Emergence and persistent spread of carbapenemase-producing Klebsiella pneumoniae high-risk clones in Greek hospitals, 2013 to 2022

BackgroundPreliminary unpublished results of the survey of carbapenem- and/or colistin-resistant Enterobacterales (CCRE survey) showed the expansion of carbapenemase-producing Klebsiella pneumoniae (CPKP) sequence type (ST) 39 in 12 of 15 participating Greek hospitals in 2019.AimWe conducted a rapid survey to determine the extent of spread of CPKP high-risk clones in Greek hospitals in 2022 and compare the distribution of circulating CPKP clones in these hospitals since 2013.MethodsWe analysed whole genome sequences and epidemiological data of 310 K. pneumoniae isolates that were carbapenem-resistant or 'susceptible, increased exposure' from Greek hospitals that participated in the European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE, 2013-2014), in the CCRE survey (2019) and in a national follow-up survey (2022) including, for the latter, an estimation of transmission events.ResultsFive K. pneumoniae STs including ST258/512 (n = 101 isolates), ST11 (n = 93), ST39 (n = 56), ST147 (n = 21) and ST323 (n = 13) accounted for more than 90% of CPKP isolates in the dataset. While ST11, ST147 and ST258/512 have been detected in participating hospitals since 2013 and 2014, KPC-2-producing ST39 and ST323 emerged in 2019 and 2022, respectively. Based on the defined genetic relatedness cut-off, 44 within-hospital transmission events were identified in the 2022 survey dataset, with 12 of 15 participating hospitals having at least one within-hospital transmission event.ConclusionThe recent emergence and rapid spread of new high-risk K. pneumoniae clones in the Greek healthcare system related to within-hospital transmission is of concern and highlights the need for molecular surveillance and enhanced infection prevention and control measures.

Plasmids pick a bacterial partner before committing to conjugation

Bacterial conjugation was first described by Lederberg and Tatum in the 1940s following the discovery of the F plasmid. During conjugation a plasmid is transferred unidirectionally from one bacterium (the donor) to another (the recipient), in a contact-dependent manner. Conjugation has been regarded as a promiscuous mechanism of DNA transfer, with host range determined by the recipient downstream of plasmid transfer. However, recent data have shown that F-like plasmids, akin to tailed Caudovirales bacteriophages, can pick their host bacteria prior to transfer by expressing one of at least four structurally distinct isoforms of the outer membrane protein TraN, which has evolved to function as a highly sensitive sensor on the donor cell surface. The TraN sensor appears to pick bacterial hosts by binding compatible outer membrane proteins in the recipient. The TraN variants can be divided into specialist and generalist sensors, conferring narrow and broad plasmid host range, respectively. In this review we discuss recent advances in our understanding of the function of the TraN sensor at the donor-recipient interface, used by F-like plasmids to select bacterial hosts within polymicrobial communities prior to DNA transfer.

Clonal expansion and rapid characterization of Klebsiella pneumoniae ST1788, an otherwise uncommon strain spreading in Wales, UK

A multidrug-resistant strain of Klebsiella pneumoniae (Kp) sequence type (ST) 1788, an otherwise uncommon ST worldwide, was isolated from 65 patients at 11 hospitals and 11 general practices across South and West Wales, UK, between February 2019 and November 2021. A collection of 97 Kp ST1788 isolates (including 94 from Wales) was analysed to investigate the diversity and spread across Wales and to identify molecular marker(s) to aid development of a strain-specific real-time PCR. Whole genome sequencing (WGS) was performed with Illumina technology and the data were used to perform phylogenetic analyses. Pan-genome analysis of further Kp genome collections was used to identify an ST1788-specific gene target; a real-time PCR was then validated against a panel of 314 strains and 218 broth-enriched screening samples. Low genomic diversity was demonstrated amongst the 94 isolates from Wales. Evidence of spread within and across healthcare facilities was found. A yersiniabactin locus and the KL2 capsular locus were identified in 85/94 (90.4 %) and 94/94 (100 %) genomes respectively; bla SHV-232, bla TEM-1, bla CTX-M-15 and bla OXA-1 were simultaneously carried by 86/94 (91.5 %) isolates; 4/94 (4.3 %) isolates also carried bla OXA-48 carbapenemase. Aminoglycoside and fluoroquinolone resistance markers were found in 94/94 (100 %) and 86/94 (91.5 %) isolates respectively. The ST1788-specific real-time PCR was 100 % sensitive and specific. Our analyses demonstrated recent clonal expansion and spread of Kp ST1788 in the community and across healthcare facilities in South and West Wales with isolates carrying well-defined antimicrobial resistance and virulence markers. An ST1788-specific marker was also identified, enabling rapid and reliable preliminary characterization of isolates by real-time PCR. This study confirms the utility of WGS in investigating novel strains and in aiding proactive implementation of molecular tools to assist infection control specialists.

Global scenario of the RmtE pan-aminoglycoside-resistance mechanism: emergence of the rmtE4 gene in South America associated with a hospital-related IncL plasmid

Antimicrobial resistance (AMR) mechanisms, especially those conferring resistance to critically important antibiotics, are a great concern for public health. 16S rRNA methyltransferases (16S-RMTases) abolish the effectiveness of most clinically used aminoglycosides, but some of them are considered sporadic, such as RmtE. The main goals of this work were the genomic analysis of bacteria producing 16S-RMTases from a 'One Health' perspective in Venezuela, and the study of the epidemiological and evolutionary scenario of RmtE variants and their related mobile genetic elements (MGEs) worldwide. A total of 21 samples were collected in 2014 from different animal and environmental sources in the Cumaná region (Venezuela). Highly aminoglycoside-resistant Enterobacteriaceae isolates were selected, identified and screened for 16S-RMTase genes. Illumina and Nanopore whole-genome sequencing data were combined to obtain hybrid assemblies and analyse their sequence type, resistome, plasmidome and pan-genome. Genomic collections of rmtE variants and their associated MGEs were generated to perform epidemiological and phylogenetic analyses. A single 16S-RMTase, the novel RmtE4, was identified in five Klebsiella isolates from wastewater samples of Cumaná. This variant possessed three amino acid modifications with respect to RmtE1-3 (Asn152Asp, Val216Ile and Lys267Ile), representing the most genetic distant among all known and novel variants described in this work, and the second most prevalent. rmtE variants were globally spread, and their geographical distribution was determined by the associated MGEs and the carrying bacterial species. Thus, rmtE4 was found to be confined to Klebsiella isolates from South America, where it was closely related to ISVsa3 and an uncommon IncL plasmid related with hospital environments. This work uncovered the global scenario of RmtE and the existence of RmtE4, which could potentially emerge from South America. Surveillance and control measures should be developed based on these findings in order to prevent the dissemination of this AMR mechanism and preserve public health worldwide.

Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae

Oxford Nanopore Technologies (ONT) sequencing has rich potential for genomic epidemiology and public health investigations of bacterial pathogens, particularly in low-resource settings and at the point of care, due to its portability and affordability. However, low base-call accuracy has limited the reliability of ONT data for critical tasks such as antimicrobial resistance (AMR) and virulence gene detection and typing, serotype prediction, and cluster identification. Thus, Illumina sequencing remains the standard for genomic surveillance despite higher capital and running costs. We tested the accuracy of ONT-only assemblies for common applied bacterial genomics tasks (genotyping and cluster detection, implemented via Kleborate, Kaptive and Pathogenwatch), using data from 54 unique Klebsiella pneumoniae isolates. ONT reads generated via MinION with R9.4.1 flowcells were basecalled using three alternative models [Fast, High-accuracy (HAC) and Super-accuracy (SUP), available within ONT's Guppy software], assembled with Flye and polished using Medaka. Accuracy of typing using ONT-only assemblies was compared with that of Illumina-only and hybrid ONT+Illumina assemblies, constructed from the same isolates as reference standards. The most resource-intensive ONT-assembly approach (SUP basecalling, with or without Medaka polishing) performed best, yielding reliable capsule (K) type calls for all strains (100 % exact or best matching locus), reliable multi-locus sequence type (MLST) assignment (98.3 % exact match or single-locus variants), and good detection of acquired AMR genes and mutations (88-100 % correct identification across the various drug classes). Distance-based trees generated from SUP+Medaka assemblies accurately reflected overall genetic relationships between isolates. The definition of outbreak clusters from ONT-only assemblies was problematic due to inflation of SNP counts by high base-call errors. However, ONT data could be reliably used to 'rule out' isolates of distinct lineages from suspected transmission clusters. HAC basecalling + Medaka polishing performed similarly to SUP basecalling without polishing. Therefore, we recommend investing compute resources into basecalling (SUP model), wherever compute resources and time allow, and note that polishing is also worthwhile for improved performance. Overall, our results show that MLST, K type and AMR determinants can be reliably identified with ONT-only R9.4.1 flowcell data. However, cluster detection remains challenging with this technology.

RADT-08. DOSIMETRIC FEASIBILITY OF DIRECT POST-OPERATIVE MRI-LINAC-BASED STEREOTACTIC RADIOSURGERY FOR RESECTION CAVITIES OF BRAIN METASTASES

Background

Post-operative stereotactic radiosurgery (SRS) of patients with brain metastases with single resection cavities is typically planned on a post-recovery MRI, 4-6 weeks after resection. However, meanwhile the intracranial metastasis may (re-)grow, and postponing adjuvant systemic treatment increases chance on extracranial progression as well. Anticipating direct post-operative SRS to minimize this interval would enable rapid start of systemic therapy. In this study, we considered treatment with MRI-Linac (MRL) SRS, because of the possibility to execute the post-operative MRI and SRS treatment combined on the MRL instead of on two separate systems, improving logistics and increasing patient comfort. However, it is unclear whether MRL-based SRS may be feasible from a dosimetric perspective. This study aims to shed light on the dosimetric feasibility of MRL-based SRS.

METHODS

We simulated MRL treatments including thirteen patients with resectable single brain metastases treated with single fraction CT-Linac (CTL) SRS. We therefore contoured direct post-operative gross tumor volumes (GTV) and compared them to post-recovery MRI GTV. Next, we compared a non-coplanar VMAT technique for CTL (ncVMAT) to a coplanar IMRT technique for MRL (cIMRT), creating three plans per patient: a ncVMAT plan and a cIMRT plan for the direct post-operative GTV, and a post-recovery ncVMAT plan as current clinical standard. RESULTSCompared to GTVs defined on direct post-operative MRI, on post-recovery MRI 15.5% of cavities shrunk by > 2cc, and 46% expanded by > 2cc. Although direct post-operative ncVMAT plans had lower median gradient index and higher median V3Gy of the skin, they were clinically acceptable according to clinical guidelines.

CONCLUSION

Although slightly inferior to non-coplanar CTL plans, direct post-operative MRL-based SRS for resection cavities of brain metastases is dosimetrically acceptable, at the trade-off between increased patient comfort and logistics. Additionally, MRL-based SRS enables substantially earlier start with adjuvant systemic therapies, thereby maximizing tumor control.

Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of Klebsiella pneumoniae

Mutations in outer membrane porins act in synergy with carbapenemase enzymes to increase carbapenem resistance in the important nosocomial pathogen, Klebsiella pneumoniae (KP). A key example is a di-amino acid insertion, Glycine-Aspartate (GD), in the extracellular loop 3 (L3) region of OmpK36 which constricts the pore and restricts entry of carbapenems into the bacterial cell. Here we combined genomic and experimental approaches to characterise the diversity, spread and impact of different L3 insertion types in OmpK36. We identified L3 insertions in 3588 (24.1%) of 14,888 KP genomes with an intact ompK36 gene from a global collection. GD insertions were most common, with a high concentration in the ST258/512 clone that has spread widely in Europe and the Americas. Aspartate (D) and Threonine-Aspartate (TD) insertions were prevalent in genomes from Asia, due in part to acquisitions by KP sequence types ST16 and ST231 and subsequent clonal expansions. By solving the crystal structures of novel OmpK36 variants, we found that the TD insertion causes a pore constriction of 41%, significantly greater than that achieved by GD (10%) or D (8%), resulting in the highest levels of resistance to selected antibiotics. We show that in the absence of antibiotics KP mutants harbouring these L3 insertions exhibit both an in vitro and in vivo competitive disadvantage relative to the isogenic parental strain expressing wild type OmpK36. We propose that this explains the reversion of GD and TD insertions observed at low frequency among KP genomes. Finally, we demonstrate that strains expressing L3 insertions remain susceptible to drugs targeting carbapenemase-producing KP, including novel beta lactam-beta lactamase inhibitor combinations. This study provides a contemporary global view of OmpK36-mediated resistance mechanisms in KP, integrating surveillance and experimental data to guide treatment and drug development strategies.

Rapidly rising rates of antibiotic resistance among Klebsiella pneumoniae (KP) necessitate a comprehensive understanding of the diversity, spread and clinical impact of resistance mutations. In KP, mutations in outer membrane porins play an important role in mediating resistance to carbapenems, a key class of antibiotics. Here we show that resistance mutations in the extracellular loop 3 (L3) region of the OmpK36 porin are found at high prevalence among clinical genomes and we characterise their diversity and impact on resistance and virulence. They include amino acid insertions of Aspartate (D), Glycine-Aspartate (GD) and Threonine-Aspartate (TD), which act by decreasing the pore size and restricting entry of carbapenems into the bacterial cell. We show that these L3 insertions are associated with large clonal expansions of resistant lineages and impose a fitness cost evident during in vivo competition. Critically, strains harbouring L3 insertions remain susceptible to novel drugs, including beta lactam-beta lactamase inhibitor combinations. This study highlights the importance of monitoring the emergence and spread of strains with OmpK36 L3 insertions for the control of resistant KP infections and provides crucial data for drug development and treatment strategies.

