical isolates from a general hospital between December 2018 and April 2019 were used.

Results

The exact molecular mass of the intact KPC-2 protein was 28 718.13 Da and KPC peaks were observed at m/z 28 708.87–28 728.34 using MALDI Microflex. Most of the KPC-2 (99.1%, 335/338) and KPC-3 (100%, 6/6) producers presented a clear peak via this method, while 12.0% (3/25) of the KPC-4 producers had a peak of weak intensity associated with low levels of gene expression. It took less than 20 min for the entire assay to be performed with colonies on an agar plate. External validation showed that the analytical sensitivity and specificity of the method compared with PCR were 100% (59/59) and 99.50% (397/399), respectively.

Conclusions

The MALDI-TOF MS-based method for directly detecting the intact KPC protein is applicable to routine tests in clinical microbiology laboratories, supported by its speed, low cost and excellent sensitivity and specificity.

Tracking the environmental dissemination of carbapenem-resistant Klebsiella pneumoniae using whole genome sequencing

The emergence and dissemination of infections caused by carbapenem-resistant Klebsiella pneumoniae (CRKP) are of great concern worldwide, as there are limited options for their treatment. Thus, in this study, whole-genome sequencing (WGS) was applied to assess CRKP distribution and dissemination from hospital settings to the aquatic environment in order to identify the extent of the problem. Samples were collected from hospital wastewaters and receiving water bodies. Susceptible K. pneumoniae and CRKP were enumerated and isolated using standard methods. Seventeen CRKP were DNA-sequenced using an Illumina HiSeq X™ platform. De novo assembly and annotation were performed using SPAdes and RAST, respectively. The study analysed antibiotic resistance traits (antibiotic resistant genes, mobile genetic elements, and virulence genes) in CRKP isolates. Although influent of wastewater harboured the highest CRKP, wastewater treatment plants were efficient in reducing the threat. In terms of resistance per matrix, benthic sediment proved to harbour more CRKP (22.88%) versus susceptible K. pneumoniae, as revealed by their resistant quotient analysis, while effluent of wastewaters (4.21%) and water bodies (4.64%) had the lowest CRKP loads. The disseminating CRKP consisted of six sequence types (ST) - ST307 (n = 7), a novel ST3559 (n = 5), ST15 (n = 2), and one isolate of each of ST39, 152 and 298. All CRKP isolates harboured β-lactams (bla_CTX-M-15 and bla_OXA-1), quinolone (oqxA and oqxB) and fosfomycin (fosA) resistance genes as well as virulence genes. This study highlights the dissemination of 'high' importance and novel ST CRKP from hospital wastewater to waterbodies. This is concerning, particularly in the African context where a sizable number of people still rely on direct water resources for household use, including drinking. Further research is needed to systematically track the occurrence and distribution of these bacteria so as to mitigate their threat.

MCR1 and KPC2 Co-producing Klebsiella pneumoniae Bacteremia: First Case in Korea

Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-KP) has been disseminating nationwide due to clonal spread and is taking a serious action at the national level in Korea. The mobilized colistin resistance (MCR1) gene confers plasmid-mediated resistance to colistin and is known to be capable of horizontal transfer between different strains of a bacterial species. We have experienced a fatal case of the patient who developed MCR1-possessing, ST307/Tn4401a[blaKPC2] K. pneumonia bacteremia in the community of non-capital region after being diagnosed as pancreatic cancer with multiple liver metastases and treated in the capital region. The ST307/Tn4401a[blaKPC2] K. pneumonia was the most commonly disseminated clone in Korea. Our strain is the first MCR1 and KPC2 co-producing K. pneumonia in Korea and our case is the critical example that the multi-drug resistant clone can cause inter-regional spread and the community-onset fatal infections. Fortunately, our patient was admitted to the intensive care unit on the day of visit, and the contact precaution was well maintained throughout and KPC-KP was not spread to other patients. The high risk patients for KPC-KP need to be screened actively, detected rapidly and preemptively isolated to prevent outbreak of KPC-KP. Inter-facility communications are essential and the nationwide epidemiologic data of KPC-KP should be analyzed and reported regularly to prevent spread of KPC-KP. The prompt identification of species and antimicrobial susceptibilities for successful treatment against KPC-KP should be emphasized as well.

An Outbreak of KPC-Producing Klebsiella pneumoniae Linked with an Index Case of Community-Acquired KPC-Producing Isolate: Epidemiological Investigation and Whole Genome Sequencing Analysis

Aims: A hospital outbreak of Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae (KPN) linked with an index case of community-acquired infection occurred in an urban tertiary care hospital in Seoul, South Korea. Therefore, we performed an outbreak investigation and whole genome sequencing (WGS) analysis to trace the outbreak and investigate the molecular characteristics of the isolates. Results: From October 2014 to January 2015, we identified a cluster of three patients in the neurosurgery ward with sputum cultures positive for carbapenem-resistant KPN. An epidemiological investigation, including pulsed-field gel electrophoresis analysis was performed to trace the origins of this outbreak. The index patient's infection was community acquired. Active surveillance cultures using perirectal swabbing from exposed patients, identified one additional patient with KPC-producing KPN colonization. WGS analyses using PacBio RSII instruments were performed for four linked isolates. WGS revealed a genetic linkage of the four isolates belonging to the same sequence type (ST307). All KPN isolates harbored conjugative resistance plasmids, which has bla_KPC-2 carbapenemase genes contained within the Tn4401 "a" isoform and other resistance genes. However, WGS showed only three isolates among four KPC-producing KPN were originated from a common origin. Conclusions: This report demonstrates the challenge that KPC-2-producing KPN with the conjugative resistance plasmid may spread not only in hospitals but also in community, and WGS can help to accurately characterize the outbreak.

