The emergence of the hypervirulent Klebsiella pneumoniae (hvKp) strains among circulating clonal complex 147 (CC147) harbouring blaNDM/OXA-48 carbapenemases in a tertiary care center of Iran

New insights and perspectives on the virulence of hypervirulent Klebsiella pneumoniae

Klebsiella pneumoniae, a Gram-negative bacterium, comprises strains with diverse virulence potentials, ranging from classical to hypervirulent variants. Understanding the genetic basis underlying the virulence disparities between hypervirulent (hvKp) and classical K. pneumoniae (cKp) strains is crucial. hvKp strains are characterized by hypermucoviscosity, attributed to the presence of specific virulence genes and the production of molecules that aid in their ability to survive, evade host immune defenses, and cause infection. In contrast, classical strains exhibit a broader array of antimicrobial resistance determinants, conferring resistance to multiple antibiotics. Although current definitions of hvKp incorporate clinical features, phenotypes, and genotypes, identifying hvKp strains in clinical settings remains challenging. Genomic studies have been pivotal and have helped to identify distinct genetic profiles in hvKp strains, including unique virulence plasmids and chromosomal variations, underscoring the genetic diversity within K. pneumoniae populations. This review examines the virulence and genetic determinants associated with hvKp. The presence of genes defining hypervirulence, alongside considerations of their utility as biomarkers and targets for therapeutic strategies, is discussed, while also providing insight into biofilm formation by hvKp and key questions that need urgent responses in understanding hvKp.

Systematic review and meta-analysis on the carbapenem-resistant hypervirulent Klebsiella pneumoniae isolates

BACKGROUND

The global dissemination of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) poses a critical threat to public health. However, comprehensive data on the prevalence and resistance rates of CR-hvKp are limited. This systematic review and meta-analysis aim to estimate the pooled prevalence of carbapenem resistance among hvKp strains and assess the distribution of carbapenemase genes.

MATERIALS AND METHODS

A systematic search of ISI Web of Science, PubMed, and Google Scholar was conducted to identify studies reporting carbapenem resistance rates in hvKp strains. The pooled prevalence of carbapenem resistance and carbapenemase genes was calculated using event rates with 95% confidence intervals.

RESULTS

A total of 36 studies encompassing 1,098 hvKp strains were included. The pooled resistance rates were 49% for imipenem, 53.2% for meropenem, and 38.2% for ertapenem. Carbapenemase gene prevalence was 19.1% for blaVIM, 22.0% for blaNDM, 43.4% for blaOXA-48, and 58.8% for blaKPC.

CONCLUSION

The high prevalence of carbapenem resistance and the widespread distribution of carbapenemase genes among hvKp strains underscore their significant threat to global health. These findings highlight the urgent need for enhanced surveillance, rapid diagnostic tools, and stringent infection control measures to mitigate the spread of CR-hvKp. Future research should focus on understanding resistance mechanisms and developing targeted therapeutic strategies to address this critical challenge.

Antibiotic resistance rates in hypervirulent Klebsiella pneumoniae strains: A systematic review and meta-analysis

OBJECTIVES

In response to the growing global concerns regarding antibiotic resistance, we conducted a meta-analysis to assess the prevalence of antibiotic resistance in hypervirulent Klebsiella pneumoniae (hvKp) strains.

METHODS

We conducted a meta-analysis of antibiotic resistance in the hvKp strains. Eligible studies published in English until April 10, 2023, were identified through a systematic search of various databases. After removing duplicates, two authors independently assessed and analysed the relevant publications, and a third author resolved any discrepancies. Data extraction included publication details and key information on antibiotic resistance. Data synthesis employed a random-effects model to account for heterogeneity, and various statistical analyses were conducted using R and the metafor package.

RESULTS

This meta-analysis of 77 studies from 17 countries revealed the prevalence of antibiotic resistance in hvKp strains. A high resistance rates have been observed against various classes of antibiotics. Ampicillin-sulbactam faced 45.3% resistance, respectively, rendering them largely ineffective. The first-generation cephalosporin cefazolin exhibited a resistance rate of 38.1%, whereas second-generation cefuroxime displayed 26.7% resistance. Third-generation cephalosporins, cefotaxime (65.8%) and ceftazidime (57.1%), and fourth-generation cephalosporins, cefepime (51.3%), showed substantial resistance. The last resort carbapenems, imipenem (45.7%), meropenem (51.0%) and ertapenem (40.6%), were not spared.

CONCLUSION

This study emphasizes the growing issue of antibiotic resistance in hvKp strains, with notable resistance to both older and newer antibiotics, increasing resistance over time, regional disparities and methodological variations. Effective responses should involve international cooperation, standardized testing and tailored regional interventions.

Occurrence of carbapenem-resistant hypervirulent Klebsiella pneumoniae in oysters in Egypt: a significant public health issue

BACKGROUND

The global dissemination of critical-priority carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) via food sources represents a significant public health concern. Epidemiological data on CR-hvKp in oysters in Egypt is limited. This study aimed to investigate the potential role of oysters sold in Egypt as a source for carbapenem-resistant K. pneumoniae (CRKP), hypervirulent K. pneumoniae (hvKp), and CR-hvKp and assess associated zoonotic risks.

METHODS

A sample of 330 fresh oysters was randomly purchased from various retail fish markets in Egypt and divided into 33 pools. Bacteriological examination and the identification of Klebsiella pneumoniae were performed. Carbapenem resistance in K. pneumoniae isolates was determined by phenotypic and molecular methods. Additionally, the presence of hypervirulent K. pneumoniae was identified based on virulence gene markers (peg-344, rmpA, rmpA2, iucA, and iroB), followed by a string test. The clustering of CR-hvKp strains was carried out using R with the pheatmap package.

RESULTS

The overall prevalence of K. pneumoniae was 48.5% (16 out of 33), with 13 isolates displaying carbapenem resistance, one intermediate resistance, and two sensitive. Both carbapenem-resistant K. pneumoniae and carbapenem-intermediate-resistant K. pneumoniae strains exhibited carbapenemase production, predominantly linked to the blaVIM gene (68.8%). HvKp strains were identified at a rate of 62.5% (10/16); notably, peg-344 was the most prevalent gene. Significantly, 10 of the 13 CRKP isolates possessed hypervirulence genes, contributing to the emergence of CR-hvKp. Moreover, cluster analysis revealed the clustering of two CR-hvKp isolates from the same retail fish market.

CONCLUSION

This study provides the first insight into the emergence of CR-hvKp among oysters in Egypt. It underscores the potential role of oysters as a source for disseminating CR-hvKp within aquatic ecosystems, presenting a possible threat to public health.

