Characterization of antibiotic resistance in clinical isolates of Klebsiella pneumoniae in Denmark

Klebsiella pneumoniae (KP) is a major global health problem as it leads to hospital outbreaks all over the world and is becoming more difficult to treat due to its increasing antimicrobial resistance (AMR). Optimization and development of new treatments of KP requires understanding of its population structure and AMR properties. Therefore, in this study, we collected and sequenced 491 KP strains from four major Danish microbiology departments covering 51% of the Danish population. The isolates were whole genome sequenced (WGS), phenotypically characterized and compared with 2,124 KP strains from 13 different countries (PATRIC strains). We found that while genomic content varies significantly across the Danish strains, they also differ significantly from strains from other countries, due to the lack of certain AMR sequence types (e.g. ST258 and ST307) in Denmark. Genomic and experimental analysis suggest that Danish strains contain fewer virulence mechanisms and are more susceptible to antimicrobials compared to strains from other countries, likely due to the relatively low antibiotic usage in Denmark where 70% of hospital antibiotic usage is penicillins. We also identified potential novel AMR determinants to tigecycline through statistical analysis of genomic and phenotypic data. To conclude, we obtained a more comprehensive understanding of the KP strains in Denmark and provided valuable insights for future experiments and strategies to combat AMR in KP.

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Phenotypic and Molecular Characteristics of the MDR Efflux Pump Gene-Carrying Stenotrophomonas maltophilia Strains Isolated in Warsaw, Poland

Biology ◽

10.3390/biology11010105 ◽

2022 ◽

Vol 11 (1) ◽

pp. 105

Author(s):

Olga M. Zając ◽

Stefan Tyski ◽

Agnieszka E. Laudy

Keyword(s):

Molecular Typing ◽

Stenotrophomonas Maltophilia ◽

Efflux Pump ◽

Pulsed Field Gel Electrophoresis ◽

Molecular Characteristics ◽

The World ◽

Genes Encoding ◽

Resistance Nodulation Division ◽

Sequence Types

An increase of nosocomial infections caused by Stenotrophomonas maltophilia strains has recently been observed all over the world. The isolation of these bacteria from the blood is of particular concern. In this study we performed the phenotypic and genotypic characterization of 94 S. maltophilia isolates, including isolates from patients hospitalized in a tertiary Warsaw hospital (n = 79) and from outpatients (n = 15). All isolates were found to be susceptible to trimethoprim-sulfamethoxazole and minocycline, while 44/94 isolates demonstrated a reduction in susceptibility to levofloxacin. A large genetic variation was observed among the isolates tested by pulsed-field gel electrophoresis. A clonal relationship with 100% similarity was observed between isolates within two sub-pulsotypes: the first included nine bloodstream isolates and the second involved six. Multilocus sequence typing showed two new sequence types (ST498 and ST499) deposited in public databases for molecular typing. Moreover, the presence of genes encoding ten different efflux pumps from the resistance-nodulation-division family and the ATP-binding cassette family was shown in the majority of the 94 isolates. The obtained knowledge about the prevalence of efflux pump genes in clinical S. maltophilia strains makes it possible to predict the scale of the risk of resistance emergence in strains as a result of gene overexpression.

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Detection and characterization of VIM-52, a new variant of VIM-1 from Klebsiella pneumoniae clinical isolate

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02660-20 ◽

2021 ◽

Author(s):

Marie de Barsy ◽

Paola Sandra Mercuri ◽

Saoussen Oueslati ◽

Eddy Elisée ◽

Te-Din Huang ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Substrate Specificity ◽

Clinical Isolate ◽

Targeted Mutagenesis ◽

Kinetic Measurements ◽

Steady State Kinetic ◽

New Variant ◽

State Kinetic ◽

Global Health Problem

Over the last two decades, antimicrobial resistance has become a global health problem. In Gram-negative bacteria, metallo-β-lactamases (MBLs), which inactivate virtually all β-lactams, increasingly contribute to this phenomenon. The aim of this study is to characterize VIM-52, a His224Arg variant of VIM-1, identified in a Klebsiella pneumoniae clinical isolate. VIM-52 conferred lower MICs to cefepime and ceftazidime as compared to VIM-1. These results were confirmed by steady state kinetic measurements, where VIM-52 yielded a lower activity towards ceftazidime and cefepime but not against carbapenems. Residue 224 is part of the L10 loop (residues 221-241), which borders the active site. As Arg 224 and Ser 228 are both playing an important and interrelated role in enzymatic activity, stability and substrate specificity for the MBLs, targeted mutagenesis at both positions were performed and further confirmed their crucial role for substrate specificity.

