Whole genome sequencing of carbapenem-resistant Klebsiella pneumoniae: evolutionary analysis for outbreak investigation

2020 ◽  
Vol 15 (3) ◽  
pp. 203-212 ◽  
Author(s):  
Carla Fontana ◽  
Silvia Angeletti ◽  
Walter Mirandola ◽  
Eleonora Cella ◽  
Lai Alessia ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Minimum Spanning Tree ◽  
Blood Stream Infection ◽  
Hospital Setting ◽  
Blood Stream ◽  
Resistant Bacteria ◽  
Klebsiella Pneumonia ◽  
Evolutionary Analysis ◽  
Carbapenem Resistant

Aim: Carbapenemase-resistant Enterobacteriaceae represents a major concern in hospital setting. Materials & methods: The evolutionary history of carbapenem-resistant Klebsiella pneumonia strains was analyzed by core genome multilocus sequence typing and Bayesian phylogenesis by whole genomes sequencing. Results: A great increase carbapenem-resistant K. pneumoniae causing blood stream infection was observed in the years 2015–2016. At multilocus sequence typing (MLST), they were prevalently ST512 and ST101. ST512 were core genome (cg)MLST 53, while ST101 mainly cgMLST453. The minimum-spanning tree, based on cgMLST, showed strains clustering based on the different STs. By Bayesian phylogenetic analysis, maximum clade credibility tree showed that strains were introduced in the year 2005 with the most probable location in the ICU ward. Two outbreaks by ST101 and ST512 strains with Tower T8 as the probable location were evidenced. Conclusion: Molecular epidemiology is a powerful tool to track the way of transmission of resistant bacteria within the hospital setting.

scholarly journals 223. The Value of Neutrophil to Lymphocyte Count Ratio for Predicting the Clinical Outcomes of Patients with Carbapenem-resistant Klebsiella pneumonia Blood Stream Infection

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S219-S219
Author(s):  
Heng Wu
Keyword(s):  
Lymphocyte Count ◽  
Blood Stream Infection ◽  
Significant Risk ◽  
Blood Stream ◽  
Apache Ii ◽  
Apache Ii Score ◽  
Klebsiella Pneumonia ◽  
Record System ◽  
Count Ratio ◽  
Carbapenem Resistant

Abstract Background The neutrophil to lymphocyte count ratio (NLR) has been recognized as a useful marker of inflammation. But, the prognostic function of NLR in patients with Carbapenem-resistant Klebsiella pneumonia (CRKP) blood stream infection is still largely unknown. The aim of this study was to explore the relationship between postoperative NLR and mortality in those patients. Methods We performed a retrospective study based on the database from Computerized Patient Record System in Sir Run Run Shaw Hospital from 1/1/2017 to 31/10/2020. Logistic analysis was performed to assess the associations between NLR and 28-day mortality. Multivariate analyses were used to control for confounders. Results A total of 134 CRKP blood stream infection inpatients were included in this study, including 54 fatal cases and 80 survival cases on the 28-day after the onset of CRKP BSI, the overall 28-day mortality rate of patients with a CRKP BSI episode was 40.3% (54/134). We conducted a multivariate analysis on these 134 patients and found that APACHE II score on the 4th day (OR 1.379 95% CI 1.065- 1.785, p = 0.015), NLR on the 4th day (OR 1.134 95% CI 1.054- 1.221, p = 0.001) were significant risk factors for the 28-day mortality of CRKP BSI patients Conclusion Elevated NLR was significantly associated with increased 28-day mortality as well as APACHE II score on the 4th day after first positive culture.NLR is promising to be a readily available and independent prognostic biomarker for patients with CRKP blood stream infection. Disclosures All Authors: No reported disclosures

Polymyxin B infusion related respiratory arrest: A case report

2021 ◽  
Vol 6 (4) ◽  
pp. 241-244
Author(s):  
Subhajit Sen ◽  
Suresh Ramasubban ◽  
M. Surya Kumar ◽  
Sanjay Bhaumik ◽  
Debasis Rout
Keyword(s):  
Blood Stream Infection ◽  
Stable Condition ◽  
Kidney Injury ◽  
Polymyxin B ◽  
Blood Stream ◽  
Respiratory Arrest ◽  
Klebsiella Pneumonia ◽  
Carbapenem Resistant ◽  
History Of ◽  
Work Up