Carbapenem-resistant Klebsiella pneumoniae: the role of plasmids in emergence, dissemination, and evolution of a major clinical challenge

INTRODUCTION

Klebsiella pneumoniae is a major agent of healthcare-associated infections and a cause of some community-acquired infections, including severe bacteremic infections associated with metastatic abscesses in liver and other organs. Clinical relevance is compounded by its outstanding propensity to evolve antibiotic resistance. In particular, the emergence and dissemination of carbapenem resistance in K. pneumoniae has posed a major challenge due to the few residual treatment options, which have only recently been expanded by some new agents. The epidemiological success of carbapenem-resistant K. pneumoniae (CR-Kp) is mainly linked with clonal lineages that produce carbapenem-hydrolyzing enzymes (carbapenemases) encoded by plasmids.

AREAS COVERED

Here, we provide an updated overview on the mechanisms underlying the emergence and dissemination of CR-Kp, focusing on the role that plasmids have played in this phenomenon and in the co-evolution of resistance and virulence in K. pneumoniae.

EXPERT OPINION

CR-Kp have disseminated on a global scale, representing one of the most important contemporary public health issues. These strains are almost invariably associated with complex multi-drug resistance (MDR) phenotypes, which can also include recently approved antibiotics. The heterogeneity of the molecular bases responsible for these phenotypes poses significant hurdles for therapeutic and diagnostic purposes.

Decoding the genetic structure of conjugative plasmids in international clones of Klebsiella pneumoniae: A deep dive into blaKPC, blaNDM, blaOXA-48, and blaGES genes

Carbapanem-resistant Klebsiella pneumoniae is a globally healthcare crisis. The distribution of plasmids carrying carbapenemase genes among K. pneumoniae poses a serious threat in clinical settings. Here, we characterized the genetic structure of plasmids harboring major carbapenemases (e.g. blaKPC, blaNDM, blaOXA-48-like, and blaGES) from K. pneumoniae using bioinformatics tools. The plasmids carrying at least one major carbapenemase gene were retrieved from the GenBank database. The DNA length, Inc type, and conjugal apparatus of these plasmids were detected. Additionally, allele types, co-existence, co-occurrence of carbapenemase genes, gene repetition, and sequence types of isolates, were characterized. There were 2254 plasmids harboring carbapenemase genes in the database. This study revealed that blaKPC-2, blaNDM-1, blaOXA-48, and blaGES-5 were the most prevalent allele types. Out of 1140 (50%) plasmids were potentially conjugative. IncFII, IncR, IncX3, and IncL replicon types were predominant. The co-existence analysis revealed that the most prevalent of other resistance genes were blaTEM-1 (related to blaKPC), blaOXA-232 (related to blaOXA-48), bleMBL (related to blaNDM), and aac (6')-Ib4 (related to blaGES). The co-occurrence of carbapenemases was detected in 42 plasmids while 15 plasmids contained carbapenemase gene repetitions. Sequence alignments highlighted that plasmids carrying blaKPC and blaOXA-48-like were more homogeneous whereas the plasmids carrying blaNDM were divergent. It seems that K. pneumoniae utilizes diversity of genetic flexibility and recombination for resistance against carbapenems. The genetic structure of the plasmids showed that class I and III, Tn3 family, Tn5403 family derivatives, and Tn7-like elements were strongly associated with carbapenemases. The mobilizable plasmids carrying carbapenemases play an important role in the spread of these genes. In addition, gene repetition maybe is related to carbapenem heteroresistance. According to MST (minimum spanning tree) results, the majority of plasmids belonged to sequence type (ST) 11, ST14, and ST12. These international clones have a high capacity to acquire the carbapenemase-containing plasmids.

Various arrangements of mobile genetic elements among CC147 subpopulations of Klebsiella pneumoniae harboring blaNDM-1: a comparative genomic analysis of carbapenem resistant strains

BACKGROUND

Certain clonal complexes (CCs) of Klebsiella pneumoniae such as CC147 (ST147 and ST392) are major drivers of blaNDM dissemination across the world. ST147 has repeatedly reported from our geographical region, but its population dynamics and evolutionary trajectories need to be further studied.

METHODS

Comparative genomic analysis of 51 carbapenem-nonsusceptible strains as well as three hypervirulent K. pneumoniae (hvKp) recovered during 16-months of surveillance was performed using various bioinformatics tools. We investigated the genetic proximity of our ST147 strains with publicly available corresponding genomes deposited globally and from neighbor countries in our geographic region.

RESULTS

While IncL/M plasmid harboring blaOXA-48 was distributed among divergent clones, blaNDM-1 was circulated by twenty of the 25 CC147 dominant clone and were mostly recovered from the ICU. The NDM-1 core structure was bracketed by a single isoform of mobile genetic elements (MGEs) [ΔISKpn26-NDM-TnAs3-ΔIS3000-Tn5403] and was located on Col440I plasmid in 68.7% of ST392. However, various arrangements of MGEs including MITESen1/MITESen1 composite transposon or combination of MITESen1/ISSen4/IS903B/IS5/ISEhe3 on IncFIb (pB171) were identified in ST147. It seems that ST392 circulated blaNDM-1 in 2018 before being gradually replaced by ST147 from the middle to the end of sample collection in 2019. ST147 strains possessed the highest number of resistance markers and showed high genetic similarity with four public genomes that harbored blaNDM-1 on the same replicon type. Mainly, there was a convergence between clusters and isolated neighboring countries in the minimum-spanning tree. A conserved arrangement of resistance markers/MGEs was linked to methyltransferase armA which was embedded in class 1 integron in 8 isolates of ST147/ST48 high-risk clones.

CONCLUSION

Our findings highlight the dynamic nature of blaNDM-1 transmission among K. pneumoniae in Iran that occurs both clonally and horizontally via various combinations of MGEs. This is the first analysis of Iranian ST147/NDM + clone in the global context.

Fluoroquinolone-resistance mechanisms and molecular epidemiology of ciprofloxacin-resistant Klebsiella pneumoniae isolates in Iran

Klebsiella pneumoniae is an important cause of nosocomial infections and displays increasing resistance to fluoroquinolones (FQ). This study surveyed the mechanisms of FQ resistance and molecular typing of K. pneumoniae isolates from intensive care units patients in Tehran, Iran. A total of 48 ciprofloxacin (CIP) resistant K. pneumoniae isolates from urine samples were included in this study. Broth microdilution assays revealed high-level CIP resistance (MIC > 32 μg/mL) in 31.25% of the isolates. Plasmid-mediated quinolone resistance genes were detected in 41 (85.4%) isolates. Among which, qnrS (41.67%) was the most prevalent followed by qnrD (35.42%), qnrB (27.1%), qnrA (25%), qepA (22.9%), aac(6')-Ib-cr (20.83%), and qnrC (6.25%). Target site mutations (gyrA and parC) were assessed using PCR and sequencing on all isolates. A single mutation in gyrA (S83I) was found in 13 (27.1%) isolates and two isolates harbored six simultaneous mutations. Fourteen isolates (29.2%) had mutations in parC and S129A and A141V mutations were the most prevalent. Real time PCR showed an increase in the expression level of acrB and oqxB efflux genes in 68.75 and 29.16% isolates, respectively. Enterobacterial repetitive intergenic consensus (ERIC)-PCR revealed 14 genotypes and 11 of them were classified by multilocus sequence typing (MLST) into 11 different sequence types belonging to seven clonal complexes and two singletons, most of them have not been reported in Iran yet. We are concerned about the spread of these clones throughout our country. Most FQ resistance mechanisms were detected among our isolates. However, target site mutation had the greatest effect on CIP resistance among our isolates.