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Molecular and Clinical Characterization of Multidrug-Resistant and Hypervirulent Klebsiella pneumoniae Strains from Liver Abscess in Taiwan

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00174-20 ◽

2020 ◽

Vol 64 (5) ◽

Cited By ~ 6

Author(s):

Yi-Tsung Lin ◽

Yi-Hsiang Cheng ◽

Chien Chuang ◽

Sheng-Hua Chou ◽

Wan-Hsin Liu ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Klebsiella Pneumoniae ◽

Liver Abscess ◽

Multidrug Resistant ◽

Resistance Mechanisms ◽

Virulence Plasmid ◽

Content Type ◽

Sequence Types

ABSTRACT Hypervirulent Klebsiella pneumoniae strains are the major cause of liver abscesses throughout East Asia, and these strains are usually antibiotic susceptible. Recently, multidrug-resistant and hypervirulent (MDR-HV) K. pneumoniae strains have emerged due to hypervirulent strains acquiring antimicrobial resistance determinants or the transfer of a virulence plasmid into a classic MDR strain. In this study, we characterized the clinical and microbiological properties of K. pneumoniae liver abscess (KPLA) caused by MDR-HV strains in Taiwan. Patients with community onset KPLA were retrospectively identified at Taipei Veterans General Hospital during January 2013 to May 2018. Antimicrobial resistance mechanisms, capsular types, and sequence types were determined. MDR-HV strains and their parental antimicrobial-susceptible strains further underwent whole-genome sequencing (WGS) and in vivo mice lethality tests. Thirteen MDR-HV strains were identified from a total of 218 KPLA episodes. MDR-HV strains resulted in similar outcomes to antimicrobial-susceptible strains. All MDR-HV strains were traditional hypervirulent clones carrying virulence capsular types. The major resistance mechanisms were the overexpression of efflux pumps and/or the acquisition of ESBL or AmpC β-lactamase genes. WGS revealed that two hypervirulent strains had evolved to an MDR phenotype due to mutation in the ramR gene and the acquisition of an SHV-12-bearing plasmid, respectively. Both these MDR-HV strains retained high virulence compared to their parental strains. The spread of MDR-HV K. pneumoniae strains in the community raises significant public concerns, and measures should be taken to prevent the further acquisition of carbapenemase and other resistance genes among these strains in order to avoid the occurrence of untreatable KPLA.

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Characterization of Tigecycline Resistance Among Tigecycline Non-susceptible Klebsiella pneumoniae Isolates From Humans, Food-Producing Animals, and in vitro Selection Assay

Frontiers in Microbiology ◽

10.3389/fmicb.2021.702006 ◽

2021 ◽

Vol 12 ◽

Author(s):

Mohaddeseh Moghimi ◽

Mehri Haeili ◽

Hanieh Mohajjel Shoja

Keyword(s):

Klebsiella Pneumoniae ◽

In Vitro Selection ◽

Nonsense Mutations ◽

Frameshift Mutations ◽

Distinct Sequence ◽

Broth Macrodilution ◽

Sequence Types ◽

Animal Isolates

Emergence of extensively drug-resistant isolates of Klebsiella pneumoniae has prompted increased reliance on the last-resort antibiotics such as tigecycline (TGC) for treating infections caused by these pathogens. Consumption of human antibiotics in the food production industry has been found to contribute to the current antibiotic resistance crisis. In the current study, we aimed to investigate the mechanisms of TGC resistance among 18 TGC-non-susceptible (resistant or intermediate) K. pneumoniae (TGC-NSKP) isolates obtained from human (n = 5), food animals (n = 7), and in vitro selection experiment (n = 6). Isolates were genotyped by multilocus sequence typing (MLST). ramR, acrR, rpsJ, tetA, and mgrB (for colistin resistance) genes were sequenced. The presence of tetX, tetX1, and carbapenemase genes was examined by PCR. Susceptibility to different classes of antibiotics was evaluated by disc diffusion and broth macrodilution methods. The expression level of acrB was quantified by RT-qPCR assay. The 12 TGC-NSKP isolates [minimum inhibitory concentrations (MICs) = 4–32 mg/l] belonged to 10 distinct sequence types including ST37 (n = 2), ST11, ST15, ST45, ST1326 (animal isolates); ST147 (n = 2, human and animal isolates); and ST16, ST377, ST893, and ST2935 (human isolates). Co-resistance to TGC and colistin was identified among 57 and 40% of animal and human isolates, respectively. All human TGC-NSKP isolates carried carbapenemase genes (blaOXA–48, blaNDM–1, and blaNDM–5). tetX/X1 genes were not detected in any isolates. About 83% of TGC-NSKP isolates (n = 15) carried ramR and/or acrR alterations including missense/nonsense mutations (A19V, L44Q, I141T, G180D, A28T, R114L, T119S, Y59stop, and Q122stop), insertions (positions +205 and +343), or deletions (position +205) for ramR, and R90G substitution or frameshift mutations for acrR. In one isolate ramR amplicon was not detected using all primers used in this study. Among seven colistin-resistant isolates, five harbored inactivated/mutated MgrB due to premature termination by nonsense mutations, insertion of IS elements, and frameshift mutations. All isolates revealed wild-type RpsJ and TetA (if present). Increased expression of acrB gene was detected among all resistant isolates, with the in vitro selected mutants showing the highest values. A combination of RamR and AcrR alterations was involved in TGC non-susceptibility in the majority of studied isolates.