Mating pair stabilization mediates bacterial conjugation species specificity

Bacterial conjugation mediates contact-dependent transfer of DNA from donor to recipient bacteria, thus facilitating the spread of virulence and resistance plasmids. Here we describe how variants of the plasmid-encoded donor outer membrane (OM) protein TraN cooperate with distinct OM receptors in recipients to mediate mating pair stabilization and efficient DNA transfer. We show that TraN from the plasmid pKpQIL (Klebsiella pneumoniae) interacts with OmpK36, plasmids from R100-1 (Shigella flexneri) and pSLT (Salmonella Typhimurium) interact with OmpW, and the prototypical F plasmid (Escherichia coli) interacts with OmpA. Cryo-EM analysis revealed that TraN_pKpQIL interacts with OmpK36 through the insertion of a β-hairpin in the tip of TraN into a monomer of the OmpK36 porin trimer. Combining bioinformatic analysis with AlphaFold structural predictions, we identified a fourth TraN structural variant that mediates mating pair stabilization by binding OmpF. Accordingly, we devised a classification scheme for TraN homologues on the basis of structural similarity and their associated receptors: TraNα (OmpW), TraNβ (OmpK36), TraNγ (OmpA), TraNδ (OmpF). These TraN-OM receptor pairings have real-world implications as they reflect the distribution of resistance plasmids within clinical Enterobacteriaceae isolates, demonstrating the importance of mating pair stabilization in mediating conjugation species specificity. These findings will allow us to predict the distribution of emerging resistance plasmids in high-risk bacterial pathogens.

Combining conjugation and structural analyses, the authors show that TraN-OMP pairings determine bacterial conjugation species specificity, with implications in resistance plasmid distribution within Enterobacteriaceae.

Testing the Limit Range of Motion Safety Function of Upper Limb Rehabilitation Robots with an Anthropometrically Adjustable and Sensorized Dummy Limb. IEEE Int Conf Rehabil Robot 2022;2022:1-6. [PMID: 36176113 DOI: 10.1109/icorr55369.2022.9896575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Arm type or exoskeleton type rehabilitation robots move the patient's upper limb through one or more, either free or restrained connection points. The rehabilitation robot is unsafe if it moves the patient's upper limb beyond the limits of the anatomical joint ranges. A validation toolkit was developed to assess the risks of "limit anatomical joint range of movement" and "limit anatomical joint overreaching" during the regular operation of a rehabilitation robot. The validation toolkit includes an anthropometrically adjustable and sensorised dummy limb attached to the RACA (rehabilitation, assessment, compensation, or alleviation) rehabilitation robot; and a software tool for off-line risk assessment and reporting.

POS1566-PARE BEYOND MEDICATION – SELF MANAGEMENT AS A COMPLEMENTARY APPROACH FOR TREATING RMDS

Background

Upon diagnosis Rheumatoid Patients declare that the feeling that prevails is fear. Fear over the unknown over their health condition, their professional future, and their personal and social life. The person experiences a vicious cycle. Loss of control leads to anxiety which triggers pain which enhances psychological distress, thus the person feels completely helpless.

Objectives

The Self-Management education workshop is offered as a complementary aid, next to the arranged medical plan and the medications prescribed. The primary goal of the Workshop is for patients to accept their new reality which is, living with RMD. Further on, grounds for change are set. Patients within the program are taught in great detail how to engage new healthy, daily activities, such as appropriate exercise, appropriate use of medications, healthier nutrition, communicating effectively their fatigue, anxiety and psychological distress to family and friends. Patients are also taught, how to communicate to health professionals their condition, seek for information so as to evaluate new treatments, and demand the right for shared decision over their treatment. Moreover they receive information about the Cyprus League of people with Rheumatism, the social and psychological help provided, practicalities that concerns them, availability of Doctors, and new medications. Information, provides a strong Know-how, to deal with everyday problems. Such achievement enhances the confidence that a new well-being could be within the persons reach.

Methods

Participants meet for two hours once a week, for five weeks. Two trained leaders conduct the workshop, one being a health professional and one patient. Participants are to the maximum 15. Major rules of a therapeutic group apply, such as empathy, confidentiality, respect in every sharing, time keeping, simple language. All activities are Interactive. Discussions, questions and answers, brain storming, action-planning exercises and feedback, role playing, problem-solving techniques, and decision making. Moreover, symptom management activities are included, such as exercise, relaxation, communication, healthy eating, medication management, and managing sleep and fatigue. During the workshop, participants experience rapport, and trust thus they are motivated to manage the challenges associated with their condition.

Results

Participants demonstrated significant improvements in exercise, ability to do social and household activities, less depression, less fear and frustration about their health, reduction in symptoms like pain, improve mobility, increase energy, and boost confidence in their ability to manage their condition. Results of every workshop are scientifically documented.

Conclusion

Self-Management workshops are often described by new coming participants as “render of last hope”. The structure and the facilitators create a safe environment for the patient to release the pain, seek knowledge, express the despair, set all the nightmares free. Acceptance, Respect, Rapport, Trust, knowledge aid the participants to experience the rebirth of hope. Self-Management workshops, are designed to complement clinical treatment and when delivered with empathy, lead RMD patients to physical and psychological well-being.

References

[1]Private practice, Self-Management education workshops at the Cyprus League of people with Rheumatism.

Disclosure of Interests

None declared

CT fractional flow reserve: an alternative to stress ECHO for gatekeeping to invasive coronary angiography

Funding Acknowledgements

Type of funding sources: None.

Introduction

Stress echocardiography (SE) can assess the significance of moderate/severe stenoses found on CT coronary angiography (CTCA), as a gatekeeper to invasive coronary angiography (ICA). In 2017, the UK National Institute for Health and Care Excellence (NICE), recommended CT fractional flow reserve (CTFFR) on all patients with coronary stenoses on CTCA to reduce downstream ICA and reduce costs.

Aim

We describe our experience of using CTFFR and compare this with previously accepted practice of judicious use of SE in patients with moderate/severe CTCA stenosis, and subsequent rate of ICA.

Method

An electronic patient record identified patients undergoing CTFFR between January 2019 and March 2020, and CTCA between January 2017 and June 2018, at our centre. We assessed downstream testing following CT evidence of moderate/severe stenoses and undertook a cost analysis per patient (PP) with the following NHS tariffs; CTCA=£220, CTFFR=£530, SE=£177, ICA=£1000.

Results

140 patients were referred for CTFFR with 125 analysed (rejection rate 11%) of which 81 had moderate/severe stenoses. The baseline audit comprised 652 patients undergoing CTCA of which 92 had moderate/severe stenoses.

Moderate CTCA stenosis: Baseline audit

58 had moderate stenosis, 18 (31%) underwent SE, with 1 positive and subsequent ICA. 36 (62%) were referred directly for ICA. In total 17 (46%) were revascularised. Cost of £1224 PP.

CTFFR audit

44 had moderate stenosis, with 35 negative and 9 positive CTFFR.  9 (26%) and 7 (78%) following negative and positive CTFFR respectively, were subsequently referred for ICA. In total 16 (36%) were referred for ICA, and 44% revascularised. Cost of £1425 PP.

Severe CTCA stenosis: Baseline audit

34 had severe stenosis, 1 (3%) underwent SE. 33 (97%) were referred directly for ICA. In total 18 (60%) were revascularised. Cost of £1418 PP.

CTFFR audit

37 had severe stenoses, with 10 negative CTFFR and 27 positive CTFFR.  5 (50%) and 22 (81%) following negative and positive CTFFR respectively were referred for ICA. In total 27 (73%) were referred for ICA and 70% revascularised. Cost of £1719 PP.

Importantly 14 patients underwent ICA following negative CTFFR with 29% revascularised.

Conclusion

CTFFR use in all patients with moderate/severe stenosis reduced the rate of downstream ICA compared with previous judicious use of SE, albeit at greater cost and similar revascularisation rates. A small number of patients underwent ICA despite negative CTFFR due to clinical concerns.