High Prevalence of blaOXA-48 and blaNDM-Producing Carbapenem-Resistant Klebsiella pneumoniae Isolated from Clinical Samples in Shahid Rajaei Hospital in Tehran, Iran

Background: Due to the increasing antibiotic resistance, treating infections caused by Klebsiella pneumoniae has become more challenging. Objectives: The present study aimed to investigate the prevalence of blaOXA-48 and blaNDM producing carbapenem-resistant K. pneumoniae isolated from clinical samples in Shahid Rajaei hospital in Tehran, Iran. Methods: Various clinical samples were collected from 1,186 patients admitted with open heart surgery in two wards (ICU and surgery) in Shahid Rajaei Heart Hospital in Tehran, Iran. Klebsiella pneumoniae isolates were identified by standard microbiologic tests. Antimicrobial susceptibility of isolates were determined by disk diffusion and E-test methods. A modified carbapenem inactivation method (mCIM) was performed to detect the presence of carbapenemase. Antibiotic resistance genes were detected using conventional polymerase chain reaction (PCR) by primers targeting blaOXA-48, blaSPM, blaIMP, blaVIM, and blaNDM genes. Results: A total of 131 clinical isolates of K. pneumoniae were isolated and 45.8% (60/131) of them were resistant to carbapenem. Klebsiella pneumoniae isolates showed the highest resistance rate (100%) to ceftriaxone, ceftazidime, cefazolin, and cefepime and the maximum sensitivity to tigecycline (96.7%). The carbapenemase-encoding blaOXA-48 and blaNDM-1 genes were detected in 96.7% and 66.7% of isolates, respectively. Eight different clusters of the isolates, considering a ≥ 80% homology cut-off, were shown with the same rep-PCR pattern. Clusters A, B, C, D, E, F, G, and H included 20, 11, 7, 6, 6, 3, 2, and 2 members, respectively. Conclusions: The RAPD-PCR method reveals the clonal relationship between isolates and may help improve infection control procedures.

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.

Detection of Extended-spectrum Beta-lactamases (ESBLs), Carbapenemase, Metallo-β-lactamase Production Bacteria and Antibiotic Susceptibility Pattern in Hospitalized Patients with Ventilator-associated Pneumonia

Background: Due to the increase in microbial resistance, nosocomial multidrug resistance infections, including ventilator-associated pneumonia (VAP), are presently one of the main causes of death in hospitals since they are difficult to treat. Objectives: This study aimed to investigate the bacterial etiology of VAP and their microbial resistance pattern in Dezful Hospital, southwest of Iran. Methods: In this cross-sectional study, 131 bacterial isolates were isolated from the respiratory secretions of the patients with VAP in ICU wards. Antibiotic susceptibility testing (AST) of all isolates was carried out after the identification. Then the extended-spectrum beta-lactamases (ESBLs), carbapenemase, and metallobetalactamase were identified by phenotyping and genotyping. Results: The most frequent isolates were Staphylococcus aureus (30.5%), Acinetobacter baumannii (25.2%), and Klebsiella pneumoniae (24.4%). All strains of S. aureus were sensitive to vancomycin, ticoplanin, quinupristin-dalfopristin, and linezolid. Escherichia coli and Klebsiella showed high resistance to cephalosporins. More than 93% of Acinetobacter isolates were resistant to carbapenem and quinolones. The overall prevalence of ESBLs and carbapenemase producing bacteria were 80.43% and 73.6%, respectively. The most frequent ESBLs gene was blaCTX-M gene (78.3%) followed by blaAMP-C gene (67.5%), blaSHV gene (64.8%), and blaTEM gene (54%). Conclusions: In sum, there was a possibility that the treatment of nosocomial multidrug resistant infections such as VAP would become a major challenge. Therefore, it was recommended that AST results should always be considered when selecting the appropriate treatment regimen. Furthermore, it was found important to emphasize the principles of antibiotic stewardship and to constantly monitor the pattern of microbial susceptibility.

Beta-lactamase determinants and molecular typing of carbapenem-resistant classic and hypervirulent Klebsiella pneumoniae clinical isolates from southwest of Iran

This study investigated the molecular epidemiology of carbapenem-resistant classic Klebsiella pneumoniae (CR-cKp) and carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) isolates in southwestern Iran. From 2019 to 2021, 136 (88.9%) cKp and 17 (11.1%) hvKp isolates were identified using biochemical tests and polymerase chain reaction (PCR). Antibiotic resistance, beta-lactamases, and clonal relatedness of carbapenem-resistant isolates were investigated using disk diffusion, PCR, and enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR), respectively. The different markers of hvKp isolates were as follows: string test (35.3%, n = 6/17), magA (11.8%, n = 2/17), rmpA (11.8%, n = 2/17), rmpA2 (52.9%, n = 9/17), iucA (52.9%, n = 9/17), and peg344 (35.3%, n = 6/17). Also, 55.1% (n = 75/136) of cKp and 47.1% (n = 8/17) of hvKp isolates were CR-cKp and CR-hvKp, respectively. All CR-hvKp (100.0%, n = 8) isolates were MDR. Colistin, tetracycline, and tigecycline were the most effective antibiotics. The occurrence of beta-lactamase genes in 75 CR-cKp and 8 CR-hvKp isolates was as follows: bla NDM (41.3, 25.0%), bla IMP (4.0, 0.0%), bla VIM (8.0, 0.0%), bla GES (14.7, 25.0%), bla OXA-48-like (20.0, 0.0%), bla CTX-M (26.7, 12.5%), bla SHV (24.0, 12.5%), bla TEM (10.7, 0.0%), bla FOX (6.7, 0.0%), bla DHA (6.7, 0.0%), bla CMY (5.3, 0.0%), bla LAT (12.0, 0.0%), and bla ACT (8.0, 0.0%). ERIC-PCR showed a high diversity among isolates. In this study, the occurrence of MDR CR-hvKp isolates harboring bla NDM and bla GES was detected for the first time in southwestern Iran. To prevent the spread of CR-hvKp and reduce selection pressure, long-term surveillance and more effective treatment strategies should be implemented.

Epidemiological characteristics and molecular evolution mechanisms of carbapenem-resistant hypervirulent Klebsiella pneumoniae

Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP), a type of Klebsiella pneumoniae (KP) that exhibits hypervirulence and carbapenem resistance phenotypes, can cause severe infections, both hospital- and community-acquired infections. CR-hvKP has brought great challenges to global public health and is associated with significant morbidity and mortality. There are many mechanisms responsible for the evolution of the hypervirulence and carbapenem resistance phenotypes, such as the horizontal transfer of the plasmid carrying the carbapenem resistance gene to hypervirulent Klebsiella pneumoniae (hvKP) or carbapenemase-producing Klebsiella pneumoniae (CRKP) acquiring a hypervirulence plasmid carrying a virulence-encoding gene. Notably, KP can evolve into CR-hvKP by acquiring a hybrid plasmid carrying both the carbapenem resistance and hypervirulence genes. In this review, we summarize the evolutionary mechanisms of resistance and plasmid-borne virulence as well as the prevalence of CR-hvKP.