A 73 years old male, known hypertensive on medication, with the history of SARS-CoV-2 infection nine months ago, presented to us with mucormycosis, he was treated with Liposomal amphotericin B initially. He developed acute kidney injury with recurrent pulmonary oedema requiring ICU admission and Haemodialysis. He later developed catheter related blood stream infection that grew Carbapenem resistant Klebsiella pneumonia and was started on Polymyxin B. However from day 3 of antibiotics he started to develop recurrent respiratory arrest with no apparent cause. He required a brief period of mechanical ventilation and was successfully weaned. He had recurrent such episodes with no apparent cause. After extensive work up and literature search it was diagnosed as Polymyxin B induced respiratory failure. Polymyxins were stopped, patient was discharged in a stable condition after five days of further observation and is currently on follow up with no such episode of dyspnoea.

scholarly journals Use of Next Generation Sequencing and Synergy Susceptibility Testing in Diagnosis and Treatment of Carbapenem-Resistant Klebsiella pneumoniae Blood Stream Infection

2018 ◽  
Vol 2018 ◽  
pp. 1-4
Author(s):  
Yuetian Yu ◽  
Fupin Hu ◽  
Cheng Zhu ◽  
Erzhen Chen ◽  
Liangjing Lu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Klebsiella Pneumoniae ◽  
Lupus Erythematosus ◽  
Susceptibility Testing ◽  
Blood Stream Infection ◽  
Blood Stream ◽  
Next Generation ◽  
Carbapenem Resistant ◽  
Appropriate Treatment ◽  
Generation Sequencing

Early diagnosis and appropriate treatment for carbapenem-resistant Klebsiella pneumoniae (CR-Kp) infection is a big challenge for clinicians due to its high mortality. Every effort has been made to improve its clinical outcomes. However, treatment according to synergy susceptibility testing has never been reported in the literature. We reported a 29-year-old systemic lupus erythematosus female with CR-Kp blood stream infection. We highlighted the identification by next generation sequencing and treatment according to synergy susceptibility testing in the case.

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.

Successful Treatment of a Case of Intracranial Infection Caused by Carbapenem-Resistant Klebsiella Pneumonia After Craniocerebral Operation in Patient with Severe Traumatic Brain Injury

2018 ◽  
Vol 10 (3) ◽  
pp. 447-450
Author(s):  
Xianchun Zhu ◽  
Jing Wang ◽  
Youmei Huang ◽  
Huaping Zhang
Keyword(s):  
Traumatic Brain Injury ◽  
Brain Injury ◽  
Severe Traumatic Brain Injury ◽  
Bacterial Infections ◽  
Present Report ◽  
Resistant Bacteria ◽  
Klebsiella Pneumonia ◽  
Beta Lactam ◽  
Intracranial Infection ◽  
Carbapenem Resistant

Klebsiella pneumoniae (KP) is one of the most common clinical drug-resistant bacteria, which is mainly related to the production of broad-spectrum beta lactamase and cephalosporin hydrolase. Carbapenems, an atypical beta lactam antibiotic, has been the most effective antibiotic for the treatment of bacterial infections caused by KP in hospital. However, with the extensive application of carbapenem antibiotics in clinic, many reports on carbapenem-resistant Klebsiella Pneumonia (CRKP) have appeared in many parts of the world. The CRKP could cause a higher mortality and morbidity. Here, we report a 26-year-old male patient with severe traumatic brain injury who underwent intracranial infection caused by CRKP after craniocerebral operation. He was successfully cured with a combination of emergency craniotomy, multidisciplinary consultation, effective nursing and strict quarantine measures. In the present report, we emphasize the effective nursing and strict quarantine measures, which contribute to the treatment of bacterial infections caused by KP.

scholarly journals Usefulness of surveillance Cultures for Carbapenem-resistant Enterobacteriaceae, Carbapenem-resistant Pseudomonas aeruginosa and Vancomycin-resistant Enterococci in Hematopoietic Stem Cell Transplant Unit