The NICE guidance recommending CTFFR on all patients with moderate/severe CTCA stenosis reduces ICA. However, assuming equal efficacy, based on the non-invasive arm of the Platform trial1, SE would achieve this at lower cost. Notably, CTFFR benefits from completing assessment within a single visit, which is pertinent in the COVID-19 era and negates inherent delays between multiple tests.

A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings

The Klebsiella group, found in humans, livestock, plants, soil, water and wild animals, is genetically and ecologically diverse. Many species are opportunistic pathogens and can harbour diverse classes of antimicrobial resistance genes. Healthcare-associated Klebsiella pneumoniae clones that are non-susceptible to carbapenems can spread rapidly, representing a high public health burden. Here we report an analysis of 3,482 genome sequences representing 15 Klebsiella species sampled over a 17-month period from a wide range of clinical, community, animal and environmental settings in and around the Italian city of Pavia. Northern Italy is a hotspot for hospital-acquired carbapenem non-susceptible Klebsiella and thus a pertinent setting to examine the overlap between isolates in clinical and non-clinical settings. We found no genotypic or phenotypic evidence for non-susceptibility to carbapenems outside the clinical environment. Although we noted occasional transmission between clinical and non-clinical settings, our data point to a limited role of animal and environmental reservoirs in the human acquisition of Klebsiella spp. We also provide a detailed genus-wide view of genomic diversity and population structure, including the identification of new groups.

Clones and Clusters of Antimicrobial-Resistant Klebsiella From Southwestern Nigeria

BACKGROUND

Klebsiella pneumoniae is a World Health Organization high-priority antibiotic-resistant pathogen. However, little is known about Klebsiella lineages circulating in Nigeria.

METHODS

We performed whole-genome sequencing (WGS) of 141 Klebsiella isolated between 2016 and 2018 from clinical specimens at 3 antimicrobial-resistance (AMR) sentinel surveillance tertiary hospitals in southwestern Nigeria. We conducted in silico multilocus sequence typing; AMR gene, virulence gene, plasmid, and K and O loci profiling; as well as phylogenetic analyses, using publicly available tools and Nextflow pipelines.

RESULTS

Phylogenetic analysis revealed that the majority of the 134 K. pneumoniae and 5 K. quasipneumoniae isolates from Nigeria characterized are closely related to globally disseminated multidrug-resistant clones. Of the 39 K. pneumoniae sequence types (STs) identified, the most common were ST307 (15%), ST5241 (12%), ST15 (~9%), and ST25 (~6%). ST5241, 1 of 10 novel STs detected, is a single locus variant of ST636 carrying dfrA14, tetD, qnrS, and oqxAB resistance genes. The extended-spectrum β-lactamase (ESBL) gene blaCTX_M-15 was seen in 72% of K. pneumoniae genomes, while 8% encoded a carbapenemase. No isolate carried a combination of carbapenemase-producing genes. Four likely outbreak clusters from 1 facility, within STs 17, 25, 307, and 5241, were ESBL but not carbapenemase-bearing clones.

CONCLUSIONS

This study uncovered known and novel K. pneumoniae lineages circulating in 3 hospitals in Southwest Nigeria that include multidrug-resistant ESBL producers. Carbapenemase-producing isolates remain uncommon. WGS retrospectively identified outbreak clusters, pointing to the value of genomic approaches in AMR surveillance for improving infection prevention and control in Nigerian hospitals.

Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch

BACKGROUND

Klebsiella species, including the notable pathogen K. pneumoniae, are increasingly associated with antimicrobial resistance (AMR). Genome-based surveillance can inform interventions aimed at controlling AMR. However, its widespread implementation requires tools to streamline bioinformatic analyses and public health reporting.

METHODS

We developed the web application Pathogenwatch, which implements analytics tailored to Klebsiella species for integration and visualization of genomic and epidemiological data. We populated Pathogenwatch with 16 537 public Klebsiella genomes to enable contextualization of user genomes. We demonstrated its features with 1636 genomes from 4 low- and middle-income countries (LMICs) participating in the NIHR Global Health Research Unit (GHRU) on AMR.

RESULTS

Using Pathogenwatch, we found that GHRU genomes were dominated by a small number of epidemic drug-resistant clones of K. pneumoniae. However, differences in their distribution were observed (eg, ST258/512 dominated in Colombia, ST231 in India, ST307 in Nigeria, ST147 in the Philippines). Phylogenetic analyses including public genomes for contextualization enabled retrospective monitoring of their spread. In particular, we identified hospital outbreaks, detected introductions from abroad, and uncovered clonal expansions associated with resistance and virulence genes. Assessment of loci encoding O-antigens and capsule in K. pneumoniae, which represent possible vaccine candidates, showed that 3 O-types (O1-O3) represented 88.9% of all genomes, whereas capsule types were much more diverse.

CONCLUSIONS

Pathogenwatch provides a free, accessible platform for real-time analysis of Klebsiella genomes to aid surveillance at local, national, and global levels. We have improved representation of genomes from GHRU participant countries, further facilitating ongoing surveillance.

Assessment of soil quality in agroecosystems based on soil fauna

Soil arthropods respond sensitively to land management practices and correlate with beneficial soil functions. The aim of this research was to determine soil quality using the QBS index in different types of crops and influence of soil variables (pH soil, soil moisture, potassium, phosphorus and nitrogen) on soil arthropods. Between the years 2018 and 2020, we studied different types of crops (Brassica napus, Pisum sativum, Triticum aestivum, T. spelta, Zea mays, Grass mixture and Hordeum vulgare) and recorded 14 taxa. Our results suggest a higher QBS index value in crops grass mixture, Pisum sativum, Triticum aestivum, T. spelta. The EMI value grew with increasing values of soil moisture, soil pH, phosphorus, potassium and nitrogen; indicating the presence of soil arthropods occurring in higher quality soil. Our results suggest that agricultural intensification affects soil arthropods, which are important for the production of biomass, which also affects crop yields.

Assessment of soil quality in agroecosystems based on soil fauna

Soil arthropods respond sensitively to land management practices and correlate with beneficial soil functions. The aim of this research was to determine soil quality using the QBS index in different types of crops and influence of soil variables (pH soil, soil moisture, potassium, phosphorus and nitrogen) on soil arthropods. Between the years 2018 and 2020, we studied different types of crops (Brassica napus, Pisum sativum, Triticum aestivum, T. spelta, Zea mays, Grass mixture and Hordeum vulgare) and recorded 14 taxa. Our results suggest a higher QBS index value in crops grass mixture, Pisum sativum, Triticum aestivum, T. spelta. The EMI value grew with increasing values of soil moisture, soil pH, phosphorus, potassium and nitrogen; indicating the presence of soil arthropods occurring in higher quality soil. Our results suggest that agricultural intensification affects soil arthropods, which are important for the production of biomass, which also affects crop yields.

Morphological changes after cranial fractionated photon radiotherapy: Localized loss of white matter and grey matter volume with increasing dose

PURPOSE

Numerous brain MR imaging studies have been performed to understand radiation-induced cognitive decline. However, many of them focus on a single region of interest, e.g. cerebral cortex or hippocampus. In this study, we use deformation-based morphometry (DBM) and voxel-based morphometry (VBM) to measure the morphological changes in patients receiving fractionated photon RT, and relate these to the dose. Additionally, we study tissue specific volume changes in white matter (WM), grey matter (GM), cerebrospinal fluid and total intracranial volume (TIV).

