Publications tagged "AMR"

Bacterial plasmids often carry antibiotic resistance genes and are a significant factor in the spread of antibiotic resistance. The ability to completely assemble plasmid sequences would facilitate ...

Genomic surveillance can inform effective public health responses to pathogen outbreaks. However, integration of non-local data is rarely done. We investigate two large hospital outbreaks of a carba...

The foodborne pathogen Yersinia enterocolitica causes gastrointestinal infections worldwide. In the spring of 2019, the Swedish Public Health Agency and Statens Serum Institut in Denmark independent...

Objectives The emergence of carbapenem-resistant Enterobacteriaceae has become a serious public-health threat. Here we report the complete genome sequence of a multidrug-resistant (MDR) Escherichia...

Extended-spectrum cephalosporin (ESC)-resistant Escherichia coli were isolated from fecal samples enriched in ESC-containing broth over two years from broiler chickens raised with and without therap...

Objectives The genus Burkholderia comprises rod-shaped, non-spore-forming, obligately aerobic Gram-negative bacteria that is found across diverse ecological niches. Burkholderia contaminans, an eme...

The rising of multi-resistant bacterial pathogens is currently one of the most critical threats to global health and requires urgent actions for its control and a better understanding of the origin,...

The emergence of carbapenem resistance (CR) caused by hydrolytic enzymes called carbapenemases has become a major concern worldwide. So far, CR genes have been widely detected in various bacteria. H...

Background The prevalence of clinical multidrug-resistant (MDR) Pseudomonas aeruginosa has been increasing rapidly worldwide over the years and responsible for a wide range of acute and chronic inf...

Outbreak investigations are essential to control and prevent the dissemination of pathogens. This study developed and validated a complete analysis protocol for faster and more accurate surveillance...

The resistance to broad-spectrum antibiotic ciprofloxacin is detected in high rates for a wide range of bacterial pathogens. To investigate dynamics of ciprofloxacin resistance development we propos...

Carbapenemase-producing Klebsiella pneumoniae (cpKP) poses serious threats to public health. Previous studies showed that only ST11/CG258-cpKP successfully disseminated in China, however, the underl...

Pseudomonas aeruginosa is a frequent cause of antibiotic-resistant infections. Although P. aeruginosa is intrinsically resistant to many antimicrobial agents, aminoglycosides are active against this...

Background Infections by Carbapenem-resistant Pseudomonas aeruginosa (CRPA) are difficult to treat and novel antibiotics are desperately needed. Till today, ceftazidime-avibactam (CAZ-AVI) has been ...

Objectives Colistin resistance in Acinetobacter spp. is increasing, causing potentially untreatable nosocomial infections. Plasmid-mediated colistin resistance is of particular concern due to its l...

International efforts to curb antimicrobial resistance have focused on drug development and limiting unnecessary use. However, in areas where water, sanitation, and hygiene infrastructure is lacking...

This study was conducted to characterize carbapenemase-producing Klebsiella pneumoniae and Acinetobacter baumannii isolated from fresh vegetables in Japan. Two K. pneumoniae (AO15, and AO22) and one...

Plasmids can provide a selective advantage for microorganisms to survive and adapt to new environmental conditions. Plasmid-encoded traits, such as antimicrobial resistance (AMR) or virulence, impac...

The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates in Egyptian hospitals has been reported. However, the genetic basis and the analysis of the plasmids associated with CR-hy...

An extensively drug-resistant (XDR) Klebsiella pneumoniae isolate MS3802 from a tracheostomy exudate was whole-genome sequenced using MiSeq and Oxford Nanopore MinION platforms in order to identify ...

Objectives The global spread of carbapenem-resistant Enterobacterales is a leading public-health threat. Lack of effective treatment has resulted in use of colistin as a last-resort therapeutic opt...

Molecular characterization was performed for 46 vancomycin-resistant E. faecium (VREfm) isolates and one vancomycin-sensitive comparator obtained during routine fecal surveillance of high-risk patie...

Objectives To characterize a blaOXA-58- and blaNDM-1-containing MDR plasmid from a rare Acinetobacter baumannii lineage and compare it with related plasmids to explore the distribution and evolutio...

Background We aimed to characterise the genetic determinants and context of two meropenem-resistant clinical isolates of Acinetobacter baumannii isolated from children hospitalised with bloodstream...

Respiratory infection during childhood is a key risk factor in early cystic fibrosis (CF) lung disease progression. Haemophilus influenzae (Hi) and Haemophilus parainfluenzae (Hpi) are routinely iso...