2020 ◽  
Author(s):  
Elisa Teixeira Mendes ◽  
Matias Chiarastelli Salomão ◽  
Lísia Moura Tomichi ◽  
Maura Salaroli Oliveira ◽  
Mariana Graça ◽  
...  
Keyword(s):  
Blood Stream Infection ◽  
Blood Stream ◽  
Cell Transplant ◽  
Surveillance Culture ◽  
Hematopoietic Stem ◽  
Carbapenem Resistant ◽  
Vancomycin Resistant Enterococci ◽  
Surveillance Cultures ◽  
Vancomycin Resistant ◽  
Carbapenem Resistant Enterobacteriaceae

Abstract Surveillance strategies to detect colonization is an important tool to prevent and control the spread of microorganisms especially among Hematopoietic Stem Cell Transplant (HSCT) patients. Colonization by Multidrug-resistant organisms (MDRO) has been evaluated as a risk factor for blood stream infection (BSI) in HSCT patients. The aim of this study was to evaluate the use of routine surveillance culture to screening colonization and infection by carbapenem-resistant Enterobacteriaceae (CRE), carbapenem-resistant Pseudomonas aeruginosa (CRPa) and vancomycin-resistant enterococci (VRE) in a HSCT unit. Methods Surveillance cultures were collected from patients admitted to the HSCT unit over one-year, with swabs for cultures on admission and then weekly until discharge. We compared surveillance culture positivity for each site and agent, also clinical and epidemiological data according to the colonization status. Results 200 HSCT patients underwent surveillance, with 1.323 samples collected. Infection due to MDRO occurred in 52 (21.5%) patients, among them 45 (86.5%) were blood stream infection (BSI) and 12 (23%) had positive surveillance culture before infection. 554 (41.8%) surveillance cultures were performed for CRPa, 413 (31.2%) for VRE, and 356 (27%) for CRE. Of these, 179 (13.5%) surveillance culture were positive, with greater positivity for oropharynx (6, 35.3%) CRPa, and rectal samples (16, 20.7%) for CRE. Being colonized by any MDRO, CRE (p <0.001) and CRPa (p = 0.027) was associated with a higher risk of infection in the bivariate analysis but being colonized was not associated with risk of death. Conclusion Previous colonization by MDRO was a significant risk factor for infection by these pathogens, mainly colonization by CRE. Overall, rectal swab was the best site with the higher positivity, and the oropharynx was also an option for CRPa investigation. Feces culture showed low positivity and should be avoided. Although the impact of the strategy on the mortality of patients undergoing HSCT is not clear, VRE surveillance should be questioned in auto-HSCT patients as it has an additional cost and little impact on survival.

scholarly journals Risk factors for carbapenem-resistant Acinetobacter baumanii blood stream infections in a neonatal intensive care unit, Delhi, India

2014 ◽  
Vol 8 (08) ◽  
pp. 1049-1054 ◽  
Author(s):  
Ajay Kumar ◽  
Valinderjeet Singh Randhawa ◽  
Nilay Nirupam ◽  
Yogita Rai ◽  
Arvind Saili
Keyword(s):  
Risk Factors ◽  
Breast Milk ◽  
Acinetobacter Baumannii ◽  
Neonatal Intensive Care ◽  
Blood Stream Infection ◽  
Blood Stream ◽  
Acinetobacter Baumanii ◽  
Carbapenem Resistant ◽  
Expressed Breast Milk ◽  
All Cause Mortality

Introduction: Carbapenem-resistant Acinetobacter baumannii (CRAB) infection is being increasingly observed and is associated with significant morbidity and mortality in newborns. In this study, we determined the epidemiology, risk factors, and outcomes of blood stream infection (BSI) caused by CRAB in neonates. Methodology: The clinical charts of neonates who developed Acinetobacter baumannii BSI in the period between 1 January 2010 and 31 December 2012 were reviewed. Results: During the study period, 65 neonates developed Acinetobacter baumannii BSI; 33 were CRAB at an incidence of 0.50 case per 1,000 patient-days. Compared with carbapenem-sensitive Acinetobacter baumannii (CSAB), patients with CRAB BSI had significantly higher prior antimicrobial use, longer duration of ventilation, and late isolation of organisms. Feeding with expressed breast milk was protective. All isolates of Acinetobacter baumenii were sensitive to colistin and tigecycline. The all-cause mortality rates were 27.3% in CRAB and 9.4% in CSAB BSI, respectively (p = 0.074). Conclusions: Neonatal BSI caused by CRAB was not common but caused high mortality. Feeding with breast milk was protective. Lack of effective antibiotics was the major challenge in treating these patients.