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Characterization of Klebsiella pneumoniae isolated from patients suspected of pulmonary or bubonic plague during the Madagascar epidemic in 2017

10.21203/rs.3.rs-449539/v1 ◽

2021 ◽

Author(s):

Andriniaina Rakotondra ◽

Lova Andrianonimiadana ◽

Soloandry Rahajandraibe ◽

Solohery Razafimahatratra ◽

Voahangy Andrianaivoarimanana ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Susceptibility Testing ◽

Sensu Stricto ◽

Community Acquired Pneumonia ◽

Short Period ◽

Wide Range ◽

Tract Infections ◽

Sequence Types ◽

National Surveillance System

Abstract Klebsiella pneumoniae can lead to a wide range of diseases including pneumonia, bloodstream, and urinary tract infections. During a short period of a plague epidemic in October 2017 in Madagascar, 12 K. pneumoniae isolates were identified in ten sputum and two buboes aspirate samples. These isolates were from 12 patients suspected of plague, without epidemiological relationships, but were negative for Yersinia pestis in culture. Data were collected from the plague national surveillance system. The isolates were characterized by antimicrobial susceptibility testing and whole-genome sequencing. Real-time PCR was performed to confirm the presence of K. pneumoniae DNA in buboes. All isolates were identified as K. pneumoniae sensu stricto. Five isolates were extended-spectrum β-lactamases producers; eight different sequence types were identified. Five isolates belonged to known hypervirulent sequence types. Our results demonstrate community-acquired pneumonia caused by K. pneumoniae isolates in patients suspected of plague, showing that plague epidemics can hide other etiologies.

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Emergence of carbapenemase-producing and colistin resistant Klebsiella pneumoniae ST101 high-risk clone in Turkey

Acta Microbiologica et Immunologica Hungarica ◽

10.1556/030.2020.01275 ◽

2020 ◽

Author(s):

Gülşen Hazırolan ◽

Alper Karagöz

Keyword(s):

Klebsiella Pneumoniae ◽

Gel Electrophoresis ◽

Low Frequency ◽

Pulsed Field Gel Electrophoresis ◽

University Hospital ◽

Bacterial Isolates ◽

Colistin Resistance ◽

Global Threat ◽

Sequence Types

AbstractCarbapenemase-producing and colistin resistant Klebsiella pneumoniae has become a worldwide healthcare problem. This study describes molecular characterization of carbapenemase-producing and colistin resistant clinical K. pneumoniae isolates.A total of 93 non-replicate carbapenem and colistin resistant K. pneumoniae were recovered from clinical specimens in a university hospital during 2017–2019. Detection of blaOXA-48, blaKPC, blaNDM-1, blaIMP, blaVIM-1 and mcr-1, -2, -3, -4, -5, -6, -7, and -8 genes was performed by PCR. The bacterial isolates were assigned to clonal lineages by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).All isolates harbored blaOXA-48 and only two isolates harbored blaOXA-48, and blaNDM-1 genes together. In colistin resistant K. pneumoniae, mcr-1 was detected in two (2.1%) isolates. Ninety three isolates of K. pneumoniae were categorized into three clusters and five pulsotypes. MLST revealed two different sequence types, ST101 (89/93) and ST147 (4/93).In our study ST101 was found to be a significantly dominant clone carrying blaOXA-48 and among our strains a low frequency of mcr-1 gene was determined. The emergence of colistin resistance was observed in K. pneumoniae ST101 isolates. ST101 may become a global threat in the dissemination of carbapenem and colistin resistance.