Objectives To characterize the clonal spread of carbapenem-resistant Klebsiella pneumoniae and Escherichia coli isolates between different healthcare institutions in Catalonia, Spain. Methods Ant...

Increased knowledge about the role of horizontal gene transfer is key to improve our understanding of the spread of antimicrobial resistance (AMR) in human populations. We therefore studied the diss...

The emergence of multidrug-resistant bacterial strains worldwide has become a serious problem for public health over recent decades. The increase in antimicrobial resistance has been expanding via p...

Here we report the whole genome sequence of Lactobacillus fermentum HFD1 strain, the producer of antibacterial peptides. The genome consists of one circular chromosome with 2101878 bp in length and ...

Extended turnaround times and large economic costs hinder the usage of currently applied screening methods for bacterial pathogen identification (ID) and antimicrobial susceptibility testing. This r...

Background: An ESBL, carbapenemase- and MCR-1-producing Escherichia coli ST648 strain was isolated from the urine sample of a patient in a Chinese tertiary hospital in 2016. Methods: The strain was ...

Fluoroquinolones are widely used as an empirical therapy for pseudomonal ocular infections. Based on increasing reports on acquired fluoroquinolone resistance genes in clinical isolates of Pseudomon...

Tailocins are phage-derived bacteriocins that demonstrate great potential as agricultural antimicrobials given their high killing efficiency and their precise strain-specific targeting ability. Our ...

Escherichia coli is a ubiquitous bacterium that has widely been exposed to antibiotics over the last 70 years. It has adapted by acquiring different antibiotic resistance genes (ARG), which we aim a...

Campylobacter jejuni and Campylobacter coli are the leading causes of human gastroenteritis in the developed world and an emerging threat in developing countries. There is increasing evidence that t...

Tigecycline is one of the last-resort antibiotics to treat severe infections. Recently, tigecycline resistance has sporadically emerged with an increasing trend, and Tet(X) family represents a new r...

Escherichia coli Strain Type 131 are a globally disseminated environmental E. coli that has been linked to the capture and spread of plasmid mediated blaCTX-M type extended spectrum beta-lactamase (...

IncF plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacteriacea...

In-depth studies of the microbiome and mobile resistome profile of different environments is central to understanding the role of the environment in antimicrobial resistance (AMR), which is one of t...

Background Environmental surveillance of antibiotic resistance can contribute towards better understanding and management of human and environmental health. This study applied a combination of long...

Objectives To investigate the prevalence of the optrA, poxtA and cfr linezolid resistance genes in linezolid-resistant enterococci from Irish hospitals and to characterize associated plasmids. Met...

The emergence of plasmid-borne mcr genes among pathogens poses great public concern. Different mcr variants have been identified from various sources and the plasmids encoding mcr genes are diverse ...

Tandem gene amplification is a frequent and dynamic source of antibiotic resistance in bacteria. Ongoing expansions and contractions of repeat arrays during population growth are expected to manifes...

Shiga toxin-producing Escherichia coli (STEC) contamination of agricultural water might be an important factor to recent foodborne illness and outbreaks involving leafy greens. Closed bacterial geno...

Objectives Escherichia coli is regarded as one of the most commonly isolated Gram-negative pathogens from bloodstream infections. Increasing antimicrobial resistance (AMR) among E. coli is a threat...

The Asian citrus psyllid (Diaphorina citri) is a key pest of Citrus spp. worldwide, as it acts as a vector for “Candidatus Liberibacter asiaticus (Las)”, the bacterial pathogen associated with the d...

The safety of microbial cultures utilized for consumption is vital for public health and should be thoroughly assessed. Although general aspects on the safety assessment of microbial cultures have b...

In this work, we report 2 cases of vancomycin-resistant Enterococcus faecium bacteremia with development of daptomycin resistance in 2 patients with acute myeloid leukemia and myelodysplastic syndro...

The extensively drug-resistant NDM-1-producing Klebsiella quasipneumoniae subsp. quasipneumoniae M17277 (Kqsq-M17277) was only susceptible to colistin and fosfomycin. Whole genome sequencing of Kqsq...

Abstract Objectives To investigate the genomic context of a novel resistance island (RI) in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates and global isolates. Methods ...

Escherichia coli and other Enterobacteriaceae are highly diverse species with ‘open’ pangenomes, where genes move intra- and inter-species via horizontal gene transfer. These species can cause clini...

Background Bacterial heteroresistance has been increasingly identified as an important phenomenon for many antibiotic/bacterium combinations. Objectives To investigate ciprofloxacin heteroresista...