scholarly journals Σχέση μεταξύ επίπτωσης βακτηριαιμίας και πολυμορφισμού των Toll like receptors (TLRs) – 2,4,9 σε ασθενείς της ΜΕΘ

2018 ◽  
Author(s):  
Μαρία Χατζή
Keyword(s):  
Blood Stream Infection ◽  
Central Nervous System Infection ◽  
Blood Stream ◽  
Klebsiella Pneumonia ◽  
Ventilator Associated Pneumonia ◽  
Nucleotide Polymorphisms ◽  
Toll Like Receptors ◽  
Chain Reaction ◽  
Single Nucleotide ◽  
Polymerase Chain

Σκοπός : Οι μονονουκλεοτιδικοί πολυμορφισμοί των Toll like υποδοχέων [Toll-like Receptors - Single Nucleotide Polymorphisms (TLR-SNPs)] μπορούν να επηρεάσουν σημαντικά την ευαισθησία του ξενιστή στις λοιμώξεις. Σκοπός της μελέτης ήταν να διερευνηθεί ο συχνότητα τεσσάρων κοινών πολυμορφισμών των Toll-Like Receptors (TLRs) σε βαρέως πάσχοντες ασθενείς των Μονάδων Εντατικής Θεραπείας (ΜΕΘ) και η συσχέτισή τους με την επίπτωση των λοιμώξεων και την έκβαση των ασθενών στην κεντρική Ελλάδα.Μέθοδος: Η συχνότητα εμφάνισης των TLR2-Arg753Gln, TLR4-Asp299Gly, TLR4-Thr399Ile και πολυμορφισμών TLR9-T-1237C, η συσχέτισή τους με την επίπτωση των λοιμώξεων και τις κλινικές εκβάσεις των ασθενών αξιολογήθηκαν προοπτικά σε ασθενείς ΜΕΘ που υποβλήθηκαν σε μηχανικό αερισμό για περισσότερο από 48 ώρες. Η ανίχνευση των πολυμορφισμών έγινε με την αλυσιδωτή αντίδραση πολυμεράσης (Real-time Polymerase-Chain-Reaction –PCR).Αποτελέσματα: Κατά τη διάρκεια περιόδου 15 μηνών (Νοέμβριος 2011- Ιανουάριος 2013), 224 ασθενείς συμπεριελήφθησαν στην μελέτη και έγινε έλεγχος γονοτύπου. Οι 136 (60,7%) ασθενείς δεν παρουσίασαν μεταλλάξεις των TLRs, ενώ 88 (39,3%) έδειξαν πολυμορφισμούς των TLRs [μονών / μικτών: 56 (25 %) / 32 (14,3%), αντίστοιχα]. Η επίπτωση των γενετικών πολυμορφισμών TLR4-Asp299Gly, TLR4-Thr399Ile, μικτών TLR4-Asp299Gly / Thr399Ile, TLR9-T-1237C και TLR2-Arg753Gln ήταν 14,4%, 14,7%, 11,2%, 24,5% και 2,2%, αντίστοιχα. Οι πολυμορφισμοί TLR4 σχετίστηκαν με αυξημένη ευπάθεια προς συγκεκριμένες λοιμώξεις που σχετίζονται με την νοσηλεία στην ΜΕΘ, δηλαδή gram-αρνητικών λοιμώξεων του κεντρικού νευρικού συστήματος (Central Nervous System Infection - CNSI) και λοιμώξεων της ουροφόρου οδού (Urinary Tract Infection - UTI), από Acinetobacter baumannii και Klebsiella pneumonia, καθώς και με την πνευμονία που σχετίζεται με τον αναπνευστήρα (Ventilator-associated pneumonia -VAP) από Pseudomonas aeruginosa (Ρ <0.05). Ο πολυμορφισμός TLR9-T-1237C σχετίστηκε με χαμηλότερη επίπτωση καθώς και μικρότερο αριθμών υποτροπών των CNSI και UTI σε σύγκριση με την ομάδα μικτών TLR4 πολυμορφισμών (P≤0.039). Δεν βρέθηκε καμία συσχέτιση των TLRs πολυμορφισμών με την βακτηριαιμία (Blood Stream Infection -BSI). Οι πολυμορφισμοί των TLR4 σχετίστηκαν με αυξημένη διάρκεια νοσηλείας στην ΜΕΘ (P<0,0416). Ωστόσο, η χρονική εξέλιξη της σήψης και η έκβαση των ασθενών στην ΜΕΘ δεν συσχετίστηκαν με μεταλλάξεις των TLRs.Συμπεράσματα: Τα ευρήματά μας υποδηλώνουν ότι κοινοί πολυμορφισμοί των TLRs μπορεί να επιδρούν στον κλινικό φαινότυπο των λοιμώξεων που σχετίζονται με την νοσηλεία των ασθενών σε ΜΕΘ στην Ελλάδα. Έτσι, οι TLR4-SNPs μπορεί να σχετίζονται με την επίπτωση των CNSI, UTI και της VAP από gram αρνητικά παθογόνα και μπορεί να επηρεάσουν δυσμενώς τη νοσηρότητα της ΜΕΘ. Αντίθετα, η μετάλλαξη TLR9-T-1237C μπορεί να ασκήσει προστατευτική επίδραση έναντι συγκεκριμένων λοιμώξεων στη ΜΕΘ.