METHODS AND MATERIALS

From our database, we selected 28 patients with MRI of high quality available at baseline and 1 year after RT. Scans were rigidly registered to each other, and to the planning CT and dose file. We used DBM to study non-tissue-specific volumetric changes, and VBM to study volume loss in grey matter. Observed changes were then related to the applied radiation dose (in EQD2). Additionally, brain tissue was segmented into WM, GM and cerebrospinal fluid, and changes in these volumes and TIV were tested.

RESULTS

Performing DBM resulted in clusters of dose-dependent volume loss 1 year after RT seen throughout the brain. Both WM and GM were affected; within the latter both cerebral cortex and subcortical nuclei show volume loss. Volume loss rates ranging from 5.3 to 15.3%/30 Gy were seen in the cerebral cortical regions in which more than 40% of voxels were affected. In VBM, similar loss rates were seen in the cortex and nuclei. The total volume of WM and GM significantly decreased with rates of 5.8% and 2.1%, while TIV remained unchanged as expected.

CONCLUSIONS

Radiotherapy is associated with dose-dependent intracranial morphological changes throughout the entire brain. Therefore, we will consider to revise sparing of organs at risk based on future cognitive and neurofunctional data.

Return to work and quality of life after trauma: A systematic review

Background

Globally, one-tenth of the disability-adjusted life-years (DALYs) are due to injuries. Injuries can reduce employment opportunities and significantly affect the quality of life (QOL). Most research on these outcomes tend to focus on specific mechanisms of injury like road traffic crashes or falls, or body regions affected such as brain or limbs. But rarely do patients come with just body region injured nor does the healthcare system only treat one specific mechanism of injury. Therefore, we aimed to assess and provide a systematic overview of current knowledge about return to work (RTW) and QOL among adult injured patients up to 1-year after discharge.

Methods

We conducted a systematic review of the literature published since 2010 on RTW and QoL among injured patients. Three databases (MEDLINE, EMBASE, the Cochrane Library) were used. Meta-analysis was performed based on outcome, measurement tool, and the effect measure. Methodological quality of the studies were evaluated using the Joanna Briggs Institute (JBI) Critical Appraisal Tool Checklist.

Results

41 articles were included in this review. More than one-third (36%) of patients had not yet returned to back to work even after 1-year. Those who did get back to work took an average time of more than 3 months. The QOL scores of the injured patients had not reached the general population or pre-injury levels even up to a year post-discharge. Women and the elderly tended have poorer outcomes and were under-represented in the studies. Over 75% of the included studies were from high-income countries (HICs) and had higher methodological quality. There were no studies from low-income countries (LICs).

Conclusions

RTW and QOL continue to remain a challenge even up to year since discharge after an injury, more so among women and the elderly. Health policy and practice should address this burden. Future studies should focus on building of high-quality evidence from LMICs on RTW and QOL among injury survivors.

Key messages

Return to work and quality of life were significantly low even after 1-year in trauma patients, especially among elderly and females. Larger representation of elderly, females, and participants from low- and middle-income setting in future long-term research on trauma patients.

High-resolution sweep metagenomics using fast probabilistic inference

Determining the composition of bacterial communities beyond the level of a genus or species is challenging because of the considerable overlap between genomes representing close relatives. Here, we present the mSWEEP pipeline for identifying and estimating the relative sequence abundances of bacterial lineages from plate sweeps of enrichment cultures. mSWEEP leverages biologically grouped sequence assembly databases, applying probabilistic modelling, and provides controls for false positive results. Using sequencing data from major pathogens, we demonstrate significant improvements in lineage quantification and detection accuracy. Our pipeline facilitates investigating cultures comprising mixtures of bacteria, and opens up a new field of plate sweep metagenomics.

OS03.4.A Irradiation of the subventricular and subgranular zone and overall survival in high-grade glioma patients

BACKGROUND

Previous research has shown that neural stem cells (NSCs) in the subventricular zone (SVZ) may support the growth of glioma by recruiting new cells to the tumor. NSCs are located in the SVZ as well as in the subgranular zone (SGZ) of the hippocampus, the two neurogenic niches of the brain. This might indicate that irradiation of the SVZ and SGZ, and thereby damaging NSCs, reduces tumor growth and improves overall survival (OS). However, irradiation may also inhibit the repair capacity of healthy brain tissue by these neurogenic niches. Therefore, we investigated the effects of SVZ and SGZ irradiation dose on OS, in a cohort of high-grade glioma patients.

MATERIAL AND METHODS

We have retrospectively selected 221 patients (2014–2020) with WHO grade III and IV gliomas that underwent radiotherapy. Next to clinical baseline characteristics, T1 weighted MRI- and CT-images were collected. The SVZ and SGZ regions on the individual T1 images were delineated via non-linear registration of brain atlases. SVZ labels were created in 0.5mm isotropic MNI T1 and T2 templates, while SGZ atlas labels were available via the Hippocampus and Subfields CoBrA atlas. Next, the mean dose from the acquired SVZ and SGZ labels were extracted. The relationship between SVZ doses, SGZ doses and OS were examined using the Cox proportional hazards model and the Kaplan-Meier method (using the Log Rank test for significance).

RESULTS

For the mean dose in the SVZ, the hazard ratio (HR) was 1.024 per Gy (P = 0.002, [95% confidence interval, 1.009–1.040]) and the mean SGZ dose had a HR of 1.021 per Gy (P< 0.001, [95% confidence interval, 1.012–1.031]). These results were then corrected for the following covariates: sex, age, total intracranial volume and extent of surgery. This resulted in a HR of 1.031 per Gy (P = 0,001, [95% confidence interval, 1.014–1.050]) for the mean SVZ dose, and a HR of 1.025 per Gy (P< 0.001, [95% confidence interval, 1.015–1.036]) for the mean SGZ dose. Patients whose SVZ received greater than the median SVZ dose (= 31.3 Gy) showed a significant decrease in OS compared to patients who received less than the median dose (10.7 months vs 13.5 months median OS, P = 0.001). Patients whose SGZ received greater than the median SGZ dose (= 31.9) showed a significant decrease in OS compared to patients who received less than the median dose (10.7 months vs 15.1 months median OS, P< 0.001).

CONCLUSION

Here, we present a large cohort of high-grade glioma patients, in which we show a statistically significant decrease in overall survival with increasing radiation dose on the SGZ and SVZ. This correlation suggests that both neurogenic niches might need to be spared during radiotherapy treatment to improve overall survival even in high-grade glioma patients. Modern radiotherapy planning and delivery options are available to implement this.

P14.23 Relation between neurological deficits and location of postsurgical ischemia in glioma resection

BACKGROUND

Postoperative ischemia is a known complications of glioma resection and can lead to neurological deficits. New or worsened postoperative deficits are often transient, but some patients experience persisting effects after surgery. Neuroanatomical location of ischemia is suspected to play an important role in the development as well as persistence of neurological deficits. Therefore, the aim of this study was to investigate the spatial relation between postoperative ischemia and short-term and long-term neurological deficits.

