scholarly journals Klebsiella quasipneumonaiae provides a window into carbapenemase gene transfer, plasmid rearrangements and nosocomial acquisition from the hospital environment

2018 ◽  
Author(s):  
Amy J Mathers ◽  
Derrick W Crook ◽  
Alison Vaughan ◽  
Katie E Barry ◽  
Kasi Vegesana ◽  
...  
Keyword(s):  
Horizontal Transmission ◽  
Hospital Environment ◽  
Clinical Microbiology Laboratory ◽  
Emerging Pathogens ◽  
Antimicrobial Resistance Genes ◽  
Carbapenemase Gene ◽  
Transfer Plasmid ◽  
A New Species ◽  
Plasmid Rearrangements ◽  
Genetic Rearrangements

Several emerging pathogens have arisen as a result of selection pressures exerted by modern healthcare. Klebsiella quasipneumoniae was recently defined as a new species, yet its prevalence, niche, and propensity to acquire antimicrobial resistance genes are not fully described. We have been tracking inter- and intra-species transmission of the Klebsiella quasipneumoniae carbapenemase (KPC) gene, blaKPC, between bacteria isolated from a single institution. We applied a combination of Illumina and PacBio whole-genome sequencing to identify and compare K. quasipneumoniae from patients and the hospital environment over 10 and five-year periods respectively. There were 32 blaKPC-positive K. quasipneumoniae isolates, all of which were identified as K. pneumoniae in the clinical microbiology laboratory, from eight patients and 11 sink drains, with evidence for seven separate blaKPC plasmid acquisitions. Analysis of a single subclade of K. quasipneumoniae subspecies quasipneumoniae (n=23 isolates) from three patients and six rooms demonstrated seeding of a sink by a patient, subsequent persistence of the strain in the hospital environment, and then probable transmission to another patient. Longitudinal analysis of this strain demonstrated the acquisition of two unique blaKPC plasmids and then subsequent within-strain genetic rearrangement through transposition and homologous recombination. Our analysis highlights the apparent molecular propensity of K. quasipneumoniae to persist in the environment as well as acquire carbapenemase plasmids from other species and enabled an assessment of the genetic rearrangements which may facilitate horizontal transmission of carbapenemases.

scholarly journals Klebsiella quasipneumoniae Provides a Window into Carbapenemase Gene Transfer, Plasmid Rearrangements, and Patient Interactions with the Hospital Environment

2019 ◽  
Vol 63 (6) ◽  
Author(s):  
Amy J. Mathers ◽  
Derrick Crook ◽  
Alison Vaughan ◽  
Katie E. Barry ◽  
Kasi Vegesana ◽  
...  
Keyword(s):  
Horizontal Transmission ◽  
Hospital Environment ◽  
Clinical Microbiology Laboratory ◽  
Emerging Pathogens ◽  
Content Type ◽  
Modern Health Care ◽  
Antimicrobial Resistance Genes ◽  
Carbapenemase Gene ◽  
Transfer Plasmid ◽  
Genetic Rearrangements

ABSTRACT Several emerging pathogens have arisen as a result of selection pressures exerted by modern health care. Klebsiella quasipneumoniae was recently defined as a new species, yet its prevalence, niche, and propensity to acquire antimicrobial resistance genes are not fully described. We have been tracking inter- and intraspecies transmission of the Klebsiella pneumoniae carbapenemase (KPC) gene, blaKPC, between bacteria isolated from a single institution. We applied a combination of Illumina and PacBio whole-genome sequencing to identify and compare K. quasipneumoniae from patients and the hospital environment over 10- and 5-year periods, respectively. There were 32 blaKPC-positive K. quasipneumoniae isolates, all of which were identified as K. pneumoniae in the clinical microbiology laboratory, from 8 patients and 11 sink drains, with evidence for seven separate blaKPC plasmid acquisitions. Analysis of a single subclade of K. quasipneumoniae subsp. quasipneumoniae (n = 23 isolates) from three patients and six rooms demonstrated seeding of a sink by a patient, subsequent persistence of the strain in the hospital environment, and then possible transmission to another patient. Longitudinal analysis of this strain demonstrated the acquisition of two unique blaKPC plasmids and then subsequent within-strain genetic rearrangement through transposition and homologous recombination. Our analysis highlights the apparent molecular propensity of K. quasipneumoniae to persist in the environment as well as acquire carbapenemase plasmids from other species and enabled an assessment of the genetic rearrangements which may facilitate horizontal transmission of carbapenemases.

