scholarly journals A67 Bloodstream infections by carbapenem-resistant Klebsiella pneumoniae subsp. pneumoniae: Bayesian phylogenetic analysis of whole genomes

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
Eleonora Cella ◽  
Davide Leoni ◽  
Walter Mirandola ◽  
Carla Fontana ◽  
Loredana Sarmati ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Klebsiella Pneumoniae ◽  
Infection Control ◽  
Minimum Spanning Tree ◽  
Hospital Setting ◽  
Bloodstream Infections ◽  
Multidrug Resistant ◽  
Epidemiological Surveillance ◽  
Health Concern ◽  
Hospital Infection Control

Abstract Bloodstream infection (BSI) caused by carbapenemase-producing Enterobacteriaceae (CPE) is a major public health concern, particularly in the hospital setting. The rapid detection of resistance patterns is of paramount importance for establishing the proper antibiotic regime. In addition, in countries where CPE are endemic, it is also important to evaluate genetic relationship among the isolates in order to trace pathogen circulation and to improve the infection control programs. This study is an application of a rapid blood culture (BC) workflow consisting of fast reporting of Gram stain results, rapid pathogen identification (using MALDI TOF technology), and a molecular assay for the detection of the major genes conferring resistance, all of them performed directly from positive BCs. The application of phylogenetic and phylodynamic analyses to bacterial whole-genome sequencing (WGS) data have become essential in the epidemiological surveillance of multidrug-resistant nosocomial pathogens. We analyzed 40 strains of Klebsiella pneumoniae subsp. pneumoniae (KP) carrying blaKPC (KP-KPC), randomly selected among 147 CPE identified from BCs collected from consecutive patients from 2013 to 2016. The number of BSIs-related CPE were 23, 31, 43, and 50 in 2013, 2014, 2015, and 2016, respectively. Among 147 CPE isolates, 143 were KP and four were Escherichia coli (EC). The gene blaKPC was detected in 117 strains of KP and in four strains of EC. Other carbapenemase genes, such as blaVIM and blaOXA-48, were detected in four and nine different isolates of KP, respectively. Moreover, 13 KP strains carried two resistance genes: twelve vehicled blaKPC plus blaVIM and one blaKPC plus blaOXA-48. Phylogenetic analysis of bacterial WGS data was used to investigate the evolution and spatial dispersion of KP in support of hospital infection control. The maximum likelihood tree showed two main clades statistically supported, with statistical support for several subclusters within as well. The minimum spanning tree showed mixing between sequences from different years and wards with only few specific groups. Bayesian analyses are ongoing, as the aid of Bayesian genomic epidemiology in combination with active microbial surveillance is highly informative regarding the development of effective infection prevention in healthcare settings or constant strain reintroduction.

scholarly journals Molecular Epidemiological Surveillance of CTX-M-15-producing Klebsiella pneumoniae from the patients of a teaching hospital.

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 444
Author(s):  
Muzaheed Muzaheed ◽  
Naveed Sattar Shaikh ◽  
Saeed Sattar Shaikh ◽  
Sadananda Acharya ◽  
Shajiya Sarwar Moosa ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Hospital Setting ◽  
Multidrug Resistant ◽  
Influential Factor ◽  
Detection Methods ◽  
Epidemiological Surveillance ◽  
Clinical Samples ◽  
Resistant Bacteria ◽  
Drug Resistant ◽  
Drug Resistant Bacteria

Background  The presence of Extended-spectrum β-lactamase (ESBL) positive bacteria in hospital setting is an aggravating influential factor for hospitalized patients, and its consequences may be hazardous. Therefore, there is a need for rapid detection methods for newly emerging drug-resistant bacteria. This study was aimed at the molecular characterization of ESBL-positive Klebsiella pneumoniae isolates recovered from clinical samples.   Methods  A total of 513 K. pneumoniae isolates were obtained from various clinical samples during June 2019 to May 2020. The collected isolates were investigated for antimicrobial susceptibility (antibiogram), and PCR and DNA sequencing were performed to analyse the ESBL genes.   Results  Among the 513 isolates, as many as 359 (69.9%) were ESBL producers and 87.5% were multi-drug resistant, while none had resistance to imipenem. PCR scored 3% blaTEM, 3% blaSHV, and 60% blaCTX-M-15 genes for the tested isolates.   Conclusion  The study showed that CTX-M-15 was the major prevalent ESBL type among the isolates. Additionally, all the isolates were susceptible to carbapenems. Screening and detection of ESBL tests are necessary among all isolates from the enterobacteriaceae family in routine microbiology laboratory to prevent associated nosocomial infections. A larger study is essential to understand molecular epidemiology of ESBL producing organisms to minimize morbidities due to these multidrug resistant organisms.

