From isolate to answer: how whole genome sequencing is helping us rapidly characterise nosocomial bacterial outbreaks

2017 ◽  
Vol 38 (3) ◽  
pp. 127
Author(s):  
Leah Roberts
Keyword(s):  
Clinical Diagnostics ◽  
Hospital Environment ◽  
Whole Genome Sequence ◽  
Clinical Settings ◽  
Whole Genome ◽  
Major Focus ◽  
New Techniques ◽  
Hospital Acquired Infections ◽  
Sequence Techniques ◽  
Hospital Acquired

The occurrence of highly resistant bacterial pathogens has risen in recent years, causing immense strain on the healthcare industry. Hospital-acquired infections are arguably of most concern, as bacterial outbreaks in clinical settings provide an ideal environment for proliferation among vulnerable populations. Understanding these outbreaks beyond what can be determined with traditional clinical diagnostics and implementing these new techniques routinely in the hospital environment has now become a major focus. This brief review will discuss the three main whole genome sequence techniques available today, and how they are being used to further discriminate bacterial outbreaks in nosocomial settings.

scholarly journals First Whole-Genome Sequence of a Highly Resistant Klebsiella pneumoniae Sequence Type 14 Strain Isolated from Sudan

2019 ◽  
Vol 8 (32) ◽  
Author(s):  
Sofia B. Mohamed ◽  
Sumaya Kambal ◽  
Abdalla Munir ◽  
Nusiba Abdalla ◽  
Mohamed Hassan ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Genomic Sequence ◽  
Significant Proportion ◽  
Opportunistic Pathogen ◽  
Sequence Type ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Hospital Acquired Infections ◽  
Hospital Acquired

Klebsiella pneumoniae is an opportunistic pathogen that accounts for a significant proportion of hospital-acquired infections and is a leading cause of nosocomial outbreaks. Here, we describe the genomic sequence of a highly resistant K. pneumoniae sequence type 14 (ST14) strain isolated from Sudan.

scholarly journals Transmission of ESBL-producing Enterobacteriaceae and their mobile genetic elements—identification of sources by whole genome sequencing: study protocol for an observational study in Switzerland

BMJ Open ◽  
2018 ◽  
Vol 8 (2) ◽  
pp. e021823 ◽  
Author(s):  
Tanja Stadler ◽  
Dominik Meinel ◽  
Lisandra Aguilar-Bultet ◽  
Jana S Huisman ◽  
Ruth Schindler ◽  
...  
Keyword(s):  
Observational Study ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bacterial Species ◽  
Mobile Genetic Elements ◽  
University Hospital ◽  
Whole Genome ◽  
Hospital Acquired Infections ◽  
Genetic Elements ◽  
Hospital Acquired

IntroductionExtended-spectrum beta-lactamases (ESBL)-producing Enterobacteriaceae were first described in relation with hospital-acquired infections. In the 2000s, the epidemiology of ESBL-producing organisms changed as especially ESBL-producingEscherichia coliwas increasingly described as an important cause of community-acquired infections, supporting the hypothesis that in more recent years ESBL-producing Enterobacteriaceae have probably been imported into hospitals rather than vice versa. Transmission of ESBL-producing Enterobacteriaceae is complicated by ESBL genes being encoded on self-transmissible plasmids, which can be exchanged among the same and different bacterial species. The aim of this research project is to quantify hospital-wide transmission of ESBL-producing Enterobacteriaceae on both the level of bacterial species and the mobile genetic elements and to determine if hospital-acquired infections caused by ESBL producers are related to strains and mobile genetic elements predominantly circulating in the community or in the healthcare setting. This distinction is critical in prevention since the former emphasises the urgent need to establish or reinforce antibiotic stewardship programmes, and the latter would call for more rigorous infection control.Methods and analysisThis protocol presents an observational study that will be performed at the University Hospital Basel and in the city of Basel, Switzerland. ESBL-producing Enterobacteriaceae will be collected from any specimens obtained by routine clinical practice or by active screening in both inpatient and outpatient settings, as well as from wastewater samples and foodstuffs, both collected monthly over a 12-month period for analyses by whole genome sequencing. Bacterial chromosomal, plasmid and ESBL-gene sequences will be compared within the cohort to determine genetic relatedness and migration between humans and their environment.Ethics and disseminationThis study has been approved by the local ethics committee (Ethikkommission Nordwest-und Zentralschweiz) as a quality control project (Project-ID 2017–00100). The results of this study will be published in peer-reviewed medical journals, communicated to participants, the general public and all relevant stakeholders.

scholarly journals Evolution of Acinetobacter baumannii infections and antimicrobial resistance. A review