Antimicrobial resistance (AMR) genes in bacteria are often carried on plasmids and these plasmids can transfer AMR genes between bacteria. For molecular epidemiology purposes and risk assessment, it...

Background: In recent years, the emergence of multidrug resistant hypervirulent K. pneumoniae (MDR hvKp) isolates poses severe therapeutic challenge to global public health. The present study used t...

Antibiotic persisters are a small subpopulation of bacteria that tolerate antibiotics due to a physiologically dormant state. As a result, this phenomenon (persistence) is considered a major contrib...

Summary The bacterial resistome is the collection of all the antibiotic resistance genes, virulence genes, and other resistance elements within a bacterial isolate genome including plasmids and bact...

Multi-drug resistant (MDR) Acinetobacter baumannii is one of the most concerning pathogens in hospital infections. A. baumannii is categorized as an “Urgent Threat” by the U.S. Centers for Disease C...

Corynebacterium diphtheriae, the agent of diphtheria, is a genetically diverse bacterial species. Although antimicrobial resistance has emerged against several drugs including first-line penicillin,...

Objectives Pathogen identification is crucial for the diagnosis and management of periprosthetic joint infection (PJI). Although culturing methods are the foundation of pathogen detection in PJI, f...

Chickens and guinea fowl are commonly reared in Gambian homes as affordable sources of protein. Using standard microbiological techniques, we obtained 68 caecal isolates of Escherichia coli from ten...

A tigecycline-resistance gene, tet(X6), was detected on a 159-kb novel plasmid carried by a tigecycline-susceptible livestock-associated Acinetobacter towneri isolate. The genetic context of tet(X6)...

Background: Linezolid is an antibiotic used to treat infections caused by multi-drug-resistant Gram-positive bacteria. Linezolid resistance in enterococci has been reported with increasing frequency...

Objectives Staphylococcus aureus Smith strain is a historical strain widely used for research purposes in animal infection models for testing the therapeutic activity of antimicrobial agents. We fou...

A total of four strains of the ‘environmental superbug’ Pedobacter isolated from sludge produced at Norwegian drinking water treatment plants, were characterized by whole genome sequencing and antib...

Purpose: Several subtypes of plasmid-mediated fosfomycin resistance gene fosA in Enterobacteriaceae have been reported worldwide and have caused concern. The present study characterized a novel memb...

Staphylococcus aureus is a leading human pathogen associated with both hospital-acquired and community-acquired infections. The bacterium has steadily gained resistance to β-lactams and other import...

In the present study, we have analyzed the metagenomic DNA from the pooled sediment sample of the river Ganges to explore the abundance and diversity of phages, microbial community and antibiotic re...

Introduction: The importance of plasmid-mediated quinolone resistance (PMQR) in Enterobacterales and its high incidence has been emphasised many times. However, a clinical strain carrying more than ...

Purpose Antimicrobial resistance (AMR) is a public health threat where efficient surveillance is needed to prevent outbreaks. Existing methods for detection of gastrointestinal colonization of multi...

Objectives To characterize the novel cfr(D) gene identified in an Enterococcus faecium clinical isolate (15-307.1) collected from France. Methods The genome of 15-307.1 was entirely sequenced usi...

Current knowledge about the microbial communities inhabiting the stormwater quality improvement devices (SQIDs) for road runoff is scarce. However, as a bioactive compound of these systems, microbes...

Conventional culture-based diagnostics of orthopaedic-implant-associated infections (OIAIs) are arduous. Hence, the aim of this study was to evaluate a culture-independent, rapid nanopore-based diag...

Colistin resistance in Acinetobacter baumannii is mediated by multiple mechanisms. Recently, mutations within pmrAB two component system and overexpression of eptA due to upstream insertion of ISAba...

Objectives To characterise the genetic environment of optrA in linezolid-resistant Enterococcus faecalis isolates from Scotland. Methods Linezolid-resistant E. faecalis were identified in three Sco...

Klebsiella species are problematic pathogens in neonatal units and may cause outbreaks, for which the sources of transmission may be challenging to elucidate. We describe the use of whole-genome seq...

Two billion people are infected with Mycobacterium tuberculosis, leading to 10 million new cases of active tuberculosis and 1.5 million deaths annually. Universal access to drug susceptibility testi...

Antimicrobial resistance (AMR) is one of the most prominent public health threats. AMR genes localized on plasmids can be easily transferred between bacterial isolates by horizontal gene transfer, t...

Objectives To characterize genomes of Klebsiella pneumoniae ST11 NDM-1 responsible for a countrywide outbreak in Poland and compare them phylogenetically with other Polish and international ST11 st...