scholarly journals Carbapenem-Resistant Pseudomonas aeruginosa Strains-Distribution of the Essential Enzymatic Virulence Factors Genes

Antibiotics ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 8
Author(s):  
Tomasz Bogiel ◽  
Małgorzata Prażyńska ◽  
Joanna Kwiecińska-Piróg ◽  
Agnieszka Mikucka ◽  
Eugenia Gospodarek-Komkowska
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Alkaline Protease ◽  
Virulence Genes ◽  
Virulence Gene ◽  
Hospital Environment ◽  
Gene Encoding ◽  
Virulence Gene Expression ◽  
Carbapenem Resistant ◽  
Antimicrobial Resistance Genes ◽  
The Difference

Pseudomonas aeruginosa is one of the most commonly isolated bacteria from clinical specimens, with increasing isolation frequency in nosocomial infections. Herein, we investigated whether antimicrobial-resistant P. aeruginosa strains, e.g., metallo-beta-lactamase (MBL)-producing isolates, may possess a reduced number of virulence genes, resulting from appropriate genome management to adapt to a changing hospital environment. Hospital conditions, such as selective pressure, may lead to the replacement of virulence genes by antimicrobial resistance genes that are crucial to survive under current conditions. The study aimed to compare, using PCR, the frequency of the chosen enzymatic virulence factor genes (alkaline protease-aprA, elastase B-lasB, neuraminidases-nan1 and nan2, and both variants of phospholipase C-plcH and plcN) to MBL distribution among 107 non-duplicated carbapenem-resistant P. aeruginosa isolates. The gene encoding alkaline protease was noted with the highest frequency (100%), while the neuraminidase-1 gene was observed in 37.4% of the examined strains. The difference in lasB and nan1 prevalence amongst the MBL-positive and MBL-negative strains, was statistically significant. Although P. aeruginosa virulence is generally more likely determined by the complex regulation of the virulence gene expression, herein, we found differences in the prevalence of various virulence genes in MBL-producers.

Two high-risk clones of carbapenemase-producing Klebsiella pneumoniae that cause infections in pets and are present in the environment of a veterinary referral hospital

2021 ◽  
Author(s):  
Michael Brilhante ◽  
Stefanie Gobeli Brawand ◽  
Andrea Endimiani ◽  
Helene Rohrbach ◽  
Sonja Kittl ◽  
...  
Keyword(s):  
High Risk ◽  
Klebsiella Pneumoniae ◽  
Genetic Relationships ◽  
Clinical Environment ◽  
Structural Variations ◽  
Veterinary Clinic ◽  
Antimicrobial Resistance Genes ◽  
Carbapenemase Gene ◽  
Genetic Features ◽  
Almost All

Abstract Objectives Infections with carbapenem-resistant Enterobacterales (CRE) are an emerging problem in pets and a major threat to public health. We determined the genetic relationships among carbapenemase-producing Klebsiella pneumoniae (CPKp) strains causing infections in hospitalized pets in a veterinary clinic and those found in the environment. Methods WGS was performed with both the Illumina and Nanopore platforms. Searches of genetic features were performed using several databases and bioinformatics tools, and phylogeny was assessed by whole-genome MLST (wgMLST) using SeqSphere and SNP calling with Snippy. Results WGS analysis of the CPKp strains identified all environmental and almost all animal strains as the high-risk clone ST11, with the exception of two strains that belonged to ST307. All CPKp belonged to novel complex types (CTs) and carried a conjugative 63 kb IncL plasmid encoding the carbapenemase gene blaOXA-48, yersiniabactin and other virulence factors. Although all CPKp ST11 strains carried additional similar IncR plasmids harbouring multiple antimicrobial resistance genes (ARGs), such as the plasmid-mediated blaDHA-1 AmpC gene, some structural variations were observed. The two ST307 strains carried identical 156 kb MDR IncFIB(K) plasmids with several ARGs, including the blaCTX-M-15 ESBL gene. Both wgMLST and cgSNP analysis confirmed that CPKp strains of the same ST were genetically highly related independent of the source of isolation. Conclusions This study demonstrated that the clinical CPKp strains were highly related to those contaminating the clinical environment. These findings confirmed nosocomial spread and highlight veterinary hospitals as a source of CPKp, which may further spread to animals, the environment and humans.