2019 ◽  
Vol 2 (1) ◽  
pp. 28-36
Author(s):  
Sonia Elena Popovici ◽  
Ovidiu Horea Bedreag ◽  
Dorel Sandesc
Keyword(s):  
Antimicrobial Agents ◽  
Resistance Mechanisms ◽  
Hospital Environment ◽  
Medical Community ◽  
Molecular Testing ◽  
Medical Systems ◽  
Antimicrobial Drugs ◽  
Hospital Acquired Infections ◽  
Acinetobacter Spp ◽  
Hospital Acquired

AbstractThe emergence of multi-drug resistantAcinetobacter sppinvolved in hospital-acquired infections, once considered an easily treatable pathogen, is troublesome and an immense burden for the modern medical systems worldwide. In the last 20 years the medical community recorded an increase in the incidence and severity of these infections as therapeutic means tend to be less and less effective on these strains. The ability of these bacteria to rapidly develop resistance to antimicrobial agents by continuously changing and adapting their mechanisms, their ability to survive for long periods of time in the hospital environment and the multitude of transmission possibilities raises serious issues regarding the management of these complex infections. The future lies in developing new and targeted methods for the early diagnosis ofA. baumannii, as well as in the judicious use of antimicrobial drugs. This review details the evolution of the pathogenicity of this microorganism, together with the changes that appeared in resistance mechanisms and the advancements in molecular testing for the early detection of infection.

scholarly journals Development of a Rapid, Efficient, Intelligent and Cost-Saving Tool to Diagnose Pasteurella Multocida by Using Whole Genome Sequence and Genotypes of Pasteurella Multocida From Different Hosts

2020 ◽  
Author(s):  
Zhong Peng ◽  
Junyang Liu ◽  
Wan Liang ◽  
Fei Wang ◽  
Li Wang ◽  
...  
Keyword(s):  
Cost Saving ◽  
Host Species ◽  
Pasteurella Multocida ◽  
Epidemiological Studies ◽  
Whole Genome Sequence ◽  
Clinical Settings ◽  
Whole Genome ◽  
Genome Sequences ◽  
Host Tropism ◽  
Tropism Prediction

Abstract Background: Different typing systems including capsular genotyping, lipopolysaccharide (LPS) genotyping, multilocus sequence typing (MLST), and virulence genotyping based on the detection of different virulence factor-encoding gene (VFG) profiles have been applied to characterize Pasteurella multocida strains from different host species. However, these methods require much time and effort in laboratories. Particularly, relying on one of these methods is difficult to address the biology of P. multocida from host species. Recently, we found that assigning P. multocida strains according to the combination of their capsular, LPS, and MLST genotypes (marked as capsular genotype: LPS genotype: MLST genotype) could help address the biological characteristics of P. multocida circulation in multiple hosts. However, it is still lack of a rapid, efficient, intelligent and cost-saving tool to diagnose P. multocida according to this system. Results: We have developed an intelligent genotyping and host tropism prediction tool PmGT for P. multocida strains according to their whole genome sequences by using machine learning and web 2.0 technologies. By using this tool, the capsular genotypes, LPS genotypes, and MLST genotypes as well as the main VFGs of P. multocida isolates in different host species were determined based on whole genome sequences. The results revealed a closer association between the genotypes and pasteurellosis rather than between genotypes and host species. Finally, we also used PmGT to predict the host species of P. multocida strains with the same capsular: lipopolysaccharide: MLST genotypes. Conclusions: With the advent of high-quality, inexpensive DNA sequencing, this platform represents a more efficient and cost-saving tool for P. multocida diagnosis in both epidemiological studies and clinical settings.

Plasmids and Bacterial Strains Mediating Multidrug-Resistant Hospital-Acquired Infections Are Coresidents of the Hospital Environment

2013 ◽  
Vol 19 (2) ◽  
pp. 104-109 ◽  
Author(s):  
Thu Betteridge ◽  
John Merlino ◽  
Jonathon Natoli ◽  
Elaine Y.-L. Cheong ◽  
Thomas Gottlieb ◽  
...  
Keyword(s):  
Multidrug Resistant ◽  
Hospital Environment ◽  
Bacterial Strains ◽  
Hospital Acquired Infections ◽  
Hospital Acquired

scholarly journals Whole-Genome Sequence Analysis of Streptococcus pneumoniae Strains That Cause Hospital-Acquired Pneumonia Infections

2018 ◽  
Vol 56 (5) ◽  
Author(s):  
Bin Chang ◽  
Masatomo Morita ◽  
Ken-ichi Lee ◽  
Makoto Ohnishi
Keyword(s):  
Streptococcus Pneumoniae ◽  
Clonal Complex ◽  
Underlying Disease ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Severe Underlying Disease ◽  
Hospital Acquired Pneumonia ◽  
Hospital Acquired