We describe here the complete genome sequence of an Enterobacter hormaechei ST279 coharbouring blaVIM-1 and mcr-9 recovered from uncooked beef patty in June 2017, Egypt. The tested isolate was resis...

Objectives To the best of our knowledge, we describe the first evidence in Europe of an MDR, blaNDM-4-positive Escherichia coli isolated from a food-producing animal, harboured by a novel IncFII pl...

Clinical management of tuberculosis (TB) in endemic areas is often challenged by a lack of resources including laboratories for Mycobacterium tuberculosis (Mtb) culture. Traditional phenotypic drug ...

Mycobacterium kubicae is 1 of nearly 200 species of nontuberculous mycobacteria (NTM), environmental micro-organisms that in some situations can infect humans and cause severe lung, skin and soft ti...

Background We benchmarked the hybrid assembly approaches of MaSuRCA, SPAdes, and Unicycler for bacterial pathogens using Illumina and Oxford Nanopore sequencing by determining genome completeness a...

International travel contributes significantly to the spread of extended-spectrum β-lactamase (ESBL) gene positive Escherichia coli (ESBL-Ec). We investigated bacterial determinants associated with ...

Vietnam is one of the top shrimp producing and exporting countries in the world. However, viral and bacterial epidemic diseases cause severe damages to shrimp farming, resulting in millions of US do...

The human zoonotic pathogen Escherichia coli O157 is defined by its extensive prophage repertoire including those that encode Shiga toxin, the factor responsible for inducing life-threatening pathol...

Salmonella spp. is an important foodborne pathogen associated with consumption of contaminated food, especially livestock products. Antimicrobial resistance (AMR) in Salmonella has been reported glo...

Shigella spp. commonly causes gastroenteritis known as shigellosis, and severe cases require antibiotic treatments. However, the increased presence of antibiotics in the environment in recent years ...

Antimicrobial resistance (AMR) is a global threat, including in sub-Saharan Africa. However, little is known about the genetics of resistant bacteria in the region. In Malawi, there is growing conce...

Hypervirulent K. pneumoniae (HvKp) is typically associated with ST23 clone; however, hvKp is also emerging from clones ST11, ST15 and ST147, which are also multi-drug resistant (MDR). Here, we aimed...

Carbapenem-hydrolyzing enzymes belonging to the OXA-48-like group are encoded by blaOXA-48-like alleles and are abundant among Enterobacterales in the Netherlands. Therefore, the objective was to in...

Background: An ESBL, carbapenemase- and MCR-1-producing Escherichia coli ST648 strain was isolated from the urine sample of a patient in a Chinese tertiary hospital in 2016. Methods: The strain was ...

Objectives To report the complete genome sequence of a methicillin-resistant Staphylococcus vitulinus from ground beef to allow comparison with other available S. vitulinus genomes and to investiga...

Spread of drug-resistant bacteria is a serious problem worldwide. We thus designed a new sequence-based protocol that can quickly identify bacterial compositions of clinical samples and their drug-r...

Objectives To reconstruct the evolutionary history of the clinical Acinetobacter baumannii XH1056, which lacks the Oxford scheme allele gdhB. Methods Susceptibility testing was performed using br...

Background Recent reports have established the emergence and dissemination of extensively drug resistant (XDR) H58 Salmonella Typhi clone in Pakistan. In India where typhoid fever is endemic, only s...

Objectives The availability of matched sequencing data for the same sample across different sequencing platforms is a necessity for validation and effective comparison of sequencing platforms. A c...

Multi-drug resistant (MDR) Escherichia coli are a major global threat to human health, wherein multi-drug resistance is primarily spread by MDR plasmid acquisition. MDR plasmids are not widely distr...

Incompatibility group C (IncC) plasmids have received attention due to their broad host range and because they harbor key antibiotic resistance genes. Because these resistance genes can spread from ...

Infections caused by Klebsiella pneumoniae are a major public health threat. Extensively drug-resistant and even pan-resistant strains have been reported. Understanding K. pneumoniae pathogenesis is...

Emerging resistance to cephalosporins in Neisseria gonorrhoeae (Ng) is a major public health threat, since these are considered antibiotics of last resort. Continuous surveillance is needed to monit...

Background Approximately half of clinical carbapenem-resistant Enterobacterales (CRE) isolates lack carbapenem-hydrolysing enzymes and develop carbapenem resistance through alternative mechanisms. ...

Objectives To develop a simple DNA sequencing test for simultaneous identification and antimicrobial resistance (AMR) detection of multiple sexually transmitted infections (STIs). Methods A total o...