Bacteriological characteristics of hypervirulent Klebsiella pneumoniae rmpA gene (hvKp-rmpA)-harboring strains in the south of Iran

Background and Objectives

To provide data on the occurrence of classical K. pneumoniae (cKp) and hypervirulent Klebsiella pneumoniae (hvKp) strains harboring the gene encoding regulator of mucoid phenotype A (rmpA) and evaluated characteristics of virulence biomarkers, carbapenemase, extended-spectrum-β-lactamase (ESBL)-producing, and capsule serotypes among K. pneumoniae clinical isolates collected in the south of Iran.

Materials and Methods

A total of 400 K. pneumoniae isolates were collected. First, the K. pneumoniae isolates were screened for rmpA gene by PCR, and then they were characterized for the presence of the virulence genes (pagO, iucA, iroB, luxR), capsular serotype genes (K1, K2, K5, K20, K54, and K57), carbapenemase (bla _NDM, bla _IMP, bla _VIM, bla _KPC, bla _SPM, bla _OXA-48, and bla _OXA-181) and ESBL (bla _CTX-M, bla _SHV and bla _TEM) genes. For all K. pneumoniae isolates phenotypic tests include of string test and disk diffusion test were performed.

Results

In total, 16 (4%) hvKp-rmpA+ and 384 (96%) cKp were observed. Of hvKp-rmpA+ strains, 16 (100%) were carried pagO, iroB, and luxR genes, and 13 (81.3%) strains harbored iucA gene. The most prevalent capsular type genes were K1 (62%) and K2 (19%) in hvKp-rmpA+ strains. The incidence of bla _SHV gene in hvKp and cKp was 94% (15/16) and 87.5% (336/384), respectively. The cKp isolates carried bla _NDM (30/384; 7.8%) gene.

Conclusion

Our data suggest that the incidence of hvKp was low. Also, hvKp-rmpA+ strains have less antibiotic resistance than cKp isolates. Serotypes K1 and K2, and bla _SHV gene were strongly associated with hvKp-rmpA+.

Ceftazidime-avibactam based combinations against carbapenemase producing Klebsiella pneumoniae harboring hypervirulence plasmids

The combination of carbapenem resistance and hypervirulence in Klebsiella pneumoniae is an emerging and urgent threat due to its potential to resist common antibiotics and cause life-threatening infections in healthy hosts. This study aimed to evaluate the activity of clinically relevant antibiotic regimens against carbapenem-resistant K. pneumoniae with hypervirulence plasmids and to identify pathways associated with antibiotic tolerance using transcriptomics. We studied two carbapenem-resistant K. pneumoniae isolates, CDI694 and CDI231, both harboring hypervirulence plasmids. Time-kill and dynamic one-compartment pharmacokinetic/pharmacodynamic assays were used to assess ceftazidime/avibactam-based therapies. RNAseq was performed following 48 h of antibiotic exposure. Closed genomes of CDI694 and CDI231 were obtained; each isolate harbored carbapenem-resistance and hypervirulence (containing rmpA/rmpA2 and iut genes) plasmids. Ceftazidime/avibactam-based regimens were bactericidal, though both isolates continued to grow in the presence of antibiotics despite no shifts in MIC. Transcriptomic analyses suggested that perturbations to cell respiration, carbohydrate transport, and stress-response pathways contributed to the antibiotic tolerance in CDI231. Genes associated with hypervirulence and antibiotic resistance were not strongly impacted by drug exposure except for ompW, which was significantly downregulated. Treatment of carbapenem-resistant K. pneumoniae harboring hypervirulence plasmids with ceftazidime/avibactam-based regimens may yield a tolerant population due to altered transcription of multiple key pathways.

WGS-Based Phenotyping and Molecular Characterization of the Resistome, Virulome and Plasmid Replicons in Klebsiella pneumoniae Isolates from Powdered Milk Produced in Germany

The emergence of Klebsiella pneumoniae (K. pneumoniae) in German healthcare is worrying. It is not well-investigated in the veterinary world and food chains. In the current study, antibiotic susceptibility profiles of 24 K. pneumoniae strains isolated from powdered milk samples produced in Germany were investigated by a microdilution test. Next-generation sequencing (NGS) was applied to identify genomic determinants for antimicrobial resistance (AMR), virulence-associated genes and plasmids replicons. All isolates were susceptible to the majority (14/18) of tested antibiotics. Resistance to colistin, fosfomycin, chloramphenicol and piperacillin was found. The ambler class A ß-lactamase, blaSHV variants were identified in all isolates, of which blaSHV-187 was most prevalent and found in 50% of isolates. Single-nucleotide-variants of oqxA and oqxB conferring resistance to phenicol/quinolone were found in all isolates, and the oqxB17 was the most prevalent found in 46% of isolates. 67% of isolates harbored fosA genes; however, only one was fosfomycin-resistant. Two isolates harbored genes conferring resistance to colistin, despite being susceptible. The majority of identified virulome genes were iron uptake siderophores. Two enterobactins (entB, fepC), six adherence-related genes belonging to E. coli common pilus (ECP) and one secretion system (ompA gene) were found in all isolates. In contrast, yersiniabactin was found in two isolates. One ST23 strain was susceptible to all tested antibiotics, and harbored determinants discriminatory for hypervirulent strains, e.g., aerobactin, salmochelin, yersiniabactin, enterobactin and regulator of mucoid phenotype A genes that are highly associated with hypervirulent K. pneumoniae. The IncF plasmid family was found in all strains, while almost half of the isolates harbored Col440I-type plasmids and nine isolates harbored various Inc-type plasmids. The presence of K. pneumoniae carrying different resistomes and major virulent specific virulomes in powdered milk samples is alarming. This could threaten public health, particularly of neonates and infants consuming dried milk.

Molecular Epidemiology of Hypervirulent K. pneumoniae and Problems of Health-Care Associated Infections

The review describes virulence factors of hypervirulent K. pneumoniae (hvKp) including genes determining its virulence and discusses their role in the development of health-care associated infections. The contribution of individual virulence factors and their combination to the development of the hypervirulence and the prospects of using these factors as biomarkers and therapeutic targets are described. Virulence factors of hvKp and "classical" K. pneumoniae strains (cKp) with no hypervirulence genes were compared. The mechanisms of biofilm formation by hvKp and high incidence of its antibiotic resistance are of particular importance for in health care institutions. Therefore, the development of methods for hvKp identification allowing early prevention of severe hvKp infection and novel approaches to abrogate its spreading are new challenges for epidemiology, infection diseases, and critical care medicine. New technologies including bacteriological and molecular studies make it possible to develop innovative strategies to diagnose and treat infection caused by hvKp. These include monitoring of both genetic biomarkers of hvKp and resistance plasmid that carry of virulence genes and antibiotic resistance genes, creation of immunological agents for the prevention and therapy of hvKp (vaccines, monoclonal antibodies) as well as personalized hvKp-specific phage therapies and pharmaceuticals enhancing the effect of antibiotics. A variety of approaches can reliably prepare our medicine for a new challenge: spreading of life-threatening health-care associated infections caused by antibiotic-resistant hvKp strains.