scholarly journals Group B streptococcus colonization of pregnant women and their children observed on obstetric and neonatal wards of the University Hospital in Krakow, Poland

2009 ◽  
Vol 58 (2) ◽  
pp. 228-233 ◽  
Author(s):  
Magdalena Strus ◽  
Dorota Pawlik ◽  
Monika Brzychczy-Włoch ◽  
Tomasz Gosiewski ◽  
Krzysztof Rytlewski ◽  
...  
Keyword(s):  
Pregnant Women ◽  
Molecular Typing ◽  
Horizontal Transmission ◽  
Group B Streptococcus ◽  
Normal Pregnancy ◽  
University Hospital ◽  
Hospital Environment ◽  
Eastern Region ◽  
Group B ◽  
Complicated Pregnancy

The study was arranged to assess the actual rates of colonization of pregnant women and their children with group B streptococcus (GBS) in a Polish university hospital. Resistance of these cocci to macrolides and clindamycin was also tested and routes of transmission of GBS were followed in some cases using molecular typing. Colonization with GBS was checked in 340 pregnant women living in the south-eastern region of Poland (Małopolska) in the years 2004–2006. Women with a complicated pregnancy were more often colonized than those with a normal pregnancy (20.0 % versus 17.2 %). Moreover, women with a complicated pregnancy were twice as often colonized with GBS strains with the MLSB phenotype indicating resistance to macrolides and clindamycin. Regarding neonatal colonization by GBS, we found that neonates born from the colonized mothers with a complicated pregnancy were more often colonized with GBS than those from the mothers with a normal pregnancy (35 % versus 26.7 %). By molecular typing of the GBS strains isolated from mothers and their newborns we have been able to suggest the possibility of horizontal transmission of the strains from the hospital environment to newborns. Our results clearly indicate that rates of GBS colonization among pregnant women and neonates in a Polish university hospital have reached levels comparable to those reported in other European clinical centres.

scholarly journals Genomic Investigation Reveals Contaminated Detergent as the Source of an Extended-Spectrum-β-Lactamase-Producing Klebsiella michiganensis Outbreak in a Neonatal Unit

2020 ◽  
Vol 58 (5) ◽  
Author(s):  
Paul Chapman ◽  
Brian M. Forde ◽  
Leah W. Roberts ◽  
Haakon Bergh ◽  
Debra Vesey ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Klebsiella Oxytoca ◽  
Multidrug Resistant ◽  
Hospital Environment ◽  
Nucleotide Polymorphism ◽  
Taxonomic Assignment ◽  
Single Nucleotide ◽  
Content Type ◽  
Extended Spectrum ◽  
Antimicrobial Resistance Genes

ABSTRACT Klebsiella species are problematic pathogens in neonatal units and may cause outbreaks, for which the sources of transmission may be challenging to elucidate. We describe the use of whole-genome sequencing (WGS) to investigate environmental sources of transmission during an outbreak of extended-spectrum-β-lactamase (ESBL)-producing Klebsiella michiganensis colonizing neonates. Ceftriaxone-resistant Klebsiella spp. isolated from neonates (or their mothers) and the hospital environment were included. Short-read sequencing (Illumina) and long-read sequencing (MinION; Oxford Nanopore Technologies) were used to confirm species taxonomy, to identify antimicrobial resistance genes, and to determine phylogenetic relationships using single-nucleotide polymorphism profiling. A total of 21 organisms (10 patient-derived isolates and 11 environmental isolates) were sequenced. Standard laboratory methods identified the outbreak strain as an ESBL-producing Klebsiella oxytoca, but taxonomic assignment from WGS data suggested closer identity to Klebsiella michiganensis. Strains isolated from multiple detergent-dispensing bottles were either identical or closely related by single-nucleotide polymorphism comparison. Detergent bottles contaminated by K. michiganensis had been used for washing milk expression equipment. No new cases were identified once the detergent bottles were removed. Environmental reservoirs may be an important source in outbreaks of multidrug-resistant organisms. WGS, in conjunction with traditional epidemiological investigation, can be instrumental in revealing routes of transmission and guiding infection control responses.

scholarly journals Genetic Basis of Multidrug Resistance in Acinetobacter baumannii Clinical Isolates at a Tertiary Medical Center in Pennsylvania