Mycobacterium chelonae is a rapidly growing nontuberculous mycobacterium that is a common cause of nosocomial infections. Here we describe investigation of a possible nosocomial transmission of M. c...

Objectives To identify and characterize a novel tetracycline resistance gene on a multiresistance plasmid from Staphylococcus aureus SA01 of chicken origin. Methods MICs were determined by broth ...

Klebsiella spp. are a major cause of both nosocomial and community acquired infections, with K. pneumoniae being responsible for most human infections. Although Klebsiella spp. are present in a vari...

Klebsiella pneumoniae is a major threat to human health worldwide. “Classical” K. pneumoniae (cKp) strains commonly cause multidrug-resistant (MDR) infections in debilitated patients residing in hos...

Next-generation sequencing technologies are being rapidly adopted as a tool of choice for diagnostic and outbreak investigation in public health laboratories. However, costs of operation and the nee...

Understanding the distribution and mobility of antibiotic resistance genes (ARGs) in soil bacteria from diverse ecological niches is critical in assessing their impacts on the global spread of antib...

Background Viruses are the most abundant biological entities on Earth, known to be crucial components of microbial ecosystems. However, there is little information on the viral community within agri...

Rapid identification of bacterial pathogens and their antimicrobial resistance (AMR) profiles is critical for minimising patient morbidity and mortality. While many sequencing methods allow deep gen...

Bloodstream infections (BSI) and sepsis are major causes of morbidity and mortality worldwide. Blood culture-based diagnostics usually requires 1–2 days for identification of bacterial agent and an...

Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characteriz...

This is a narrative review on the potential of rapid and point-of-care microbiological testing in pneumonia patients, focusing particularly on hospital-acquired and ventilator-associated pneumonia, ...

Background Riverine ecosystems are biogeochemical powerhouses driven largely by microbial communities that inhabit water columns and sediments. Because rivers are used extensively for anthropogenic ...

Mycobacterium tuberculosis (MTB) is the leading cause of death from bacterial infection. Improved rapid diagnosis and antimicrobial resistance determination, such as by whole genome sequencing, are ...

Surveillance of drug-resistant bacteria is essential for healthcare providers to deliver effective empirical antibiotic therapy. However, traditional molecular epidemiology does not typically occur ...

The rise of antimicrobial resistant Neisseria gonorrhoeae is a significant public health concern. Against this background, rapid culture-independent diagnostics may allow targeted treatment and prev...

The Neisseria gonorrhoeae multilocus sequence type (ST) 7827 emerged in dramatic fashion in Norway in the period 2016-2018. Here, we aim to determine what enabled it to establish and spread so quick...

Background Klebsiella pneumoniae frequently harbours multidrug resistance, and current diagnostics struggle to rapidly identify appropriate antibiotics to treat these bacterial infections. The MinIO...

Background The prevalence of multidrug-resistant Klebsiella pneumoniae is increasingly being implicated worldwide in a variety of infections with high mortalities. Here, we report the complete genom...

Novel antimicrobial resistance genes harboured by pathogens pose a great public health concern, as exemplified by the emergence of blaNDM-1 and mcr-1 over the past decade. Recently, two novel plasmi...

Genotyping methods and genome sequencing are indispensable for revealing the genomic structure of bacterial species displaying high levels of genome plasticity. However, reconstruction of the genome...

Carbapenemase-producing Klebsiella pneumoniae emerged over the past decades as an important pathogen causing morbidity and mortality in hospitalized patients. For infection prevention and control, i...

Carbapenem-resistant Enterobacteriaceae (CRE) represent an urgent threat to human health. Here we report the application of several complementary whole-genome sequencing (WGS) technologies to chara...

Background Hospital outbreaks of carbapenemase-producing organisms, such as blaIMP-4-containing organisms, are an increasing threat to patient safety. Objectives To investigate the genomic dynamics...

The New Delhi Metallo-β-lactamase (NDM) producing Enterobacteriaceae is spreading worldwide. Although the blaNDM gene has been identified in animal associated Enterobacteriaceae isolates in many cou...

Human anthrax cases necessitate rapid response. We completed Bacillus anthracis nanopore whole-genome sequencing in our high-containment laboratory from a human anthrax isolate hours after receipt. ...

Carbapenemase-producing Enterobacteriaceae (CPE) are an increasingly common cause of healthcare-associated infections and may occasionally be identified in patients without extensive healthcare expo...

One-Health studies applying massive-parallel and single-molecule sequencing are a suitable approximation to try to understand how antibiotic resistances flow between the human-animal-environment sce...

In recent years, high-throughput sequencing has revolutionized disease diagnosis by its powerful ability to provide high resolution genomic information. The Oxford Nanopore MinION sequencer has unpa...