Association of fluoroquinolone resistance and ESBL production in hypervirulent Klebsiella pneumoniae ST11 and ST893 in Iran

The spread of multidrug resistance in Klebsiella pneumoniae is a serious threat to the public health. In this study, the prevalence of fluoroquinolone resistance and virulence determinants among ESBL-producing K. pneumoniae isolates was investigated. A total of 50 third-generation cephalosporin resistant K. pneumoniae strains were collected from patients' clinical cultures between September 1st, 2019 and February 30th, 2020. Clonal relatedness of clinical isolates was determined by multilocus sequence typing. All 50 isolates were multidrug-resistant (MDR) and carried at least one of the ESBL resistance determinants. The bla CTX-M-15 gene was the major ESBL determinant found in K. pneumoniae (88%), followed by bla SHV (86%) and bla TEM (78%). PMQR was detected in 96% of the isolates and aac(6')-Ib-cr was the most common (78%) as well as multiple mutations in gyrA (S83I, D87G) and parC (S80I) were found. Selected isolates were assigned to seven sequence types (STs) (ST11, ST893, ST147, ST16, ST377, ST13, and ST392). Overall, hypervirulent phenotypes were identified in 26 (52%) of the isolates. Among the 50 isolates, 28 (56%) were positive for ybt, 23 (46%) for rmpA, 17 (34%) for iroB, 15 (30%) for magA, 4 (8%) for alls and 3 (6%) for iucA genes. The K1 capsular type was the most prevalent (11/50; 22%) among isolates. The emergence of hypervirulent K. pneumoniae (hvKp) ST11 and ST893, which co-carried ESBL, PMQR determinants and different virulence genes has become a threat to the treatment of inpatients in the clinical setting.

Occurrence of Hypervirulent Klebsiella pneumoniae in Clinical Settings and Lytic Potential of Bacteriophages Against the Isolates

Background: Antibiotic resistance is a major health hazard around the globe. Hypervirulent Klebsiella Pneumoniae (hvKp) is associated with hospital-acquired and community-acquired infections. Since there is a lack of new antibiotics against multidrug-resistant (MDR) pathogens, phage therapy might provide an alternative approach to confer antibiotic resistance. Objectives: This study aimed to estimate the occurrence of hvKp and characterize the bacteriophage against the hvKp prevalence in clinical settings, which might be used as an alternative to antibiotics. Methods: Different clinical samples (n = 50) were collected to isolate K. pneumoniae, and the assessment of multidrug resistance was carried out based on the Clinical and Laboratory Standards Institute guidelines (2020). The bacteriophage was isolated from hospital waste, and the double agar overlay method was used for phage purification and propagation. Spot test and one-step curve were performed to determine host-phage interactions. For the evaluation of phage stability in environmental conditions, the phage was incubated at various ranges of temperature, pH, and chloroform. Results: Out of the collected samples, 22 (44%) isolates were confirmed as K. pneumoniae. Among confirmed K. pneumoniae isolates, a total of 11 (50%) isolates were detected as hvKp. Moreover, 14 (64%) isolates were detected as MDR, out of which 5 (35%) isolates were among hvKp phenotypes. Maximum resistance was observed against ampicillin (86%) followed by ceftriaxone (81%) which was the highest among cephalosporins. The isolated bacteriophage showed a broad host range, short latent period, and stability. Overall, 16 isolates (85%) of K. pneumoniae were susceptible to phage infection, among which 12 isolates were MDR (75%); however, all 5 (100%) hvKp isolates were susceptible to phage infection. One-step growth analysis revealed a burst size of 190 phages/host bacterial cells with a short latent period of 24 minutes. Conclusions: Altogether, the significant prevalence of hvKp was estimated in clinical settings, and the isolated bacteriophage showed significant lytic activity as it killed all the hvKp strains. Phage therapy might be exploited and used as a potential alternative therapeutic approach against infections caused by this resistant pathogen.

Occurrence of Hypervirulent Klebsiella pneumoniae in Clinical Settings and Lytic Potential of Bacteriophages Against the Isolates

Background: Antibiotic resistance is a major health hazard around the globe. Hypervirulent Klebsiella Pneumoniae (hvKp) is associated with hospital-acquired and community-acquired infections. Since there is a lack of new antibiotics against multidrug-resistant (MDR) pathogens, phage therapy might provide an alternative approach to confer antibiotic resistance. Objectives: This study aimed to estimate the occurrence of hvKp and characterize the bacteriophage against the hvKp prevalence in clinical settings, which might be used as an alternative to antibiotics. Methods: Different clinical samples (n = 50) were collected to isolate K. pneumoniae, and the assessment of multidrug resistance was carried out based on the Clinical and Laboratory Standards Institute guidelines (2020). The bacteriophage was isolated from hospital waste, and the double agar overlay method was used for phage purification and propagation. Spot test and one-step curve were performed to determine host-phage interactions. For the evaluation of phage stability in environmental conditions, the phage was incubated at various ranges of temperature, pH, and chloroform. Results: Out of the collected samples, 22 (44%) isolates were confirmed as K. pneumoniae. Among confirmed K. pneumoniae isolates, a total of 11 (50%) isolates were detected as hvKp. Moreover, 14 (64%) isolates were detected as MDR, out of which 5 (35%) isolates were among hvKp phenotypes. Maximum resistance was observed against ampicillin (86%) followed by ceftriaxone (81%) which was the highest among cephalosporins. The isolated bacteriophage showed a broad host range, short latent period, and stability. Overall, 16 isolates (85%) of K. pneumoniae were susceptible to phage infection, among which 12 isolates were MDR (75%); however, all 5 (100%) hvKp isolates were susceptible to phage infection. One-step growth analysis revealed a burst size of 190 phages/host bacterial cells with a short latent period of 24 minutes. Conclusions: Altogether, the significant prevalence of hvKp was estimated in clinical settings, and the isolated bacteriophage showed significant lytic activity as it killed all the hvKp strains. Phage therapy might be exploited and used as a potential alternative therapeutic approach against infections caused by this resistant pathogen.