2008 ◽  
Vol 52 (11) ◽  
pp. 3837-3843 ◽  
Author(s):  
Jennifer M. Adams-Haduch ◽  
David L. Paterson ◽  
Hanna E. Sidjabat ◽  
Anthony W. Pasculle ◽  
Brian A. Potoski ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Genetic Basis ◽  
Medical Center ◽  
Multidrug Resistant ◽  
Quinolone Resistance ◽  
Clinical Isolates ◽  
Clinical Microbiology Laboratory ◽  
Carbapenemase Gene ◽  
Methylase Gene ◽  
High Level

ABSTRACT A total of 49 unique clinical isolates of multidrug-resistant (MDR) Acinetobacter baumannii identified at a tertiary medical center in Pittsburgh, Pennsylvania, between August 2006 and September 2007 were studied for the genetic basis of their MDR phenotype. Approximately half of all A. baumannii clinical isolates identified during this period qualified as MDR, defined by nonsusceptibility to three or more of the antimicrobials routinely tested in the clinical microbiology laboratory. Among the MDR isolates, 18.4% were resistant to imipenem. The frequencies of resistance to amikacin and ciprofloxacin were high at 36.7% and 95.9%, respectively. None of the isolates was resistant to colistin or tigecycline. The presence of the carbapenemase gene bla OXA-23 and the 16S rRNA methylase gene armA predicted high-level resistance to imipenem and amikacin, respectively. bla OXA-23 was preceded by insertion sequence ISAba1, which likely provided a potent promoter activity for the expression of the carbapenemase gene. The structure of the transposon defined by ISAba1 differed from those reported in Europe, suggesting that ISAba1-mediated acquisition of bla OXA-23 may occur as an independent event. Typical substitutions in the quinolone resistance-determining regions of the gyrA and parC genes were observed in the ciprofloxacin-resistant isolates. Plasmid-mediated quinolone resistance genes, including the qnr genes, were not identified. Fifty-nine percent of the MDR isolates belonged to a single clonal group over the course of the study period, as demonstrated by pulsed-field gel electrophoresis.

scholarly journals OXA-24 Carbapenemase Gene Flanked by XerC/XerD-Like Recombination Sites in Different Plasmids from Different Acinetobacter Species Isolated during a Nosocomial Outbreak

2010 ◽  
Vol 54 (6) ◽  
pp. 2724-2727 ◽  
Author(s):  
María Merino ◽  
Joshi Acosta ◽  
Margarita Poza ◽  
Francisca Sanz ◽  
Alejandro Beceiro ◽  
...  
Keyword(s):  
Horizontal Transmission ◽  
Carbapenem Resistance ◽  
Acinetobacter Calcoaceticus ◽  
Multidrug Resistant ◽  
Clinical Strain ◽  
Acinetobacter Species ◽  
Gene Comparison ◽  
Carbapenemase Gene ◽  
Large Outbreak ◽  
Culture Sample

ABSTRACT A clinical strain of Acinetobacter calcoaceticus resistant to carbapenems was isolated from a blood culture sample from an inpatient in a hospital in Madrid (Spain) during a large outbreak of infection (affecting more than 300 inpatients), caused by a multidrug-resistant Acinetobacter baumannii clone. The carbapenem resistance in both the A. calcoaceticus and A. baumannii clones was due to a bla OXA-24 gene harbored in different plasmids. The plasmids were fully sequenced, revealing the presence of site-specific recombination binding sites putatively involved in mobilization of the bla OXA-24 gene. Comparison of plasmids contained in the two strains revealed possible horizontal transmission of resistance genes between the Acinetobacter species.

scholarly journals Characterization and PCR-Based Replicon Typing of Resistance Plasmids in Acinetobacter baumannii

2010 ◽  
Vol 54 (10) ◽  
pp. 4168-4177 ◽  
Author(s):  
Alessia Bertini ◽  
Laurent Poirel ◽  
Pauline D. Mugnier ◽  
Laura Villa ◽  
Patrice Nordmann ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Horizontal Transmission ◽  
Opportunistic Pathogen ◽  
Multidrug Resistant ◽  
Conjugative Plasmid ◽  
Homogeneous Groups ◽  
Nucleotide Homology ◽  
Carbapenemase Gene ◽  
Resistance Plasmids