Colistin is considered as a last resort antibiotic. The re-use of this antibiotic highlighted the emergence of colistin resistance mediated by chromosomal and plasmidic resistance mechanisms. Five ...

Edwardsiella piscicida is a pathogenic bacterium responsible for significant losses in important wild and cultured fish species. E. piscicida strain MS-18-199 recovered from a diseased hybrid catfis...

The MinION sequencing platform offers near real-time analysis of DNA sequence; this makes the tool attractive for deployment in fieldwork or clinical settings. We used the MinION platform coupled t...

Antimicrobial resistance (AMR) in the nosocomial pathogen, Acinetobacter baumannii, is becoming a serious public health threat. While some mechanisms of AMR have been reported, understanding novel m...

Infections by multidrug resistant Gram negative bacteria are increasingly common, prompting the renewed interest in the use of colistin. Colistin specifically targets Gram negative bacteria by inter...

Gonorrhea is one of the most common sexually transmitted diseases worldwide. To cure infection and prevent transmission, timely and appropriate antimicrobial therapy is necessary. Unfortunately, Nei...

Background Metagenomic sequencing of respiratory microbial communities for pathogen identification in pneumonia may help overcome the limitations of culture-based methods. We examined the feasibilit...

Background OXA-48-like carbapenemases have become increasingly prevalent in healthcare settings worldwide. Their low-level activity against carbapenems makes them difficult to identify, causing pro...

Viable pathogenic bacteria are major biohazards that pose a significant threat to food safety. Despite the recent developments in detection platforms, multiplex identification of viable pathogens in...

Objectives Enterohaemorrhagic Escherichia coli (EHEC) infections may be complicated by haemolytic uraemic syndrome (HUS). The emerging worldwide EHEC serogroup O80 has acquired a mosaic plasmid com...

Melioidosis caused by Burkholderia pseudomallei has become an important clinical threat, especially in Northern Australia and Southeast Asia. However, the genome information on this pathogen is limi...

Enterobacteriaceae having chromosomally-encoded mcr-1 is rarely reported. In this study, we recovered a chromosomal mcr-1 carrying Escherichia coli, designated HeN100, from the feces of a diarrheal...

Multidrug-resistant bacterial pathogens pose a serious public health threat, especially in hospital settings. Horizontal gene transfer (HGT) of mobile genetic elements (MGEs) contributes to this thr...

Over the last 35 years in the UK, the burden of Shiga toxin-producing Escherichia coli (STEC) O157:H7 infection has, during different periods of time, been associated with five different sub-lineage...

Objectives blaOXA-23 is a class D carbapenemase-encoding gene typical of the Acinetobacter genus. However, its occurrence in the Enterobacteriaceae is uncommon. Here we provide the genome character...

Shigella is ranked as the second leading cause of diarrheal disease worldwide. Though infection occurs in people of all ages, most of the disease burden constitutes among the children less than 5 ye...

Bacteroides fragilis constitutes a significant part of the normal human gut microbiota and can also act as an opportunistic pathogen. Antimicrobial resistance (AMR) and the prevalence of AMR genes a...

Background Empirical gonorrhoea treatment at initial diagnosis reduces onward transmission. However, increasing resistance to multiple antibiotics may necessitate waiting for culture-based diagnosti...

National networks of laboratory-based surveillance of antimicrobial resistance (AMR) monitor resistance trends and disseminate these data to AMR stakeholders. Whole-genome sequencing (WGS) can supp...

Horizontal gene transfer, mediated by conjugative plasmids, is one of the main drivers of the global spread of antibiotic resistance. However, the relative contributions of different factors that un...

Widespread release of Bacillus anthracis (anthrax) or Yersinia pestis (plague) would prompt a public health emergency. During an exposure event, high-quality whole genome sequencing (WGS) can identi...

The global dissemination of a ciprofloxacin-resistant (cipR) S. sonnei clone outlines the mobility of this important agent of diarrheal disease, and threatens the utility of ciprofloxacin as a first...

The emergence of Mycobacterium tuberculosis strains with complex drug resistance profiles necessitates a rapid and extensive drug susceptibility test for comprehensive guidance of patient treatment....

Background blaTEM-1 encodes a narrow-spectrum β-lactamase that is inhibited by β-lactamase inhibitors and commonly present in Escherichia coli. Hyperproduction of blaTEM-1 may cause resistance to p...

We report first complete genome sequence and analysis of an extreme drug resistance (XDR) nosocomial Stenotrophomonas maltophilia that is resistant to the mainstream drugs i.e. trimethoprim/sulfamet...