Occurrence of Hypervirulent Klebsiella pneumoniae in Clinical Settings and Lytic Potential of Bacteriophages Against the Isolates

Background: Antibiotic resistance is a major health hazard around the globe. Hypervirulent Klebsiella Pneumoniae (hvKp) is associated with hospital-acquired and community-acquired infections. Since there is a lack of new antibiotics against multidrug-resistant (MDR) pathogens, phage therapy might provide an alternative approach to confer antibiotic resistance. Objectives: This study aimed to estimate the occurrence of hvKp and characterize the bacteriophage against the hvKp prevalence in clinical settings, which might be used as an alternative to antibiotics. Methods: Different clinical samples (n = 50) were collected to isolate K. pneumoniae, and the assessment of multidrug resistance was carried out based on the Clinical and Laboratory Standards Institute guidelines (2020). The bacteriophage was isolated from hospital waste, and the double agar overlay method was used for phage purification and propagation. Spot test and one-step curve were performed to determine host-phage interactions. For the evaluation of phage stability in environmental conditions, the phage was incubated at various ranges of temperature, pH, and chloroform. Results: Out of the collected samples, 22 (44%) isolates were confirmed as K. pneumoniae. Among confirmed K. pneumoniae isolates, a total of 11 (50%) isolates were detected as hvKp. Moreover, 14 (64%) isolates were detected as MDR, out of which 5 (35%) isolates were among hvKp phenotypes. Maximum resistance was observed against ampicillin (86%) followed by ceftriaxone (81%) which was the highest among cephalosporins. The isolated bacteriophage showed a broad host range, short latent period, and stability. Overall, 16 isolates (85%) of K. pneumoniae were susceptible to phage infection, among which 12 isolates were MDR (75%); however, all 5 (100%) hvKp isolates were susceptible to phage infection. One-step growth analysis revealed a burst size of 190 phages/host bacterial cells with a short latent period of 24 minutes. Conclusions: Altogether, the significant prevalence of hvKp was estimated in clinical settings, and the isolated bacteriophage showed significant lytic activity as it killed all the hvKp strains. Phage therapy might be exploited and used as a potential alternative therapeutic approach against infections caused by this resistant pathogen.

The Spread of NDM-1 and NDM-7-Producing Klebsiella pneumoniae Is Driven by Multiclonal Expansion of High-Risk Clones in Healthcare Institutions in the State of Pará, Brazilian Amazon Region

Carbapenem resistance among Klebsiella pneumoniae isolates is often related to carbapenemase genes, located in genetic transmissible elements, particularly the blaKPC gene, which variants are spread in several countries. Recently, reports of K. pneumoniae isolates harboring the blaNDM gene have increased dramatically along with the dissemination of epidemic high-risk clones (HRCs). In the present study, we report the multiclonal spread of New Delhi metallo-beta-lactamase (NDM)-producing K. pneumoniae in different healthcare institutions in the state of Pará, Northern Brazil. A total of 23 NDM-producing isolates were tested regarding antimicrobial susceptibility testing features, screening of carbapenemase genes, and genotyping by multilocus sequencing typing (MLST). All K. pneumoniae isolates were determined as multidrug-resistant (MDR), being mainly resistant to carbapenems, cephalosporins, and fluoroquinolones. The blaNDM-7 (60.9%-14/23) and blaNDM-1 (34.8%-8/23) variants were detected. MLST genotyping revealed the predomination of HRCs, including ST11/CC258, ST340/CC258, ST15/CC15, ST392/CC147, among others. To conclude, the present study reveals the contribution of HRCs and non-HRCs in the spread of NDM-1 and NDM-7-producing K. pneumoniae isolates in Northern (Amazon region) Brazil, along with the first detection of NDM-7 variant in Latin America and Brazil, highlighting the need for surveillance and control of strains that may negatively impact healthcare and antimicrobial resistance.

The Association of the Phylogenetic Typing of the Klebsiella pneumoniae Isolates with Antibiotic Resistance

Klebsiella pneumoniae complex (KPC) accounts for approximately one-third of all Gram-negative infections. Moreover, it is highly resistant and can taxonomically be distributed into KpI, KpII, and KpIII phylogroups. This study aimed to investigate the distribution of phylogenetic groups and the relationship between them and antibiotic resistance patterns. For this purpose, we collected KPC isolates from Tabriz, Iran, between 2018 and 2020. Antimicrobial susceptibility testing was performed by disk diffusion agar, and phylogenetic groups were then examined using gyrA restriction fragment length polymorphism (RFLP) and parC PCR methods. A total of 100 KPC isolates were obtained from the clinical specimens (urine, respiratory secretion, blood, wounds, and trachea). The enrolled patients included 47 men and 53 women aged from 1 to 91 years old. The highest sensitivity was found related to fosfomycin as 85%, followed by amikacin as 66%. The three phylogenetically groups by the RFLP-PCR method were found in KPC, 96% (96 isolates) as KpI, 3% (3 isolates) as KpII, and 1% (1isolate) as KpIII. The highest antibiotic resistance was observed in KpI. It was shown that a valid identification of three phylogenetic groups of KPC can be done by combining both gyrA PCR-RFLP and parC PCR. Of note, the KpI group was also observed as the dominant phylogenetic group with the highest resistance to antibiotics.

Comparative genome analysis of colistin-resistant OXA-48-producing Klebsiella pneumoniae clinical strains isolated from two Iranian hospitals

BACKGROUND

Carbapenemase-producing Klebsiella pneumoniae (CP-KP) is becoming extensively disseminated in Iranian medical centers. Colistin is among the few agents that retains its activity against CP-KP. However, the administration of colistin for treatment of carbapenem-resistant infections has increased resistance against this antibiotic. Therefore, the identification of genetic background of co-carbapenem, colistin-resistance K. pneumoniae (Co-CCRKp) is urgent for implementation of serious infection control strategies.

METHODS

Fourteen Co-CCRKp strains obtained from routine microbiological examinations were subjected to molecular analysis of antimicrobial resistance (AMR) using whole genome sequencing (WGS).

RESULTS

Nine of 14 K. pneumoniae strains belonged to sequence type (ST)-11 and 50% of the isolates had K-locus type 15. All strains carried blaOXA-48 except for P26. blaNDM-1 was detected in only two plasmids associated with P6 and P26 strains belonging to incompatibility (Inc) groups; IncFIB, IncHI1B and IncFII. No blaKPC, blaVIM and blaIMP were identified. Multi-drug resistant (MDR) conjugative plasmids were identified in strains P6, P31, P35, P38 and P40. MICcolistin of K. pneumoniae strains ranged from 4 to 32 µg/ml. Modification of PmrA, PmrB, PhoQ, RamA and CrrB regulators as well as MgrB was identified as the mechanism of colistin resistance in our isolates. Single amino acid polymorphysims (SAPs) in PhoQ (D150G) and PmrB (R256G) were identified in all strains except for P35 and P38. CrrB was absent in P37 and modified in P7 (A200E). Insertion of ISKpn72 (P32), establishment of stop codon (Q30*) (P35 and P38), nucleotides deletion (P37), and amino acid substitution at position 28 were identified in MgrB (P33 and P42). None of the isolates were positive for plasmid-mediated colistin resistance (mcr) genes. P35 and P38 strains carried iutA, iucD, iucC, iucB and iucA genes and are considered as MDR-hypervirulent strains. P6, P7 and P43 had ICEKp4 variant and ICEKp3 was identified in 78% of the strains with specific carriage in ST11.