scholarly journals Genomic Analysis of Multiresistant Staphylococcus capitis Associated with Neonatal Sepsis

2018 ◽  
Vol 62 (11) ◽  
Author(s):  
Glen P. Carter ◽  
James E. Ussher ◽  
Anders Gonçalves Da Silva ◽  
Sarah L. Baines ◽  
Helen Heffernan ◽  
...  
Keyword(s):  
Neonatal Sepsis ◽  
Neonatal Intensive Care ◽  
Genomic Analysis ◽  
Bloodstream Infections ◽  
Multidrug Resistant ◽  
Comparative Genomic ◽  
Coagulase Negative Staphylococci ◽  
Content Type ◽  
Staphylococcus Capitis ◽  
Hospital Infection Control

ABSTRACT Coagulase-negative staphylococci (CoNS), such as Staphylococcus capitis, are major causes of bloodstream infections in neonatal intensive care units (NICUs). Recently, a distinct clone of S. capitis (designated S. capitis NRCS-A) has emerged as an important pathogen in NICUs internationally. Here, 122 S. capitis isolates from New Zealand (NZ) underwent whole-genome sequencing (WGS), and these data were supplemented with publicly available S. capitis sequence reads. Phylogenetic and comparative genomic analyses were performed, as were phenotypic assessments of antimicrobial resistance, biofilm formation, and plasmid segregational stability on representative isolates. A distinct lineage of S. capitis was identified in NZ associated with neonates and the NICU environment. Isolates from this lineage produced increased levels of biofilm, displayed higher levels of tolerance to chlorhexidine, and were multidrug resistant. Although similar to globally circulating NICU-associated S. capitis strains at a core-genome level, NZ NICU S. capitis isolates carried a novel stably maintained multidrug-resistant plasmid that was not present in non-NICU isolates. Neonatal blood culture isolates were indistinguishable from environmental S. capitis isolates found on fomites, such as stethoscopes and neonatal incubators, but were generally distinct from those isolates carried by NICU staff. This work implicates the NICU environment as a potential reservoir for neonatal sepsis caused by S. capitis and highlights the capacity of genomics-based tracking and surveillance to inform future hospital infection control practices aimed at containing the spread of this important neonatal pathogen.

Spread of NDM-producing Klebsiella pneumoniae in a tertiary Greek hospital

2021 ◽  
Author(s):  
Κonstantina Kontopoulou ◽  
Georgios Meletis ◽  
Styliani Pappa ◽  
Sofia Zotou ◽  
Katerina Tsioka ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Hospital Setting ◽  
Tertiary Hospital ◽  
Whole Genome Sequence ◽  
Health Concern ◽  
Resistant Bacteria ◽  
New Delhi ◽  
Whole Genome

AbstractBacterial carbapenem resistance, especially when mediated by transferable carbapenemases, is of important public health concern. An increased number of metallo-β-lactamase (MBL)-producing Klebsiella pneumoniae strains isolated in a tertiary hospital in Thessaloniki, Greece, called for further genetic investigation.The study included 29 non-repetitive carbapenem resistant K. pneumoniae isolates phenotypically characterized as MBL-producers collected in a tertiary hospital in Greece. The isolates were screened for the detection of carbapenemase genes (K. pneumoniae carbapenemase (blaKPC), Verona-integron-encoded MBL-1 (blaVIM-1), imipenemase (blaIMP), oxacillinase-48 (blaOXA-48) and New Delhi MBL (blaNDM)). The genetic relationship of the isolates was determined by Random Amplified Polymorphic DNA (RAPD) analysis. The whole genome sequences (WGS) from two NDM-positive K. pneumoniae isolates were further characterized.The presence of New Delhi MBL (blaNDM) gene was confirmed in all K. pneumoniae isolates, while blaKPC and blaVIM-1 genes were co-detected in one and two isolates, respectively. The RAPD analysis showed that the isolates were clustered into two groups. The whole genome sequence analysis of two K. pneumoniae isolates revealed that they belonged to the sequence type 11, they carried the blaNDM-1 gene, and exhibited differences in the number and type of the plasmids and the resistant genes.All MBL-producing K. pneumoniae isolates of the study harbored a blaNDM gene, while WGS analysis revealed genetic diversity in resistance genes. Continuous surveillance is needed to detect the emergence of new clones in a hospital setting, while application of antimicrobial stewardship is the only way to reduce the spread of multi-resistant bacteria.