Pathogen monitoring, detection and removal are essential to public health and outbreak management. Systems are in place for monitoring the microbial load of hospitals and public health facilities wi...

The Elizabethkingia are a genetically diverse genus of emerging pathogens that exhibit multidrug resistance to a range of common antibiotics. Two representative species, Elizabethkingia bruuniana an...

Background Mycobacterium tuberculosis resistance to anti-tuberculosis drugs is a major threat to global public health. Whole genome sequencing (WGS) is rapidly gaining traction as a diagnostic tool...

The gold standard for clinical diagnosis of bacterial lower respiratory infections (LRIs) is culture, which has poor sensitivity and is too slow to guide early, targeted antimicrobial therapy. Metag...

Objectives Pseudomonas aeruginosa (P. aeruginosa) is a common Gram-negative bacterium that can cause a series of serious infections, such as lower respiratory tract infection, urinary-tract infecti...

The Oxford Nanopore MinION DNA sequencing device can produce large amounts of long sequences, typically several kilobases, within a few hours. This long read capacity was exploited to detect antimic...

Background Infection of patients with multidrug-resistant (MDR) bacteria often leave very limited or no treatment options. The transfer of antimicrobial resistance genes (ARG) carrying plasmids bet...

Carbapenem resistant Enterobacteriaceae (CRE) are a critical public health issue. Recent studies indicate many CRE lack carbapenemases, but contain extended spectrum β-lactamases (ESBLs). We investi...

Horizontal transfer of plasmids plays a pivotal role in the dissemination of antibiotic resistance genes and emergence of multidrug-resistant bacteria. Sequencing of plasmids is thus paramount for t...

Background The mcr-1 gene has been widely reported in both bacterial chromosomes and plasmids, while its stability in these genetic materials is not well understood. Objectives Our aim was to ch...

In this article, Che et al. performed metagenomic sequencing of wastewater treatment samples to identify the hosts of antibacterial resistance genes and monitor their spread. Nanopore long-reads gre...

Background Colistin resistance mediated by mcr-1-harbouring plasmids is an emerging threat in Enterobacteriaceae, like Salmonella. Based on its major contribution to the diarrhoea burden, the epide...

Disruptive innovations in long-range, cost-effective direct template nucleic acid sequencing are transforming clinical and diagnostic medicine. A multidrug resistant strain and a pan-susceptible str...

The incidence of infections caused by extraintestinal Escherichia coli (ExPEC) is rising globally, which is a major public health concern. ExPEC strains that are resistant to antimicrobials have bee...

Background Enterobacter hormaechei is an important emerging pathogen and a key member of the highly diverse Enterobacter cloacae complex. E. hormaechei strains can persist and spread in nosocomial ...

Shigella flexneri is a major etiological agent of shigellosis in developing countries, primarily occurring in children under five years of age. We have sequenced, for the first time, the complete ge...

Standard antimicrobial susceptibility testing (AST) approaches lead to delays in the selection of optimal antimicrobial therapy. Here, we sought to determine the accuracy of antimicrobial resistance...

Background Pathogens identification is critical for the proper diagnosis and precise treatment of infective endocarditis (IE). Although blood and valve cultures are the gold standard for IE pathoge...

Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is common, compromising gonorrhoea treatment internationally. Rapid characterisation of AMR strains could ensure appropriate and personalised ...

Background The antimicrobial resistance (AMR) phenotypic properties, multiple drug resistance (MDR) gene profiles, and genes related to potential virulence and pathogenic properties of five Enterob...

The aim of this study was to use single-molecule nanopore sequencing to explore the genomic environment of the resistance determinants in a multidrug-resistant (MDR) strain of enteroaggregative Esch...

Surveillance of circulating drug resistant bacteria is essential for healthcare providers to deliver effective empiric antibiotic therapy. However, the results of surveillance may not be available o...

A total of 416 actinomycete cultures were isolated from various unique environments in Ethiopia and tested for bioactivity. Six isolates with pronounced antimicrobial activity were chosen for taxono...

Background ISCR1 is an important mobile genetic element mediating the transfer of antibiotic resistance genes. Genetic diversity regarding distribution and copy numbers of ISCR1 within a bacterial...

Historically, Neisseria meningitidis serogroup A strains have caused large epidemics of meningitis across sub-Saharan Africa. Following mass vaccination from 2010, serogroup A outbreaks have been mo...

Here, we report the application of a portable sequencer, MinION, for genotyping the malaria parasite Plasmodium falciparum. In the present study, an amplicon mixture of nine representative genes cau...