CONCLUSION

In our study, different genetic modifications in chromosomal coding regions of some regulator genes resulted in phenotypic resistance to colistin. However, the extra-chromosomal colistin resistance through mcr genes was not detected. Continuous genomic investigations need to be conducted to accurately depict the status of colistin resistance in clinical settings.

Detection of extensively drug-resistant and hypervirulent Klebsiella pneumoniae ST15, ST147, ST377 and ST442 in Iran

In this study, we focused on the emergence of extensively drug-resistant (XDR), pandrug-resistant (PDR), and hypervirulent Klebsiella pneumoniae (hvKP) in Iran. During 2018 to 2020 a total of 52 K. pneumoniae isolates were collected from different clinical specimens. The hvKP isolates were identified by PCR amplification of virulence and capsular serotype-specific genes. Hypermucoviscous K. pneumoniae (hmKP) were identified by string test. Carbapenem-resistant hvKP (CR-hvKP), multidrug-resistant hvKP (MDR-hvKP), extensively drug-resistant hvKP (XDR-hvKP), and pandrug-resistant hvKP (PDR-hvKP) were determined by disc diffusion method, Carba-NP test and PCR method. XDR-hvKP isolates were typed by multilocus sequence typing (MLST). Among all K. pneumoniae isolates 14 (26.9%) were identified as hvKP and 78.6% (11/14) of them were hmKP however, none of the classic K. pneumoniae (cKP) isolates were hmKP. The predominant capsular serotype of hvKP was K2 (42.85%) followed by K1 (35.71%). The prevalence of MDR-hvKP, XDR-hvKP and PDR-hvKP isolates were 6 (42.9%), 5 (35.7%) and 1 (7.1%), respectively. ESBL production was found in 85.7% of hvKP isolates and most of them carried bla TEM gene (78.6%) and 6 isolates (42.9%) were CR-hvKP. Among hvKP isolates, 1 (7.1%), 2 (14.3%), 3 (21.4%), 8 (28.6%), and 11 (78.6%) carried bla NDM-6, bla OXA-48, bla CTX-M, bla SHV, and bla TEM genes, respectively. According to MLST analysis, 2, 1, 1, and 1 XDR-hvKP isolates belonged to ST15, ST377, ST442, and ST147, respectively. The occurrence of such isolates is deeply concerning due to the combination of hypervirulence and extensively drug-resistance or pandrug-resistance.

The face of hypervirulent Klebsiella pneumoniae isolated from clinical samples of two Iranian teaching hospitals

Hypervirulent Klebsiella pneumoniae (hvKp) has emerged as a pathogen of global concern. In this study, both phenotypic and genotypic tests were used to detect hvKp. Antimicrobial resistance profiles and clonal relatedness of clinical isolates were also determined. We found that 34.2% (163/477) of the isolates were tellurite resistant, and among them 102 hvKp isolates detected with iucA or iutA or peg-344 as molecular markers. The blaSHV (80.4%), followed by blaCTX-M-15 (76.5%) and blaTEM (67.6%), blaOXA-48 (53.9%), and blaNDM-1 (32.3%) were detected, while blaKPC-1 was not present in any hvKp isolates. It was found that the majority of hvKp isolates belonged to capsular serotype K20 and ompK36 group C, which is related to clonal group (CG) 23 (e.g. ST23). A high percentage of multidrug-resistant hvKp (76.6%) and high resistance to imipenem (67%) indicated a serious problem that should be addressed in the clinical setting.

Arrangements of Mobile Genetic Elements among Virotype E Subpopulation of Escherichia coli Sequence Type 131 Strains with High Antimicrobial Resistance and Virulence Gene Content

Escherichia coli sequence type 131 (ST131) is known for its contribution to multidrug resistance and the worldwide spread of this clone has become a global problem. Understanding the trends among ST131 clades will help design strategies to prevent its rapid dissemination. In this study, 72 ST131 strains were subjected to comparative genomic analysis and 64 clade C strains were compared with clade C strains reported from other regions using publicly available whole-genome sequencing data. C1 (n = 31 [48.4%]) and C2 (n = 33 [%51.5]) strains had the same prevalence in our collection, and C1-M27 (n = 22) strains were closely related, carried a unique plasmid type (F1:A2:B20), and exhibited virotype C. Removal of 11 C2 strains with varied virotype patterns and the heterogeneous IncF type identified 22 closely related virotype E/F strains with replicon type F31/F36:A4:B1, forming what we denote as the “C2-subset.” In a global context, the C2-subset constituted a distinct cluster with international virotype E strains and harbored a genomic island, GI-pheU. Association of cnf1/hlyCABD genes with 1 to 7 mobile genetic elements, mostly IS682/ISKpn37 combination within GI-pheU was identified. The C2-subset accounted for excess resistance/virulence of subclade C2 relative to C1 strains. In addition, a conserved chromosomal IS26-mediated composite transposon (IS15DIV-ISEcp1-bla_CTX-M-15-WbuC cupin fold metalloprotein-Tn2-IS15DIV) was observed in the C2-subset. The local spread of the C2-subset in the hospital studied, with the carriage of higher virulence/resistance markers and a peculiar F-type plasmid, demonstrates the potential for diversification of the ST131 lineage and the emergence of subpopulations with higher survival potential to cause health care-associated outbreaks.

IMPORTANCEEscherichia coli sequence type 131 (ST131) is a globally dominant multidrug-resistant clone that is commonly associated with extraintestinal infections. Specific sublineages have been shown to have emerged and spread within ST131, highlighting the complex nature of ST131 epidemiology. This study systematically compared the Iranian ST131 population to those reported from other countries and found a subpopulation harboring virotype E, a homogeneous profile of plasmid Inc-F type F31/F36:A4:B1 harboring cnf1/hemolysin genes on the genomic island GI-pheU, and up to seven mobile genetic elements (MGEs) flanking cnf1/hemolysin virulence markers. The results of this study highlight the importance of MGEs for virulence gene acquisition and the formation of new subpopulations among pandemic clones such as E. coli ST131.

Genetic diversity and evolution of the virulence plasmids encoding aerobactin and salmochelin in Klebsiella pneumoniae

Virulence plasmids of hypervirulent Klebsiella pneumoniae (hvKp) have the potential to transfer to drug-resistant strains or integrate with other plasmids, facilitating the genome evolution of threatening pathogens. We conducted an in-depth analysis of the publicly available 156 complete genome sequences of hvKp together with a multi-region clinical cohort of 171 hvKp strains from China to provide evidence for the virulence plasmid evolution. Virulence plasmids were frequently detected in the ST23 and ST11 K. pneumoniae strains. Multidrug-resistant hvKp (MDR-hvKp) occupied a large proportion of hvKp, and the coexistence of virulence and resistance plasmids may be the major cause. Virulence plasmids commonly possessed multiple replicons, of which IncFIB_K was the most prevalent (84.6%). We identified 49 IncFIB_K alleles among 583 IncFIB_K plasmids, and they could be divided into Clades I, II, and III. We further observed that conjugative and non-conjugative virulence plasmids could be distinguished by IncFIB_K genetic diversity, and IncFIB_K subtyping could also indirectly indicate a chimeric preference of conjugative virulence plasmids. On this basis, we developed an open-access web tool called KpVR for IncFIB_K subtyping. In conclusion, the genetic diversity of IncFIB_K virulence plasmids could be used for tracking the evolution of virulence plasmids, and further preventing the emergence of MDR-hvKp strains.