MATERIAL AND METHODS

Postoperative ischemia was defined as new confluent areas of diffusion restriction on DWI in a retrospective database of 144 adult WHO grade II-IV supratentorial glioma patients, who received MRI within 3 days after resection in 2012–2014. New or worsened neurological deficits of any grade at discharge and after 3 months was assessed in relation to postoperative ischemia by an experienced neuro-oncologist. We manually delineated ischemic lesions and spatially normalized these to stereotaxic MNI space. Next, we performed voxel-based analysis (VBA) to identify locations of ischemia associated with new or worsened neurological deficits and corrected for multiple comparisons using family-wise error correction to eliminate false positive results. Delineations were labeled using the Harvard-Oxford cortical and subcortical atlases and a white matter atlas (XTRACT).

RESULTS

Any new or worsened neurological deficits were present in 44 (30.5%) cases at discharge and in 27 (20.9%) cases after 3 months, of which respectively 26 (18%) and 21 (16.3%) were related to ischemia. Volume of ischemia was significantly associated with deficits at discharge (P = 0.003) and after 3 months (P = 0.039). No areas of ischemia were associated with a lack of new or worsened deficits. A statistically significant cluster of 42.96cc was associated with deficits at discharge and encompassed the right frontal, insular and tempo-occipital regions. Voxels associated only with deficits at discharge included lateral occipital cortices and supramarginal gyri. A cluster of 17.68cc in the right frontal and insular lobes was significantly associated with deficits after 3 months. Overlapping areas included the right thalamus, caudate nucleus, putamen, globus pallidum, insular cortex, middle and inferior temporal gyri, corticospinal tract and superior thalamic radiation.

CONCLUSION

Transient and persisting new or worsened deficits after glioma resection were significantly associated with volume of postoperative ischemia. Ischemic lesions in right frontal and insular regions, including the basal nuclei, corticospinal tract and superior thalamic radiation were significantly associated with persisting neurological deficits after 3 months, while temporo-occipital lesions were associated with transient deficits only found at discharge.

P14.30 Voxelwise analysis of spatial distribution of postoperative ischemia in diffuse glioma

BACKGROUND

Surgical treatment of diffuse glioma is performed to reduce tumor mass effect and to pave the way for adjuvant (chemo)radiotherapy. As a complication of surgery, ischemic lesions are often found in the postoperative setting. Not only can these lesion induce neurological deficits, but their volume has also been associated with reduced survival time. Prior studies suggest areas with a singular vascular supply to be more prone to postoperative ischemic lesions, although the precise cause is yet unknown. The aim of this study was to explore the volumetric and spatial distributions of postoperative ischemic lesions and their relation to arterial territories in glioma patients.

MATERIAL AND METHODS

We accessed a retrospective database of 144 adult cases with WHO grade II-IV supratentorial gliomas, who received surgery and postoperative MRI within 3 days in 2012–2014. We identified 93 patients with postoperative ischemia, defined as new confluent diffusion restriction on DWI. Ischemic lesions were manually delineated and spatially normalized to stereotaxic MNI space. Voxel-based analysis (VBA) was performed to compare presence and absence of postoperative ischemia. False positive results were eliminated by family-wise error correction. Areas of ischemia were labeled using an arterial territory map, the Harvard-Oxford cortical and subcortical atlases and the XTRACT white matter atlas.

RESULTS

Median volume of confluent ischemia was 3.52cc (IQR 2.15–5.94). 23 cases had only ischemic lesion in the left hemisphere, 46 in the right hemisphere and 24 bilateral. Median volume was 3.08cc (IQR 1.35–5.72) in left-sided lesions and 2.47cc (1.01–4.24) in right-sided lesions. Volume of ischemic lesions was not associated with survival after 1, 2 or 5 years. A cluster of 125.18cc was found to be significantly associated with development of postoperative ischemia. 73% of this cluster was situated in the arterial territory of the right middle cerebral artery (MCA), limited by the border of the posterior cerebral artery (PCA), and the watershed area between the right MCA and the right anterior cerebral artery (ACA). Significant areas were located in the frontal lobes, spanning into the right temporo-occipital region, and predominantly included right and left thalamus, caudate nucleus, putamen, pallidum, as well as right temporal gyri and insular cortex, and parts of the right corticospinal tract, longitudinal fasciculi and superior thalamic radiation.

CONCLUSION

We found slightly more and larger ischemic lesions in the right than left hemisphere after glioma resection. A statistically significant cluster of voxels of postoperative ischemia was found in the territory of the right MCA and watershed area of the right ACA. Exploration of the spatial distribution of these lesions could help elucidate their etiology and form the basis for predicting clinically relevant postoperative ischemia.

The changing epidemiology of carbapenemase-producing Klebsiella pneumoniae in Italy: toward polyclonal evolution with emergence of high-risk lineages

BACKGROUND

Previous studies showed that the epidemic of carbapenem-resistant Klebsiella pneumoniae (CR-KP) observed in Italy since 2010 was sustained mostly by strains of clonal group (CG) 258 producing KPC-type carbapenemases. In the framework of the National Antibiotic-Resistance Surveillance (AR-ISS), a countrywide survey was conducted in 2016 to explore the evolution of the phenotypic and genotypic characteristics of CR-KP isolates.

METHODS

From March to July 2016, hospital laboratories participating in AR-ISS were requested to provide consecutive, non-duplicated CR-KP (meropenem and/or imipenem MIC >1 mg/L) from invasive infections. Antibiotic susceptibility was determined according to EUCAST recommendations. A WGS approach was adopted to characterize the isolates by investigating phylogeny, resistome and virulome.

RESULTS

Twenty-four laboratories provided 157 CR-KP isolates, of which 156 were confirmed as K. pneumoniae sensu stricto by WGS and found to carry at least one carbapenemase-encoding gene, corresponding in most cases (96.1%) to blaKPC. MLST- and SNP-based phylogeny revealed that 87.8% of the isolates clustered in four major lineages: CG258 (47.4%), with ST512 as the most common clone, CG307 (19.9%), ST101 (15.4%) and ST395 (5.1%). A close association was identified between lineages and antibiotic resistance phenotypes and genotypes, virulence traits and capsular types. Colistin resistance, mainly associated with mgrB mutations, was common in all major lineages except ST395.

CONCLUSIONS

This WGS-based survey showed that, although CG258 remained the most common CR-KP lineage in Italy, a polyclonal population has emerged with the spread of the new high-risk lineages CG307, ST101 and ST395, while KPC remained the most common carbapenemase.

Population genomics and antimicrobial resistance dynamics of Escherichia coli in wastewater and river environments

Aquatic environments are key niches for the emergence, evolution and dissemination of antimicrobial resistance. However, the population diversity and the genetic elements that drive the dynamics of resistant bacteria in different aquatic environments are still largely unknown. The aim of this study was to understand the population genomics and evolutionary events of Escherichia coli resistant to clinically important antibiotics including aminoglycosides, in anthropogenic and natural water ecosystems. Here we show that less different E. coli sequence types (STs) are identified in wastewater than in rivers, albeit more resistant to antibiotics, and with significantly more plasmids/cell (6.36 vs 3.72). However, the genomic diversity within E. coli STs in both aquatic environments is similar. Wastewater environments favor the selection of conserved chromosomal structures associated with diverse flexible plasmids, unraveling promiscuous interplasmidic resistance genes flux. On the contrary, the key driver for river E. coli adaptation is a mutable chromosome along with few plasmid types shared between diverse STs harboring a limited resistance gene content.