ABSTRACT Streptococcus pneumoniae colonizes the nasopharyngeal mucus in healthy individuals and can cause otitis media, pneumonia, and invasive pneumococcal diseases. In this study, we analyzed S. pneumoniae strains that caused 19 pneumonia episodes in long-term inpatients with severe underlying disease in a hospital during a period of 14 months (from January 2014 to February 2015). Serotyping and whole-genome sequencing analyses revealed that 18 of the 19 pneumonia cases were caused by S. pneumoniae strains belonging to 3 genetically distinct groups: clonal complex 9999 (CC9999), sequence type 282 (ST282), and ST166. The CC9999 and ST282 strains appeared to have emerged separately by a capsule switch from the pandemic PMEN 1 strain (Spain 23F -ST81). After all the long-term inpatients were inoculated with the 23-valent pneumococcal polysaccharide vaccine, no other nosocomial pneumonia infections occurred until March 2016.

scholarly journals Antimicrobial resistance genetic factor identification from whole-genome sequence data using deep feature selection

2019 ◽  
Vol 20 (S15) ◽  
Author(s):  
Jinhong Shi ◽  
Yan Yan ◽  
Matthew G. Links ◽  
Longhai Li ◽  
Jo-Anne R. Dillon ◽  
...  
Keyword(s):  
Feature Selection ◽  
Antimicrobial Resistance ◽  
Genome Sequence ◽  
Sequence Data ◽  
Bacterial Species ◽  
Clinical Diagnostics ◽  
New Drugs ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data

Abstract Background Antimicrobial resistance (AMR) is a major threat to global public health because it makes standard treatments ineffective and contributes to the spread of infections. It is important to understand AMR’s biological mechanisms for the development of new drugs and more rapid and accurate clinical diagnostics. The increasing availability of whole-genome SNP (single nucleotide polymorphism) information, obtained from whole-genome sequence data, along with AMR profiles provides an opportunity to use feature selection in machine learning to find AMR-associated mutations. This work describes the use of a supervised feature selection approach using deep neural networks to detect AMR-associated genetic factors from whole-genome SNP data. Results The proposed method, DNP-AAP (deep neural pursuit – average activation potential), was tested on a Neisseria gonorrhoeae dataset with paired whole-genome sequence data and resistance profiles to five commonly used antibiotics including penicillin, tetracycline, azithromycin, ciprofloxacin, and cefixime. The results show that DNP-AAP can effectively identify known AMR-associated genes in N. gonorrhoeae, and also provide a list of candidate genomic features (SNPs) that might lead to the discovery of novel AMR determinants. Logistic regression classifiers were built with the identified SNPs and the prediction AUCs (area under the curve) for penicillin, tetracycline, azithromycin, ciprofloxacin, and cefixime were 0.974, 0.969, 0.949, 0.994, and 0.976, respectively. Conclusions DNP-AAP can effectively identify known AMR-associated genes in N. gonorrhoeae. It also provides a list of candidate genes and intergenic regions that might lead to novel AMR factor discovery. More generally, DNP-AAP can be applied to AMR analysis of any bacterial species with genomic variants and phenotype data. It can serve as a useful screening tool for microbiologists to generate genetic candidates for further lab experiments.

scholarly journals Knowledge, Attitude and Practice of nursing students on Hospital Acquired Infections in Western region of Nepal

2016 ◽  
Vol 12 (3) ◽  
pp. 103-107 ◽  
Author(s):  
Ishwari Sharama Paudel ◽  
Vivek Ghosh ◽  
Purushottam Adhikari
Keyword(s):  
Nursing Students ◽  
Hand Hygiene ◽  
Hospital Environment ◽  
Good Knowledge ◽  
Healthcare Team ◽  
Western Region ◽  
Hospital Acquired Infections ◽  
Attitude And Practice ◽  
Hospital Acquired ◽  
Knowledge Attitude And Practice

Background & Objectives: Hospital-acquired infections (HAIs) are a common problem and challenge faced by hospitals in all countries around the world. Nurses are an important part of the healthcare team that plays a unique role in the control of HAIs. Compliance on the part of healthcare workers (HCWs) including nurses with standard precautions has been recognized as being an efficient means to prevent and control HAIs. The present study was conducted with objective of understanding the level of Knowledge, attitude and practice (KAP) regarding HAIs among nursing students in the Western Region of Nepal.Materials & Methods: This descriptive cross-sectional study was conducted among nursing students posted in different wards of two hospitals of Pokhara. A self administered questionnaire containing different set of questions regarding knowledge, attitude and practice on HAI were used for data collection.Results: Among the total participants in the study 97% of the participants considered that prevention of HAIs were a valuable part of nurses’ role but only 89% had received formal training regarding hand hygiene. The results show that 74% of the participants had good knowledge regarding HAIs. 82% of the participants felt that they would be less likely to transmit infection to the patient if they performed hand-hygiene. 66% of them identified that hand hygiene agents were not readily available in current settings. Regarding practice, only 6% performed hand hygiene before patient contact.Conclusion: The nursing students had good knowledge regarding HAIs that was reflected in their attitude and practice on hand hygiene for the prevention of HAIs. However there is the need of regular training and performance feedback regarding hand hygiene and the hospital environment should be hand-hygiene friendly with easily accessible to sinks and other facilities.