Molecular characteristics of antibiotic-resistant Escherichia coli and Klebsiella pneumoniae strains isolated from hospitalized patients in Tehran, Iran

BACKGROUND

We evaluated the distribution of carbapenem and colistin resistance mechanisms of clinical E. coli and K. pneumoniae isolates from Iran.

METHODS

165 non-duplicate non-consecutive isolates of K. pneumoniae and E. coli were collected from hospitalized patients admitted to Iran's tertiary care hospitals from September 2016 to August 2018. The isolates were cultured from different clinical specimens, including wound, urine, blood, and tracheal aspirates. Antibiotic susceptibility testing was performed by disc diffusion and microdilution method according to the Clinical and Laboratory Standards Institute (CLSI) guideline. The presence of extended spectrum β-lactamases (ESBLs) genes, carbapenemase genes, as well as fosfomycin resistance genes, and colistin resistance genes was also examined by PCR-sequencing. The ability of biofilm formation was assessed with crystal violet staining method. The expression of colistin resistance genes were measured by quantitative reverse transcription-PCR (RT-qPCR) analysis to evaluate the association between gene upregulation and colistin resistance. Genotyping was performed using the multi-locus sequencing typing (MLST).

RESULTS

Colistin and tigecycline were the most effective antimicrobial agents with 90.3% and 82.4% susceptibility. Notably, 16 (9.7%) isolates showed resistance to colistin. Overall, 33 (20%), 31 (18.8%), and 95 (57.6%) isolates were categorized as strong, moderate, and weak biofilm-producer, respectively. Additionally, blaTEM, blaSHV, blaCTX-M, blaNDM-1, blaOXA-48-like and blaNDM-6 resistance genes were detected in 98 (59.4%), 54 (32.7%), 77 (46.7%), 3 (1.8%), 17 (10.30%) and 3 (1.8%) isolates, respectively. Inactivation of mgrB gene due to nonsense mutations and insertion of IS elements was observed in 6 colistin resistant isolates. Colistin resistance was found to be linked to upregulation of pmrA-C, pmrK, phoP, and phoQ genes. Three of blaNDM-1 and 3 of blaNDM-6 variants were found to be carried by IncL/M and IncF plasmid, respectively. MLST revealed that blaNDM positive isolates were clonally related and belonged to three distinct clonal complexes, including ST147, ST15 and ST3299.

CONCLUSIONS

The large-scale surveillance and effective infection control measures are also urgently needed to prevent the outbreak of diverse carbapenem- and colistin-resistant isolates in the future.

Extensively Drug-Resistant Hypervirulent Klebsiella pneumoniae From a Series of Neonatal Sepsis in a Tertiary Care Hospital, India

The recent emergence of multidrug-resistant (MDR) Klebsiella pneumoniae with hypervirulent traits causing severe infections and considerable mortality is a global cause for concern. The challenges posed by these hypermucoviscous strains of K. pneumoniae with regard to their optimal treatment, management, and control policies are yet to be answered. We studied a series of extensively drug-resistant (XDR) and hypervirulent K. pneumoniae ST5235 isolates with resistance to carbapenems and polymyxins causing neonatal sepsis in a tertiary care hospital in India. A total of 9 K. pneumoniae isolates from 9 cases of neonatal sepsis were studied with respect to their clinical relevance, antimicrobial susceptibility profile, presence of extended spectrum β lactamase (ESBL) production, and responsible genes, carbapenemases (classes A, B, and D), and aminoglycoside-resistant genes. Hypervirulence genes encoding hypermucoid nature, iron uptake, and siderophores were detected by multiplex PCR. The plasmid profile was studied by replicon typing. Isolates were typed by multilocus sequence typing (MLST) and enterobacterial repetitive intergenic consensus (ERIC) PCR to study the sequence types (STs) and clonal relation, respectively. The neonates in the studied cases had history of pre-maturity or low birth weight with maternal complications. All the cases were empirically treated with piperacillin-tazobactam and amikacin followed by imipenem/meropenem and vancomycin and polymyxin B as a last resort. However, all the neonates finally succumbed to the condition (100%). The studied isolates were XDR including resistance to polymyxins harboring multiple ESBL genes and carbapenemase genes (bla _NDM and bla _OXA-48). Hypervirulence genes were present in various combinations with rmpA/A2 genes present in all the isolates. IncFI plasmids were detected in these isolates. All belonged to ST5235. In ERIC PCR, 6 different clusters were seen. The study highlighted the emergence and burden of XDR hypervirulent isolates of K. pneumoniae causing neonatal sepsis in a tertiary care hospital.

Expansion of a Subset Within the C2 Subclade of Escherichia coli Sequence Type 131 (ST131) Is Driving the Increasing Rates of Aminoglycoside Resistance

Background

Sequence type 131 (ST131) of Escherichia coli is a pandemic clone that drives the increasing rates of antibiotic resistance. While the pervasiveness of ST131 clade C, especially subclades C2 and C1-M27, has been demonstrated in numerous global surveys, no report about the ST131 clades and their virotypes has been published from Iran so far.

Methods

A collection of 73 consecutive ST131 isolates from extraintestinal specimens was investigated for determination of virotypes, antibiotic susceptibility patterns, resistance/virulence determinants, and clade subsets.

Results

Most of the isolates belonged to subclade C2 (33/73; 45.2%), which had the highest virulence factor (VF) scores and resistance rates, followed by C1-M27 (18; 24.6%), C1-non-M27 (14; 19.1%), and A (8; 10.9%). The distinctive profiles of subclade C2 virulence genes were revealed by principle coordinates analysis testing. The distribution of the hlyA virulence gene among subclade C2 was not uniform, so that positive strains (21; 63.6%) showed significantly higher rates of resistance (bla_CTX-M-15, bla_OXA-1, aac(6’)-Ib-cr, aac(6’)-Ib, aac(3)-IIa) and virulence (hra, tia/hek, K5, cnf, papGII, papC) markers and gentamicin/tobramycin resistance. Virotype C as the most common virotype (34; 46.5%) was predominant among the subclade C1 population, while virotypes E and F (21; 28.7%) were detected among subclade C2, which had the highest VF scores and aminoglycoside resistance rates.

Conclusions

The appearance of virotypes E and F among subclade C2 strains with higher rates of aminoglycoside resistance/virulence gene content shows the shifting dynamics of this pandemic clone in response to antibiotic selection pressure by establishing subsets with higher survival potential.