A high prevalence of blaOXA-48 in Klebsiella (Raoultella) ornithinolytica and related species in hospital wastewater in South West England

Klebsiella species occupy a wide range of environmental and animal niches, and occasionally cause opportunistic infections that are resistant to multiple antibiotics. In particular, Klebsiella pneumoniae (Kpne) has gained notoriety as a major nosocomial pathogen, due principally to the rise in non-susceptibility to carbapenems and other beta-lactam antibiotics. Whilst it has been proposed that the urban water cycle facilitates transmission of pathogens between clinical settings and the environment, the level of risk posed by resistant Klebsiella strains in hospital wastewater remains unclear. We used whole genome sequencing (WGS) to compare Klebsiella species in contemporaneous samples of wastewater from an English hospital and influent to the associated wastewater treatment plant (WWTP). As we aimed to characterize representative samples of Klebsiella communities, we did not actively select for antibiotic resistance (other than for ampicillin), nor for specific Klebsiella species. Two species, Kpne and K. (Raoultella) ornithinolytica (Korn), were of equal dominance in the hospital wastewater, and four other Klebsiella species were present in low abundance in this sample. In contrast, despite being the species most closely associated with healthcare settings, Kpne was the dominant species within the WWTP influent. In total, 29 % of all isolates harboured the blaOXA-48 gene on a pOXA-48-like plasmid, and these isolates were almost exclusively recovered from the hospital wastewater. This gene was far more common in Korn (68 % of isolates) than in Kpne (3.4 % of isolates). In general plasmid-borne, but not chromosomal, resistance genes were significantly enriched in the hospital wastewater sample. These data implicate hospital wastewater as an important reservoir for antibiotic-resistant Klebsiella, and point to an unsuspected role of species within the Raoultella group in the maintenance and dissemination of plasmid-borne blaOXA-48. This article contains data hosted by Microreact.

The influence of relief morphometric characteristics upon the occurrence of the species Cordulegaster bidentata in the particular conditions of the Western Carpathians

The study concerns a monitoring survey of Cordulegaster bidentata Selys, 1843 (Odonata, Cordulegastridae), which is considered near threatened in the European Red List of Dragonflies, in order to show its habitat preferences and clarify the influence of slope and orientation of slopes on the occurrence of the species. Investigations of water habitats were carried out during the period from 2019 to 2020 in the Kysuce Region in northwest Slovakia. The protocol consists of looking for larvae and characterizing larval micro-habitat of C. bidentata so as to show their habitat preferences and clarify the influence of slope and orientation of slopes on the occurrence of the species. We sampled 32 watercourses (epicrenal, hypocrenal, rheocren, heleocren, epirhithral, metarhithral) at altitudes 420–950 m above sea level. A total of 79 larvae and 10 imagines (7♂ 3♀) of C. bidentata were found at 12 streams. In the present study, C. bidentata clearly preferred first-order stream sections, the slopes were steep and the proportion of small sediment grain sizes was high. The results show that the number of C. bidentata larvae grew with the increasing percentage of forests around streams. We also confirmed the trend for the number of C. bidentata larvae to increase with increasing values of slope and altitude of watercourses. Most of the individuals were recorded at the south and southwest oriented streams; we did not record larvae on the north and northwest oriented slopes. We assume that more suitable conditions for development of population exist in the streams on the south and southwest oriented slopes. The preference for watercourses oriented south and southwest ensures optimal conditions for the development of the population of this dragonfly species. The finding of larvae at the stages of instars shows the permanent occurrence of the species in the Kysuce Region.

ESC 2019 guidelines on chronic coronary syndromes: can calcium scoring improve the risk underestimation associated with the updated pre-test probability risk score?

Funding Acknowledgements

Type of funding sources: None.

Introduction

The European Society of Cardiology (ESC) published an updated stable chest pain guideline in 2019. It recommends the use of an updated pre-test probability (PTP) risk score (RS) to assess the likelihood of coronary artery disease (CAD), to try and reduce the risk overestimation associated with previous risk scores. We sought to assess the performance of the 2019 PTPRS in a contemporary cohort of patients undergoing CT coronary angiography (CTCA). Furthermore, we focussed on patients with PTPRS <15%, and assessed the utility of CT calcium scores as a discriminator of risk.

Methods

652 patients who were investigated with CTCA for stable chest pain between January 2017 and May 2018 were included in a retrospective analysis. CTCA reported CAD degree of stenosis as normal/minimal stenosis, mild (30-50%), moderate (50-70%), or severe (>70%). ESC 2019 pre-test probability risk scores were retrospectively calculated and compared.

Results

A total of 652 patients underwent CTCA between 01 January 2017 and 31 May 2018, of which 330 were male and 322 were female, with an average age of 55 years ±11 years.

Using the ESC 2019 PTPRS there were no patients with PTPRS >85%. 2 patients had PTPRS 50-85%; one patient had moderate stenosis and one mild stenosis on CTCA. 

There were 267 patients with PTPRS 15-50%; 23 (9%) patients had severe CTCA stenosis, 37 (14%) a moderate stenosis, and 34 (13%) a mild stenosis.

A further 379 patients had PTPRS <15%; 11 (3%) had severe stenosis and 20 (5%) moderate stenosis. A further 27 (7%) patients had mild CTCA stenosis. 

A total of 357 of 379 patients with PTPRS <15% based on ESC 2019 had a CT calcium score. 236 patients were found to have a calcium score of zero, and 121 patients had a score greater than zero, with a range between 1 and 930. Of patients with zero calcium score, only 1 (0.4%) patient had severe stenosis, 2 (0.8%) moderate stenoses and 6 (2.5%) mild stenosis. In contrast, in patients with positive calcium scores, 10 (8%) had severe stenosis, 18 (15%) moderate stenosis, and 22 (18%) mild stenosis.

Conclusions

The ESC 2019 PTPRS classified this as an overall low risk cohort. The downward risk modification of PTPRS has led to a large number of patients being classified as low risk with PTPRS <15%. No or deferred investigation is recommended by the ESC in this cohort. However, the use of CT calcium scores  in patients with PTPRS <15%, detected the majority of patients with any degree of CAD. CT calcium scores are a simple and low cost risk modifier, and may help identify patients who may benefit from primary prevention as per SCOT-Heart. Patients with calcium score greater than zero could be investigated with CTCA.

Rapid detection and differentiation of mobile colistin resistance (mcr-1 to mcr-10) genes by real-time PCR and melt-curve analysis

BACKGROUND

The emergence of multi-drug-resistant (MDR) micro-organisms prompted new interest in older antibiotics, such as colistin, that had been abandoned previously due to limited efficacy or high toxicity. Over the years, several chromosomal-encoded colistin resistance mechanisms have been described; more recently, 10 plasmid-mediated mobile colistin resistance (mcr) genes have been identified. Spread of these genes among MDR Gram-negative bacteria is a matter of serious concern; therefore, reliable and timely mcr detection is paramount.

AIM

To design and validate a multiplex real-time polymerase chain reaction (PCR) assay for detection and differentiation of mcr genes.