Systematic surveillance and meta-analysis on the prevalence of Metallo-β-Lactamase producers among carbapenem resistant clinical isolates in Pakistan

2020 ◽  
Author(s):  
Noor ul Ain ◽  
Samyyia Abrar ◽  
Rehan Ahmad Khan ◽  
Abdul Hannan ◽  
Namrah Imran ◽  
...  
Keyword(s):  
Infection Control ◽  
Meta Analysis ◽  
Carbapenem Resistance ◽  
Epidemiological Surveillance ◽  
Health Concern ◽  
New Delhi ◽  
Significant Heterogeneity ◽  
Carbapenem Resistant ◽  
Geographical Regions ◽  
Clinically Significant

Abstract Background: Rapid emergence of carbapenem resistance (CR) is a health concern of pertinent importance. Epidemiological surveillance of CR at global and indigenous level (Pakistan) can help to improve infection control strategy and establish pharmacovigilance programs. This study evaluate the prevalence of clinically significant CR isolates, and its genetic variant distribution among different geographical regions of Pakistan. Methods: A meta-analysis was conducted to present the current rate of CR infections and prevalence of Metallo-β-lactamases (MBLs). The proposed subject was researched using robustic electronic databases a) PubMed b) PubMed Central® (PMC), and c) Google Scholar to identify the available literature. Thereafter, relevant data was extracted and statistical analysis was performed using STATA version 14. Result: A total of 110 relevant studies were identified with 19 meeting the inclusion criteria for the meta-analysis of CR, while 22 for MBLs. Pooled rate for carbapenem resistance was determined to be 0.28 (95% CI: 0.26-0.31) with overall significant heterogeneity (I 2 =99.61%, p<0.001) and significant estimated score ES=0 (Z=22.65, p<0.001). In case of Pakistan, the overall pooled proportion of MBL producers was 0.34 (95% CI: 0.29-0.39) with overall heterogeneity significance (I 2 =99.62%, p<0.001) and respective significant ES=0 (Z=13.17, p<0.001). Conclusively, diverse variants of carbapenemases (VIM, IMP, NDM, KPC, GIM, SIM) along with other co-existing β-lactamase variants (OXA, TEM, SHV, CTX-M) have been reported across the country. However, New Delhi Metallo-β-lactamase (NDM)-variants were reported in predominant literature. Conclusion: The prevalence of CR isolates in Pakistan is alarming, associated with MBL production primarily evident from the studies. The study emphasizes the need for regular surveillance, pharmacovigilance and antibiotic stewardship programs to ensure the availability of data to the authorities for preemptive measures of infection control.

scholarly journals Isolation and Characterization of Two Klebsiella pneumoniae Phages Encoding Divergent Depolymerases

2020 ◽  
Vol 21 (9) ◽  
pp. 3160 ◽  
Author(s):  
Pilar Domingo-Calap ◽  
Beatriz Beamud ◽  
Lucas Mora-Quilis ◽  
Fernando González-Candelas ◽  
Rafael Sanjuán
Keyword(s):  
Klebsiella Pneumoniae ◽  
Multidrug Resistant ◽  
Health Concern ◽  
Resistant Bacteria ◽  
Isolation And Characterization ◽  
The Family ◽  
Important Challenge ◽  
Tail Spike ◽  
Reference Strains

The emergence of multidrug-resistant bacteria is a major global health concern. The search for new therapies has brought bacteriophages into the spotlight, and new phages are being described as possible therapeutic agents. Among the bacteria that are most extensively resistant to current antibiotics is Klebsiella pneumoniae, whose hypervariable extracellular capsule makes treatment particularly difficult. Here, we describe two new K. pneumoniae phages, πVLC5 and πVLC6, isolated from environmental samples. These phages belong to the genus Drulisvirus within the family Podoviridae. Both phages encode a similar tail spike protein with putative depolymerase activity, which is shared among other related phages and probably determines their ability to specifically infect K. pneumoniae capsular types K22 and K37. In addition, we found that phage πVLC6 also infects capsular type K13 and is capable of striping the capsules of K. pneumoniae KL2 and KL3, although the phage was not infectious in these two strains. Genome sequence analysis suggested that the extended tropism of phage πVLC6 is conferred by a second, divergent depolymerase. Phage πVLC5 encodes yet another putative depolymerase, but we found no activity of this phage against capsular types other than K22 and K37, after testing a panel of 77 reference strains. Overall, our results confirm that most phages productively infected one or few Klebsiella capsular types. This constitutes an important challenge for clinical applications.