Acinetobacter baumannii is a common causative agent of hospital-acquired infections and a leading cause of infection in burns patients. Carbapenem-resistant A. baumannii is considered a major public...

Objectives In this study, we characterize a concurrent disseminated infection with a virulent hypermucoviscous (HMV) Klebsiella pneumoniae and an OXA-181-producing XDR K. pneumoniae from a patient...

A better understanding of the genomic changes that facilitate the emergence and spread of drug-resistant Mycobacterium tuberculosis strains is currently required. Here, we report the use of the MinI...

Determination of HIV drug resistance (HIVDR) is becoming an integral baseline HIV evaluation for newly infected subjects, as the level of pre-treatment resistance is increasing worldwide. Until now,...

Malaria is the most significant parasitic disease affecting humans, with 212 million cases and 429,000 deaths in 20151, and resistance to existing drugs endangers the global malaria elimination camp...

Wastewater treatment plants (WWTPs) functioned as the intersection between the human society and nature environment, are receiving increasingly more attention on risk assessment of the acquisition o...

Recent advances in nanopore sequencing technology have led to a substantial increase in throughput and sequence quality. Together, these improvements may permit real-time benchtop genomic sequencing...

We characterized the genetic environment of mcr-1 in colistin-resistant Escherichia coli strains isolated in Switzerland during 2014-2016 from humans (n=3) and chicken meat (n=6). Whole genome and p...

Next generation sequencing can accurately predict antibiotic susceptibility in Neisseria gonorrhoeae (NG) allowing preservation of first-line treatments in the face of widespread antimicrobial resis...

Dissemination of carbapenem resistance among pathogenic Gram-negative bacteria is a looming medical emergency. Efficient spread of resistance within and between bacterial species is facilitated by m...

The Oxford Nanopore Technologies MinIONTM is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome...

Routine full characterization of Mycobacterium tuberculosis (TB) is culture-based, taking many weeks. Whole-genome sequencing (WGS) can generate antibiotic susceptibility profiles to inform treatmen...

Objectives: The introduction of metagenomic sequencing to diagnostic microbiology has been hampered by slowness, cost and complexity. We explored whether MinION nanopore sequencing could accelerate ...

The emergence of antibiotic resistance in human pathogens has become a major threat to modern medicine and in particular hospitalized patients. The outcome of antibiotic treatment can be affected by...

The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100~kBp were reported), however it suffers from high sequencing er...

Derrick Crook from University of Oxford gives a talk at London Calling 2016.

A talk by Stephanie Hao of Johns Hopkins University Applications of Nanopore Sequencing for Infectious Disease Detection at London Calling 2016.

A presentation to the MinION Community by Dr Justin O’Grady, Lecturer in Medical Microbiology, University of East Anglia.

Dr Catherine Arnold, Consultant Clinical Scientist in Molecular Microbiology at Public Health England talks to the MinION Community about NGS for Public Health Microbiology.

Next generation sequencing technology has revolutionised the study of microbial genomics, but most large-scale studies have focused on short-read sequencing. This use of short-read sequencing has li...

The diagnosis of infectious diseases by culture takes at least two days: one to grow the bacteria and then, at best, one to identify pathogens and test their antimicrobial susceptibility. Meanwhile ...

Clinical pathogen sequencing has been demonstrated to have a positive outcome on treatment of patients with unknown bacterial infection. However, widespread adoption of clinical pathogen sequencing ...

Human herpesvirus type 1 (HHV-1) has a large double-stranded DNA genome of approximately 152 kbp that is structurally complex and GC-rich. This makes the assembly of HHV-1 whole genomes from short-r...

Translating the Oxford Nanopore MinION sequencing technology into medical microbiology requires on-going analysis that keeps pace with technological improvements to the instrument and release of ass...

Many isolates of Escherichia coli carrying blaOXA-48 referred to Public Health England’s national reference laboratory during 2014 and 2015 shared similar pulsed-field gel electrophoresis (PFGE) pro...

Rapid and accurate detection of antibiotic resistance in pathogens is an urgent need, affecting both patient care and population-scale control. Microbial genome sequencing promises much, but many ba...

The recently introduced Oxford Nanopore MinION platform generates DNA sequence data in real-time. This has great potential to shorten the sample-to-results time and is likely to have benefits such a...

Genome sequencing will be increasingly used in the clinical setting to tailor antimicrobial prescribing and inform infection control outbreaks. A recent technological innovation that could reduce th...

Short-read, high-throughput sequencing technology cannot identify the chromosomal position of repetitive insertion sequences that typically flank horizontally acquired genes such as bacterial virule...