METHODS

All available mcr alleles were downloaded from the National Center for Biotechnology Information Reference Gene Catalogue, aligned with Clustal Omega and primers designed using Primer-BLAST. Real-time PCR monoplexes were optimized and validated using a panel of 120 characterized Gram-negative strains carrying a wide range of resistance genes, often in combination. Melt-curve analysis was used to confirm positive results.

FINDINGS

In-silico analysis enabled the design of a 'screening' assay for detection of mcr-1/2/6, mcr-3, mcr-4, mcr-5, mcr-7, mcr-8 and mcr-9/10, paired with an internal control assay to discount inhibition. A 'supplementary' assay was subsequently designed to differentiate mcr-1, mcr-2, mcr-6, mcr-9 and mcr-10. Expected results were obtained for all strains (100% sensitivity and specificity). Melt-curve analysis showed consistent melting temperature results. Inhibition was not observed.

CONCLUSIONS

The assay is rapid and easy to perform, enabling unequivocal mcr detection and differentiation even when more than one variant is present. Adoption by clinical and veterinary microbiology laboratories would aid the surveillance of mcr genes amongst Gram-negative bacteria.

Novel Subclone of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 with Enhanced Virulence and Transmissibility, China

We aimed to clarify the epidemiologic and clinical importance of evolutionary events that occurred in carbapenem-resistant Klebsiella pneumoniae (CRKP). We collected 203 CRKP causing bloodstream infections in a tertiary hospital in China during 2013-2017. We detected a subclonal shift in the dominant clone sequence type (ST) 11 CRKP in which the previously prevalent capsular loci (KL) 47 had been replaced by KL64 since 2016. Patients infected with ST11-KL64 CRKP had a significantly higher 30-day mortality rate than other CRKP-infected patients. Enhanced virulence was further evidenced by phenotypic tests. Phylogenetic reconstruction demonstrated that ST11-KL64 is derived from an ST11-KL47-like ancestor through recombination. We identified a pLVPK-like virulence plasmid carrying rmpA and peg-344 in ST11-KL64 exclusively from 2016 onward. The pLVPK-like-positive ST11-KL64 isolates exhibited enhanced environmental survival. Retrospective screening of a national collection identified ST11-KL64 in multiple regions. Targeted surveillance of this high-risk CRKP clone is urgently needed.

ESC 2019 guidelines on chronic coronary syndromes: could calcium scoring improve detection of coronary artery disease in patients with low risk score. Findings from a retrospective cohort of patients in a district general hospital

BACKGROUND

The European Society of Cardiology (ESC) published an updated stable chest pain guideline in 2019, recommending the use of an updated pre-test probability (PTP) risk score (RS) to assess the likelihood of coronary artery disease (CAD). We sought to compare the 2019 and 2013 PTPRS in a contemporary cohort of patients.

METHODS

612 patients who were investigated with computed tomography coronary angiography (CTCA) for stable chest pain were included in a retrospective analysis.

RESULTS

There were 255 patients with 2019 PTPRS 15-50% with a 9% yield of severe CAD on CTCA, compared with 402 patients and a 4% yield using the 2013 PTPRS (p = 0.01). 355 patients had a 2019 PTPRS of <15%, with 3% found to have severe CAD, compared with 67 patients and none with severe CAD using the 2013 PTPRS (p = 0.14). 336 of patients with 2019 PTPRS of <15% had a calcium score as part of the CTCA. 223 of these had a zero calcium score and only one had severe CAD. In comparison, 113 patients had a positive calcium score, and 10 (9%) had severe CAD (p < 0.001).

DISCUSSION

The ESC 2019 PTPRS classifies more patients as at lower risk of CAD and hence reduces the risk overestimation associated with the 2013 PTPRS. However, in patients with a 2019 PTPRS of <15%, who would not be investigated, the use of the calcium score detected the majority of patients with significant CAD, who may benefit from secondary prevention and an associated mortality benefit as per the SCOT-Heart trial.

[What is evidence-based in the treatment of sepsis?]

BACKGROUND

The term sepsis was redefined in 2016 as a life-threatening organ dysfunction caused by an inadequate host response to an infection. The German S3 guidelines for the treatment of sepsis were published in 2018.

OBJECTIVE

What is evidence-based in the treatment of patients with sepsis?

MATERIAL AND METHODS

Discussion of the S3 guidelines and inclusion of study results after 2018.

RESULTS

The cornerstones for the treatment of sepsis continue to consist of early hemodynamic stabilization, anti-infection treatment and organ support procedures. Supportive and extracorporeal treatments are controversially discussed and continue to be intensively investigated.

CONCLUSION

Despite an improved understanding of the pathophysiology, there is still no effective causal sepsis treatment, i.e. directed against the pathological host reaction. The treatment of patients with sepsis is therefore still based on the basic principles of correction of volume deficits, anti-infective agents, source control and organ support, including the symptomatic treatment of vasoplegia with catecholamines.

Long-term Survival with 18-Fluorodeoxyglucose Positron Emission Tomography-directed Therapy in Non-small Cell Lung Cancer with Synchronous Solitary Brain Metastasis

AIMS

At diagnosis, <1% of patients with non-small cell lung cancer (NSCLC) have synchronous solitary brain metastasis (SSBM). In prior cohorts without 18-fluorodeoxyglucose positron emission tomography/computed tomography (FDG-PET/CT) staging, definitive treatment to intracranial and intrathoracic disease showed a 5-year overall survival (OS) of 11-21%. We investigated the long-term survival outcomes for patients with SSBM NSCLC, diagnosed in the FDG-PET/CT era and treated definitively with local therapies to both intracranial and intrathoracic sites of disease.

MATERIALS AND METHODS

This retrospective study assessed patients staged with FDG-PET/CT who received definitive lung and SSBM treatment from February 1999 to December 2017. A lung-molecular graded prognostic assessment (lung-molGPA) score was assigned for each patient using age, performance status score, and, where carried out, molecular status. Overall survival and progression-free survival (PFS) were calculated using Kaplan-Meier methods. Cox proportional hazard models determined OS and PFS prognostic factors.

RESULTS

Forty-nine patients newly diagnosed with NSCLC and SSBM had a median age of 63 years (range 34-76). The median follow-up of all patients was 3.9 years. Thirty-three patients (67%) had ≥T2 disease, 23 (47%) had ≥N2. At 2 years, 45% of first failures were intracranial only (95% confidence interval 30-59). At 3 and 5 years, OS was 45% (95% confidence interval 32-63) and 30% (95% confidence interval 18-51), respectively. In ≥N1 disease, 5-year OS was 34% (95% confidence interval 18-63). The 3- and 5-year PFS was 8% (95% confidence interval 3-22) and 0%, respectively. Higher lung-molGPA was associated with longer OS (hazard ratio 0.26, 95% confidence interval 0.11-0.61, P = 0.002). Higher lung-molGPA (hazard ratio 0.33, 95% confidence interval 0.15-0.71, P = 0.005) and lower N-stage (hazard ratio 1.56, 95% confidence interval 1.13-2.15, P = 0.007) were associated with longer PFS.

CONCLUSIONS

Definitive treatment of patients with NSCLC and SSBM staged with FDG-PET/CT can result in 5-year survivors, including those with ≥N1 disease.