Persisting intrahospital transmission of multidrug-resistant Klebsiella pneumoniae and challenges for infection control

2019 ◽  
Vol 40 (8) ◽  
pp. 904-909 ◽  
Author(s):  
Isabelle Vock ◽  
Sarah Tschudin-Sutter
Keyword(s):  
Klebsiella Pneumoniae ◽  
Infection Control ◽  
Multidrug Resistant ◽  
Global Scale ◽  
Resistance Mechanisms ◽  
Healthcare Associated Infections ◽  
The Past ◽  
Healthcare Settings ◽  
Healthcare Associated ◽  
Antibiotic Agents

AbstractIn the past several decades, the incidence of Klebsiella pneumoniae harboring resistance mechanisms against multiple antibiotic agents has increased on a global scale. We discuss reasons for ongoing transmission of multidrug-resistant K. pneumoniae in healthcare settings, which has resulted in the successful spread and establishment of this pathogen. It is now one of the most important causes of healthcare-associated infections worldwide.

scholarly journals A Novel Cecropin D-Derived Short Cationic Antimicrobial Peptide Exhibits Antibacterial Activity Against Wild-Type and Multidrug-Resistant Strains of Klebsiella pneumoniae and Pseudomonas aeruginosa

2020 ◽  
Vol 16 ◽  
pp. 117693432093626
Author(s):  
Iván Darío Ocampo-Ibáñez ◽  
Yamil Liscano ◽  
Sandra Patricia Rivera-Sánchez ◽  
José Oñate-Garzón ◽  
Ashley Dayan Lugo-Guevara ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibacterial Activity ◽  
Klebsiella Pneumoniae ◽  
Multidrug Resistant ◽  
Clinical Isolates ◽  
Health Concern ◽  
Wild Type ◽  
Cationic Antimicrobial Peptide ◽  
Promising Alternative ◽  
Resistant Strains

Infections caused by multidrug-resistant (MDR) Pseudomonas aeruginosa and Klebsiella pneumoniae are a serious worldwide public health concern due to the ineffectiveness of empirical antibiotic therapy. Therefore, research and the development of new antibiotic alternatives are urgently needed to control these bacteria. The use of cationic antimicrobial peptides (CAMPs) is a promising candidate alternative therapeutic strategy to antibiotics because they exhibit antibacterial activity against both antibiotic susceptible and MDR strains. In this study, we aimed to investigate the in vitro antibacterial effect of a short synthetic CAMP derived from the ΔM2 analog of Cec D-like (CAMP-CecD) against clinical isolates of K pneumoniae (n = 30) and P aeruginosa (n = 30), as well as its hemolytic activity. Minimal inhibitory concentrations (MICs) and minimal bactericidal concentrations (MBCs) of CAMP-CecD against wild-type and MDR strains were determined by the broth microdilution test. In addition, an in silico molecular dynamic simulation was performed to predict the interaction between CAMP-CecD and membrane models of K pneumoniae and P aeruginosa. The results revealed a bactericidal effect of CAMP-CecD against both wild-type and resistant strains, but MDR P aeruginosa showed higher susceptibility to this peptide with MIC values between 32 and >256 μg/mL. CAMP-CecD showed higher stability in the P aeruginosa membrane model compared with the K pneumoniae model due to the greater number of noncovalent interactions with phospholipid 1-Palmitoyl-2-oleyl-sn-glycero-3-(phospho-rac-(1-glycerol)) (POPG). This may be related to the boosted effectiveness of the peptide against P aeruginosa clinical isolates. Given the antibacterial activity of CAMP-CecD against wild-type and MDR clinical isolates of P aeruginosa and K pneumoniae and its nonhemolytic effects on human erythrocytes, CAMP-CecD may be a promising alternative to conventional antibiotics.