Clonal Spread of Extended-Spectrum Cephalosporin-Resistant Enterobacteriaceae Between Companion Animals and Humans in South Korea

Extended-spectrum cephalosporin (ESC)-resistant Enterobacteriaceae is an increasingly important problem in both human and veterinary medicine. The aims of this study were to describe a comparative molecular characterization of Enterobacteriaceae carrying ESC resistance genes, encoding extended-spectrum β-lactamase (ESBL) and AmpC, isolated from human stool samples, rectal swabs from companion animals, and swabs from the environment of veterinarian hospitals in South Korea, and to examine their possible dissemination and transmission. The ESC resistance genes were identified by PCR and sequencing. Isolates with the predominant ESC resistance genes were assessed for their genetic relatedness by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing. A total of 195 Escherichia coli and 41 Klebsiella pneumoniae isolates that exhibited ESC resistance were recovered on CHROMagar ESBL from human, companion animal, and the veterinary hospital environmental samples. In companion animals, most of the ESC resistance genes were bla_{CMY–2–like} (26.4%), followed by bla_{CTX –M–55} (17.2%) and bla_CTX–M–14 (16.1%), whereas bla_CTX–M–15 (28.6%) was predominant in human samples. The epidemiological relatedness of isolates carrying ESC resistance genes, including 124 E. coli and 23 K. pneumoniae isolates carrying CMY-2-like, DHA-1-like, or/and CTX-M-type, were analyzed by PFGE. The pulsotypes of five E. coli isolates (three from dogs and two from humans) carrying bla_{CMY–2–like}, which were attributed to sequence type 405, from different veterinary clinics showed >85% similarity. Our results indicate direct transmission and dissemination of ESC-resistant Enterobacteriaceae between humans and companion animals.

Performance evaluation of the PANA RealTyper™ CRE Kit for detecting carbapenemase genes in Gram-negative bacilli

OBJECTIVES

The spread of carbapenemase-producing organisms has been continuously reported over the past decade. Rapid and accurate detection of carbapenemase production is essential for adequate infection control and appropriate antimicrobial treatment in the clinical setting. In this study, the performance of the newly developed PANA RealTyper™ CRE Kit (PANAGENE, Daejeon, South Korea) for the detection of six common carbapenemase genes (bla_KPC, bla_GES, bla_IMP, bla_NDM, bla_VIM and bla_OXA-48-like) was evaluated.

METHODS

A total of 479 non-duplicate clinical isolates of Gram-negative bacilli, including 391 carbapenemase-producers and 88 non-producers, were tested. Conventional PCR and sequencing were performed as reference methods for performance evaluation of the PANA RealTyper™ CRE Kit.

RESULTS

The PANA RealTyper™ CRE Kit showed a reliable performance for the detection of carbapenemase-producing organisms compared with the monoplex PCR system, with sensitivity and specificity values both >95%, with only a few discrepant results for six types of carbapenemase genes.

CONCLUSION

This kit is rapid and accurate for simultaneously detecting various carbapenemase genes in a single reaction and could contribute to early decisions for appropriate antimicrobial treatment in the clinical setting.

Antimicrobial resistance of major clinical pathogens in South Korea, May 2016 to April 2017: first one-year report from Kor-GLASS

The Korean government established an antimicrobial resistance (AMR) surveillance system, compatible with the Global AMR Surveillance System (GLASS): Kor-GLASS. We describe results from the first year of operation of the Kor-GLASS from May 2016 to April 2017, comprising all non-duplicated clinical isolates of major pathogens from blood, urine, faeces and urethral and cervical swabs from six sentinel hospitals. Antimicrobial susceptibility tests were carried out by disk diffusion, Etest, broth microdilution and agar dilution methods. Among 67,803 blood cultures, 3,523 target pathogens were recovered. The predominant bacterial species were Escherichia coli (n = 1,536), Klebsiella pneumoniae (n = 597) and Staphylococcus aureus (n = 584). From 57,477 urine cultures, 6,394 E. coli and 1,097 K. pneumoniae were recovered. Bloodstream infections in inpatients per 10,000 patient-days (10TPD) were highest for cefotaxime-resistant E. coli with 2.1, followed by 1.6 for meticillin-resistant Sta. aureus, 1.1 for imipenem-resistant Acinetobacter baumannii, 0.8 for cefotaxime-resistant K. pneumoniae and 0.4 for vancomycin-resistant Enterococcus faecium. Urinary tract infections in inpatients were 7.7 and 2.1 per 10TPD for cefotaxime-resistant E. coli and K. pneumoniae, respectively. Kor-GLASS generated well-curated surveillance data devoid of collection bias or isolate duplication. A bacterial bank and a database for the collections are under development.

The Infinity War: How to Cope with Carbapenem-resistant Enterobacteriaceae

Carbapenem-resistant Enterobacteriaceae (CRE) are now spread worldwide. In Korea, the number of CRE isolation is rapidly increasing, and impending endemicity is a concern. To cope well with CRE, thorough infection control, such as active surveillance, early detection, strict contact precaution, cleaning the environment, and antibiotic stewardship is very important. Therapeutic options include polymyxin, tigecycline, fosfomycin or the combination of them with carbapenem, which is currently the mainstay of treatment. In addition, various combination regimens with new carbapenemase inhibitors such as avibactam, vaborbactam, or relebactam, and other classes of antimicrobials such as plazomicin and siderophore cephalosporin are in the process of evaluation.