ABSTRACT Acinetobacter baumannii is an opportunistic pathogen, especially in intensive care units, and multidrug-resistant isolates have increasingly been reported during the last decade. Despite recent progress in knowledge of antibiotic resistance mechanisms in A. baumannii, little is known about the genetic factors driving isolates toward multidrug resistance. In the present study, the A. baumannii plasmids were investigated through the analysis and classification of plasmid replication systems and the identification of A. baumannii-specific mobilization and addiction systems. Twenty-two replicons were identified by in silico analysis, and five other replicons were identified and cloned from previously uncharacterized A. baumannii resistance plasmids carrying the OXA-58 carbapenem-hydrolyzing oxacillinase. Replicons were classified into homology groups on the basis of their nucleotide homology. A novel PCR-based replicon typing scheme (the A. baumannii PCR-based replicon typing [AB-PBRT] method) was devised to categorize the A. baumannii plasmids into homogeneous groups on the basis of the nucleotide homology of their respective replicase genes. The AB-PBRT technique was applied to a collection of multidrug-resistant A. baumannii clinical isolates carrying the bla OXA-58 or bla OXA-23 carbapenemase gene. A putative complete conjugative apparatus was identified on one plasmid whose self-conjugative ability was demonstrated in vitro. We showed that this conjugative plasmid type was widely diffused in our collection, likely representing the most important vehicle promoting the horizontal transmission of A. baumannii resistance plasmids.

scholarly journals First Report of an OXA-48-Producing Multidrug-Resistant Proteus mirabilis Strain from Gaza, Palestine

2015 ◽  
Vol 59 (7) ◽  
pp. 4305-4307 ◽  
Author(s):  
Liang Chen ◽  
Nahed Al Laham ◽  
Kalyan D. Chavda ◽  
Jose R. Mediavilla ◽  
Michael R. Jacobs ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Proteus Mirabilis ◽  
Draft Genome ◽  
Multidrug Resistant ◽  
Aminoglycoside Resistance ◽  
Content Type ◽  
Antimicrobial Resistance Genes ◽  
Carbapenemase Gene ◽  
Genes Encoding ◽  
Draft Genome Sequencing

ABSTRACTWe report the first multidrug-resistantProteus mirabilisstrain producing the carbapenemase OXA-48 (Pm-OXA-48) isolated at Al-Shifa hospital in Gaza, Palestine. Draft genome sequencing of Pm-OXA-48 identified 16 antimicrobial resistance genes, encoding resistance to β-lactams, aminoglycosides, fluoroquinolones, phenicols, streptothricin, tetracycline, and trimethoprim-sulfamethoxazole. Complete sequencing of theblaOXA-48-harboring plasmid revealed that it is a 72 kb long IncL/M plasmid, harboring carbapenemase geneblaOXA-48, extended spectrum β-lactamase geneblaCTX-M-14, and aminoglycoside resistance genesstrA,strB, andaph(3′)-VIb.

scholarly journals The Prevalence of Exoenzyme S Gene in Multidrug-Sensitive and Multidrug-Resistant Pseudomonas aeruginosa Clinical Strains

2017 ◽  
Vol 66 (4) ◽  
pp. 427-431 ◽  
Author(s):  
Tomasz Bogiel ◽  
Aleksander Deptuła ◽  
Joanna Kwiecińska-Piróg ◽  
Małgorzata Prażyńska ◽  
Agnieszka Mikucka ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Virulence Factors ◽  
Multidrug Resistant ◽  
Hospital Environment ◽  
Antibiotic Resistant ◽  
Exoenzyme S ◽  
Clinical Specimens ◽  
Antimicrobial Resistance Genes ◽  
The Difference ◽  
Susceptibility Patterns

Pseudomonas aeruginosa rods are one of the most commonly isolated microorganisms from clinical specimens, usually responsible for nosocomial infections. Antibiotic-resistant P. aeruginosa strains may present reduced expression of virulence factors. This fact may be caused by appropriate genome management to adapt to changing conditions of the hospital environment. Virulence factors genes may be replaced by those crucial to survive, like antimicrobial resistance genes. The aim of this study was to evaluate, using PCR, the occurrence of exoenzyme S-coding gene (exoS) in two distinct groups of P. aeruginosa strains: 83 multidrug-sensitive (MDS) and 65 multidrug-resistant (MDR) isolates. ExoS gene was noted in 72 (48.7%) of the examined strains: 44 (53.0%) MDS and 28 (43.1%) MDR. The observed differences were not statistically significant (p = 0.1505). P. aeruginosa strains virulence is rather determined by the expression regulation of the possessed genes than the difference in genes frequency amongst strains with different antimicrobial susceptibility patterns.

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