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Molecular Characterization Of Extended Spectrum Betalactamases Genes (Blactxm And Blashv) In Enterobacteria Isolates In Medical Specimens In Lomé (Togo)

10.21203/rs.2.10678/v1 ◽

2019 ◽

Author(s):

Sika Dossim ◽

Mounerou SALOU ◽

Majesté IHOU-WATEBA ◽

Bawisdom BIDJADA ◽

Amivi Mawussi GODONOU ◽

...

Keyword(s):

Escherichia Coli ◽

Klebsiella Pneumoniae ◽

Clavulanic Acid ◽

Molecular Characterization ◽

Gene Amplification ◽

Enterobacter Cloacae ◽

The World ◽

Amoxicillin Clavulanic Acid ◽

Medical Bacteriology

Abstract Background Extendum Bêtalactamases genes spread throughout the world. Many informations are known about it in Europe, Asia and elsewhere. In Africa particularly in Togo, we have lack informations although their prevalence are still increasing. The aim of this study is to identify the blaSHV and blaCTXM genes on Escherichia coli and Klebsiella pneumoniae strains isolated in two medical bacteriology laboratories in Lomé. Material and method 46 strains (20 Klebsiella pneumoniae, 23 Escherichia coli and 3 Enterobacter cloacae) isolated at Sylvanus Olympio Teaching Hospital (n = 31) and at Institut d’Hygiène (n = 15) in Lomé were investigated in search of blaSHV and blaCTXM through gene amplification. The strains were isolated from various samples in 2015 and 2016. An amplification of blaTEM was carried out in case of negativity to both genes. A sequencing of the amplicons was carried out then the sequences identified through blastX on the basis of NCBI data. Results We found 97.9% resistance to amoxicillin + clavulanic acid, gentamicin, levofloxacin and to sulfamethoxazole + trimethoprim. 8.7% of the strains were resistant to ertapenem. All the strains carried blaCTXM-15. In Klebsiella pneumoniae, blaSHV-1 blaSHV-11, blaSHV-28, blaSHV-61, blaSHV-77 were identified. Associations were found (blaSHV-1 / blaCTXM-15, blaSHV-11 / blaCTXM-15, blaSHV-28 / blaCTXM-15). blaTEM was identified on a strain of Enterobacter cloacae. Conclusion There is a diversity of blaSHV genes with a dominance of blaCTXM-15. blaTEM remains the gene to search for in case of absence of the two previous genes in ESBL strains in Lomé.

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OXA-48-Like-Producing Klebsiella pneumoniae in Southern Spain in 2014–2015

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01396-18 ◽

2018 ◽

Vol 63 (1) ◽

Cited By ~ 5

Author(s):

Jesús Machuca ◽

Lorena López-Cerero ◽

Felipe Fernández-Cuenca ◽

Laura Mora-Navas ◽

Concepción Mediavilla-Gradolph ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Gel Electrophoresis ◽

Pulsed Field Gel Electrophoresis ◽

Southern Spain ◽

Clinical Samples ◽

Sequencing Analysis ◽

Content Type ◽

Clonal Relatedness ◽

Sequence Types

ABSTRACT The aim of this study was to characterize the population structure of 56 OXA-48-like-producing Klebsiella pneumoniae isolates, as well as extended-spectrum β-lactamase (ESBL) and carbapenemase genes, recovered in 2014 and 2015 from 16 hospitals in southern Spain. XbaI pulsed-field gel electrophoresis and multilocus sequence typing were performed to assess clonal relatedness. Representative isolates belonging to OXA-48-like-producing and CTX-M-15-coproducing pulsotypes were selected for characterization of blaOXA-48-like- and blaCTX-M-15-carrying plasmids by PCR-based replicon typing, IncF subtyping, whole-genome sequencing analysis, and typing of Tn1999 structures. Forty-three OXA-48-producing isolates (77%) were recovered from clinical samples and 13 from rectal swabs. All isolates showed ertapenem MIC values of ≥1 mg/liter, although 70% remained susceptible to imipenem and meropenem. Forty-nine isolates (88%) produced OXA-48, 5 produced OXA-245, and 2 produced OXA-181. Twenty-eight different pulsotypes (5 detected in more than 1 hospital) and 16 sequence types (STs) were found. The most prevalent clones were ST15 (29 isolates [52%]) and ST11 (7 isolates [13%]). Forty-five (80%) isolates were also blaCTX-M-15 carriers. The blaCTX-M-15 gene was mostly (82%) located on IncR plasmids, although ST15 and ST11 isolates also carried this gene on IncF plasmids. The composite transposon variant Tn1999.2-like was the most frequent. Among ST15 and ST11 isolates, different transposon variants were observed. The blaOXA-48 gene was mainly located on IncL plasmids, although IncM plasmids were also observed. The spread of OXA-48-like-producing K. pneumoniae in southern Spain is mainly due to ST15 and ST11 clones. Variation within clonal lineages could indicate different acquisition events for both ESBL and carbapenemase traits.