scholarly journals Molecular epidemiology of Candida auris in Qatar using whole genome sequence data

2021 ◽  
Vol 3 (12) ◽  
Author(s):  
Husam Salah ◽  
Sathyavathi Sundararaju ◽  
Lamya Dalil ◽  
Patrick Tang ◽  
Walid Al-Wali ◽  
...  
Keyword(s):  
Sequence Data ◽  
Multidrug Resistant ◽  
Hospital Environment ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Resistance Mutations ◽  
Candida Auris ◽  
East Region ◽  
Echinocandin Resistance ◽  
Middle East Region

Candida auris is an emerging, multidrug resistant fungal pathogen that has become a public health threat worldwide. Candida auris spreads easily among patients within and between hospitals, and the incidence of infections has increased substantially in the last decade. Multiple C. auris outbreaks have been reported worldwide including India, USA and United Kingdom. Infections and outbreaks caused by C. auris have also been reported in the Middle East region including Kuwait, Oman, Saudi Arabia, and Qatar; however, the origin of these isolates is largely unknown. This study uses whole genome sequencing (WGS) data to determine the epidemiology and the drug resistance mutations from C. auris in Qatar. Forty samples isolated from the patients and the hospital environment were sequenced by Illumina Nextseq. Core genome SNPs revealed that all isolates belonged to the Indian lineage, which could be originated from the expatriate labour from South Asia. The genetic variability among the isolates was low but comprised of more than one genetic cluster. The environmental isolates were identical to the clinical isolates, and the isolates from patients of different hospitals/outbreaks clustered together, suggesting the transmission of C. auris could be linked to infected/colonized patients and the hospital environment. Mutations associated with azole and echinocandin resistance were discussed.

scholarly journals Meningococcal Deduced Vaccine Antigen Reactivity (MenDeVAR) Index: a Rapid and Accessible Tool that Exploits Genomic Data in Public Health and Clinical Microbiology Applications

2020 ◽  
Author(s):  
Charlene M.C. Rodrigues ◽  
Keith A. Jolley ◽  
Andrew Smith ◽  
J. Claire Cameron ◽  
Ian M. Feavers ◽  
...  
Keyword(s):  
Public Health ◽  
Sequence Data ◽  
Cross Reactivity ◽  
Vaccine Antigen ◽  
Whole Genome Sequence ◽  
Clinical Settings ◽  
Whole Genome ◽  
Outbreak Management ◽  
Individual Gene ◽  
Antigen Reactivity

AbstractAs microbial genomics makes increasingly important contributions to clinical and public health microbiology, the interpretation of whole genome sequence data by non-specialists becomes essential. In the absence of capsule-based vaccines, two protein-based vaccines have been used for the prevention of invasive serogroup B meningococcal disease (IMD), since their licensure in 2013/14. These vaccines have different components and different coverage of meningococcal variants. Hence, decisions regarding which vaccine to use in managing serogroup B IMD outbreaks require information about the index case isolate including: (i) the presence of particular vaccine antigen variants; (ii) the expression of vaccine antigens; and (iii) the likely susceptibility of its antigen variants to antibody-dependent bactericidal killing. To obtain this information requires a multitude of laboratory assays, impractical in real-time clinical settings, where the information is most urgently needed. To facilitate assessment for public health and clinical purposes, we synthesised genomic and experimental data from published sources to develop and implement the ‘Meningococcal Deduced Vaccine Antigen Reactivity’ (MenDeVAR) Index, which is publicly-available on PubMLST (https://pubmlst.org). Using whole genome sequences or individual gene sequences obtained from IMD isolates or clinical specimens, MenDeVAR provides rapid evidence-based information on the presence and possible immunological cross-reactivity of different meningococcal vaccine antigen variants. The MenDeVAR Index enables practitioners who are not genomics specialists to assess the likely reactivity of vaccines for individual cases, outbreak management, or the assessment of public health vaccine programmes. MenDeVAR has been developed in consultation with, but independently of, both vaccine manufacturers.

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