scholarly journals The most common bacterial isolates from wound samples – a three-year study

2021 ◽  
Vol 13 (1) ◽  
pp. 77-90
Author(s):  
Ana Kaftandzieva ◽  
Marko Kostovski ◽  
Blerta Mehmeti ◽  
Gordana Mirchevska
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Anaerobic Bacteria ◽  
Resistant Bacteria ◽  
Klebsiella Pneumonia ◽  
City Hospital ◽  
E Coli ◽  
Percentage Decrease ◽  
Carbapenem Resistant ◽  
Resistant Strains ◽  
The University

Aim: The aim of our study was to determine the most common bacteria isolated from wound samples and tо compare the frequency of the resistant bacteria isolated over a 3-year period. Material and methods: During a three years period (2017-2019) a total of 11 863 wound samples (wound swabs, punctuates, exudates, tissue, etc.) were obtained from the hospitalized patients in the University Clinics of the ,,Mother Theresa” campus, the City hospital ,,8th September” and the University Clinic for surgical diseases ,,St. Naum Ohridski” in Skopje. All samples were processed at the Institute of Microbiology and Parasitology, Faculty of Medicine, Skopje. They were examined by standard microbiology techniques. Identification and susceptibility of microorganisms were done by both standard methods and automatized Vitek 2 system. Results: Out of a total number of samples, which was 3 463 in 2017, 4 127 in 2018 and 4 273 in 2019, positive were 2 068 (60%), 2 302 (55.8%) and 2 387 (55.9%), respectively. From the total of aerobes/facultative anaerobes (2 758, 2 949 and 3 279 in three consecutive years, 2017, 2018 and 2019, respectively), Staphylococcus aureus was the most predominant isolate (19.5%, 16.6%, 16.9%) followed by Enterococcus spp (16%, 16%, 16.7%), Pseudomonas aeruginosa (12%, 13%, 12.7%) and E. coli (10%, 10.4%, 10.7%). Considering anaerobic bacteria, the percentage of Gram positive anaerobes (Peptostreptococcus) has decreased from 33% to 18% out of a total number of anaerobes, unlike Gram negative anaerobes in which the increasing percentage was mostly observed in bacteria of the genus Bacteroides (from 39% to 45%). The percentage of the resistant strains of MRSA, CNS-MR and VRE was almost the same in that period. In Gram-negatives the percentage of ESBL-positive isolates of E. coli and Enterobacter spp. increased consecutively from 2017 to 2019. The increase in the percentage of resistant strains was more noticeable in ESBL-positive isolates of Klebsiella pneumonia between 2017 and 2018, but in 2019 a percentage decrease can be observed. Considering carbapenem-resistant (CR) Enterobacterales, an increase in the resistance was noticeable in K. pneumonia. The increase in the percentage of resistant strains in Enterobacter spp. between 2017 and 2018, as well as the decrease between 2018 and 2019 was statistically significant. The percentage of CR-isolates of Pseudomonas aeruginosa was from 30% to 38% and for Acinetobacter spp. this percentage was from 81% to 85%. Conclusion: The knowledge of the most commonly isolated bacterial pathogens, especially the presence of resistant bacteria, is crucial and should be continuously monitored in order to understand, construct and update effective treatment algorithms and guidelines.

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