scholarly journals Clinical and Molecular Description of a High-Copy IncQ1 KPC-2 Plasmid Harbored by the International ST15 Klebsiella pneumoniae Clone

mSphere ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Willames M. B. S. Martins ◽  
Marisa F. Nicolas ◽  
Yang Yu ◽  
Mei Li ◽  
Priscila Dantas ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Copy Number ◽  
Carbapenem Resistance ◽  
Bloodstream Infections ◽  
Illumina Miseq ◽  
Clinical Analysis ◽  
High Copy Number ◽  
Health Concern ◽  
Helper Plasmid ◽  
Content Type

ABSTRACT This study provides the genomic characterization and clinical description of bloodstream infections (BSI) cases due to ST15 KPC-2 producer Klebsiella pneumoniae. Six KPC-K. pneumoniae isolates were recovered in 2015 in a tertiary Brazilian hospital and were analyzed by whole-genome sequencing (WGS) (Illumina MiSeq short reads). Of these, two isolates were further analyzed by Nanopore MinION sequencing, allowing complete chromosome and plasmid circularization (hybrid assembly), using Unicycler software. The clinical analysis showed that the 30-day overall mortality for these BSI cases was high (83%). The isolates exhibited meropenem resistance (MICs, 32 to 128 mg/liter), with 3/6 isolates resistant to polymyxin B. The conjugative properties of the blaKPC-2 plasmid and its copy number were assessed by standard conjugation experiments and sequence copy number analysis. We identified in all six isolates a small (8.3-kb), high-copy-number (20 copies/cell) non-self-conjugative IncQ plasmid harboring blaKPC-2 in a non-Tn4401 transposon. This plasmid backbone was previously reported to harbor blaKPC-2 only in Brazil, and it could be comobilized at a high frequency (10−4) into Escherichia coli J53 and into several high-risk K. pneumoniae clones (ST258, ST15, and ST101) by a common IncL/M helper plasmid, suggesting the potential of international spread. This study thus identified the international K. pneumoniae ST15 clone as a carrier of blaKPC-2 in a high-copy-number IncQ1 plasmid that is easily transmissible among other common Klebsiella strains. This finding is of concern since IncQ1 plasmids are efficient antimicrobial resistance determinant carriers across Gram-negative species. The spread of such carbapenemase-encoding IncQ1 plasmids should therefore be closely monitored. IMPORTANCE In many parts of the world, carbapenem resistance is a serious public health concern. In Brazil, carbapenem resistance in Enterobacterales is mostly driven by the dissemination of KPC-2-producing K. pneumoniae clones. Despite being endemic in this country, only a few reports providing both clinical and genomic data are available in Brazil, which limit the understanding of the real clinical impact caused by the dissemination of different clones carrying blaKPC-2 in Brazilian hospitals. Although several of these KPC-2-producer K. pneumoniae isolates belong to the clonal complex 258 and carry Tn4401 transposons located on large plasmids, a concomitant emergence and silent dissemination of small high-copy-number blaKPC-2 plasmids are of importance, as described in this study. Our data identify a small high-copy-number IncQ1 KPC plasmid, its clinical relevance, and the potential for conjugative transfer into several K. pneumoniae isolates, belonging to different international lineages, such as ST258, ST101, and ST15.

scholarly journals Next-Generation Epidemiology: Using Real-Time Core Genome Multilocus Sequence Typing To Support Infection Control Policy

2016 ◽  
Vol 54 (12) ◽  
pp. 2850-2853 ◽  
Author(s):  
John P. Dekker ◽  
Karen M. Frank
Keyword(s):  
Infection Control ◽  
Real Time ◽  
Core Genome ◽  
Hospital Setting ◽  
Control Policy ◽  
Multidrug Resistant ◽  
Resistant Bacteria ◽  
Multidrug Resistant Bacteria ◽  
Substantial Morbidity ◽  
Multilocus Sequencing

Multidrug-resistant bacteria are responsible for substantial morbidity and mortality worldwide. Tracking the nosocomial spread of resistant bacteria is critical to infection control. Mellmann et al. (J. Clin. Microbiol. 54:2874–2881, 2016, http://dx.doi.org/10.1128/JCM.00790-16 ) have described prospective whole-genome sequencing with core genome multilocus sequencing typing (cgMLST) analysis for real-time surveillance and have addressed the practical aspects of implementing this type of operation in the hospital setting.

Sign in / Sign up

Export Citation Format

Share Document