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The Characterization of OXA-232 Carbapenemase-Producing ST437 Klebsiella pneumoniae in China

Canadian Journal of Infectious Diseases and Medical Microbiology ◽

10.1155/2020/5626503 ◽

2020 ◽

Vol 2020 ◽

pp. 1-5

Author(s):

Xingbei Weng ◽

Qiucheng Shi ◽

Sheng Wang ◽

Yubo Shi ◽

Dinghe Sun ◽

...

Keyword(s):

Public Health ◽

High Risk ◽

Klebsiella Pneumoniae ◽

Clonal Complex ◽

Multidrug Resistant ◽

New Delhi ◽

Carbapenem Resistant ◽

The World ◽

Global Threat

Carbapenem-resistant Klebsiella pneumoniae (CRKP) was epidemic around the world and become a global threat to public health. The most important carbapenem-resistant mechanism is producing carbapenemases, especially Klebsiella pneumoniae carbapenemase (KPC), which is prevalent in the international clonal complex CC11. The high-risk multidrug-resistant CC11 is widespread worldwide, and KPC-producing and (New Delhi metallo) NDM-producing strains had been reported in this clonal complex before; moreover, cases with the CC11 strain faced more severe forms of drug resistance and treatment challenges than other clonal complexes. In this study, we identified an OXA-232-producing ST437 Klebsiella pneumoniae isolate in China, which belonged to CC11. The isolate was resistant to β-lactams, aminoglycosides, and fluoroquinolones but susceptible to fosfomycin, tigecycline, and colistin. The blaOXA-232 gene was located on a 6141 bp ColKP3-type nonconjugative plasmid, and the plasmid was transformed by chemical transformation successfully. This is the first report of OXA-232-producing ST437 K. pneumoniae in China, a new clone of high-risk multidrug-resistant CC11.

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Characterization of Siliceous Nodules in Western Kefalonia Ιsland Greece: An Initial Approach to Their Formation and Diagenetic Characteristics

Minerals ◽

10.3390/min12010101 ◽

2022 ◽

Vol 12 (1) ◽

pp. 101

Author(s):

Paraskevi Lampropoulou ◽

Vayia Xanthopoulou ◽

Małgorzata Wojtaszek-Kalaitzidi ◽

Petros Petrounias ◽

Elena Zoumpouli ◽

...

Keyword(s):

Tectonic Activity ◽

Upper Eocene ◽

Comprehensive Understanding ◽

Fine Grained ◽

Geothermal Fluids ◽

Diagenetic Processes ◽

Pelagic Environment ◽

The World ◽

Diagenetic Evolution

In this study, siliceous nodules from the world-famous Myrtos beach, as well as from Avithos beach, in the western flanks of Kefalonia Island in Greece are examined by means of petrographical, mineralogical, geochemical and micropaleontological methods. The objectives of this study are to characterize the textural and compositional features of the nodules, with the aim to provide an initial interpretation of their origin and their diagenetic evolution. The studied siliceous nodules are hosted within Lower Cretaceous thin-bedded limestones at Myrtos and Upper Eocene limestones at Avithos. Nodules from both areas display a characteristic concentric texture at a macroscopic and microscopic scale. They both have a dense fine-grained siliceous sedimentary fabric, composed mainly of microcrystalline or cryptocrystalline quartz and moganite with common residual calcite in the case of Avithos. These results, and in particular the shape of the nodules, along the textural and compositional characteristics, indicate different conditions of formation in the two localities, both during the early epigenetic stages, as well as later during the diagenetic processes. Myrtos nodules originated from Si-precursors deposited in a pelagic environment, going through intense Si-replacement. Avithos nodules were deposited in a more proximal environment, being influenced by a less intense silicification. Nevertheless, the higher degree of recrystallization of Avithos samples indicates a syn- or post-diagenetic tectonic activity that resulted in the circulation of geothermal fluids. The conclusions drawn from this work demonstrate the usefulness of thorough studies of siliceous nodules in order to get a more comprehensive understanding of the initial depositional conditions, as well as diagenetic pathways and processes.

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