18 results found
Rodriguez Manzano J, Moser N, Malpartida Cardenas K, et al., 2020, Rapid detection of mobilized colistin resistance using a nucleic acid based lab-on-a-chip diagnostic system, Scientific Reports, Vol: 10, ISSN: 2045-2322
The increasing prevalence of antimicrobial resistance is a serious threat to global public health. One of the most concerning trends is the rapid spread of Carbapenemase-Producing Organisms (CPO), where colistin has become the last-resort antibiotic treatment. The emergence of colistin resistance, including the spread of mobilized colistin resistance (mcr) genes, raises the possibility of untreatable bacterial infections and motivates the development of improved diagnostics for the detection of colistin-resistant organisms. This work demonstrates a rapid response for detecting the most recently reported mcr gene, mcr−9, using a portable and affordable lab-on-a-chip (LoC) platform, offering a promising alternative to conventional laboratory-based instruments such as real-time PCR (qPCR). The platform combines semiconductor technology, for non-optical real-time DNA sensing, with a smartphone application for data acquisition, visualization and cloud connectivity. This technology is enabled by using loop-mediated isothermal amplification (LAMP) as the chemistry for targeted DNA detection, by virtue of its high sensitivity, specificity, yield, and manageable temperature requirements. Here, we have developed the first LAMP assay for mcr−9 - showing high sensitivity (down to 100 genomic copies/reaction) and high specificity (no cross-reactivity with other mcr variants). This assay is demonstrated through supporting a hospital investigation where we analyzed nucleic acids extracted from 128 carbapenemase-producing bacteria isolated from clinical and screening samples and found that 41 carried mcr−9 (validated using whole genome sequencing). Average positive detection times were 6.58 ± 0.42 min when performing the experiments on a conventional qPCR instrument (n = 41). For validating the translation of the LAMP assay onto a LoC platform, a subset of the samples were tested (n = 20), showing average detection times o
Jauneikaite E, Ferguson T, Mosavie M, et al., 2020, Staphylococcus aureus colonisation and acquisition of skin and soft tissue infection amongst Royal Marines recruits: A prospective cohort study, Clinical Microbiology and Infection, Vol: 26, Pages: 381.e1-381.e6, ISSN: 1198-743X
Objectives: Skin and soft tissue infections (SSTIs) are a serious health issue for military personnel. Of particular importance are those caused by MRSA and PVL-positive S. aureus (PVL-SA), as they have been associated with outbreaks of SSTIs. A prospective observational study was conducted in Royal Marines recruits to investigate the prevalence of PVL-SA carriage and any association with SSTIs.Methods: 1,012 RM recruits were followed through a 32-week training programme, with nose and throat swabs obtained at weeks 1, 6, 15 and 32. S. aureus isolates were characterised by antibiotic susceptibility testing, spa typing, presence of mecA/C and PVL genes. Retrospective review of the clinical notes for SSTI acquisition was conducted.Results: S. aureus colonisation decreased from week-1 to week-32 (41% to 26%, p<0.0001). Of 1,168 S. aureus isolates, 3/1168 (0.3%) were MRSA and 10/1168 (0.9%) PVL-positive (all MSSA) and 169/1168 (14.5%) were resistant to clindamycin. Isolates showed genetic diversity with 238 different spa types associated with 25 MLST clonal complexes. SSTIs were seen in 35% (351/989) of recruits with 3 training days lost per recruit. SSTI acquisition rate was reduced amongst persistent carriers (p<0.0283). Conclusions: Nose and throat carriage of MRSA and PVL-SA was low amongst recruits, despite a high incidence of SSTIs being reported particularly cellulitis. Carriage strains were predominantly MSSA with a marked diversity of genotypes. Persistent nose and/or throat carriage was not associated with SSTI acquisition. Putative person-to-person transmission within troops was identified based on spa typing requiring further research to confirm and explore potential transmission routes.
Collin SM, Lamb P, Jauneikaite E, et al., 2019, Hospital clusters of invasive Group B Streptococcal disease: a systematic review, Journal of Infection, Vol: 79, Pages: 521-527, ISSN: 0163-4453
Objectives: To characterize outbreaks of invasive Group B Streptococcal (iGBS) disease in hospitals.Methods: Systematic review using electronic databases to identify studies describing iGBS outbreaks/clusters or cross-infection/acquisition in healthcare settings where ‘cluster’ was defined as ≥2 linked cases. PROSPERO CRD42018096297.Results: Twenty-five references were included describing 30 hospital clusters (26 neonatal, 4 adult) in 11 countries from 1966 to 2019. Cross-infection between unrelated neonates was reported in 19 clusters involving an early-onset (<7 days of life; n = 3), late-onset (7–90 days; n = 13) index case or colonized infant (n = 3) followed by one or more late-onset cases (median serial interval 9 days (IQR 3–17, range 0–50 days, n = 45)); linkage was determined by phage typing in 3 clusters, PFGE/MLST/PCR in 8, WGS in 4, non-molecular methods in 4. Postulated routes of transmission in neonatal clusters were via clinical personnel and equipment, particularly during periods of crowding and high patient-to-nurse ratio. Of 4 adult clusters, one was attributed to droplet spread between respiratory cases, one to handling of haemodialysis catheters and two unspecified.Conclusions: Long intervals between cases were identified in most of the clusters, a characteristic which potentially hinders detection of GBS hospital outbreaks without enhanced surveillance supported by genomics.
Herbert R, Hatcher J, Jauneikaite E, et al., 2019, Two-year analysis of Clostridium difficile ribotypes associated with increased severity, Journal of Hospital Infection, Vol: 103, Pages: 388-394, ISSN: 0195-6701
BackgroundCertain Clostridium difficile ribotypes have been associated with complex disease phenotypes including recurrence and increased severity, especially the well-described hypervirulent ribotype RT027. In this study we set out to determine the pattern of ribotypes causing infection and association if any with severity.MethodsAll faecal samples submitted to a large diagnostic laboratory for C. difficile testing between 2011 and 2013 were subject to routine testing and cultured. All C. difficile isolates were ribotyped and associated clinical and demographic patient data were retrieved then linked to ribotyping data.ResultsA total of 86 distinct ribotypes were identified from 705 isolates of C. difficile. Ribotypes RT002 and RT015 were the most prevalent (22.5%, n=159). Only five isolates (0.7%) were the hypervirulent RT027. Ninety of 450 (20%) patients with clinical information available died within 30-days of C. difficile isolation. Ribotype RT220, one of the ten commonest ribotypes, was associated with elevated median C-reactive protein and significantly increased 30-day all-cause mortality when compared with ribotypes RT002 and RT015, and with all other ribotypes found in the study.ConclusionsA wide range of C. difficile ribotypes were responsible for C. difficile infection presentations. Although C. difficile-associated mortality has reduced in recent years, expansion of lineages associated with increased severity could herald increases in future mortality. Enhanced surveillance for emerging lineages such as RT220 that are associated with more severe disease is required, with genomic approaches to dissect pathogenicity.
Ellington MJ, Davies F, Jauneikaite E, et al., 2019, A multi-species cluster of GES-5 carbapenemase producing Enterobacterales linked by a geographically disseminated plasmid, Clinical Infectious Diseases, ISSN: 1058-4838
BACKGROUND: Early and accurate treatment of infections due to carbapenem-resistant organisms is facilitated by rapid diagnostics but rare resistance mechanisms can compromise detection. One year after a GES-5 carbapenemase-positive Klebsiella oxytoca infection was identified by whole genome sequencing (WGS) (later found to be part of a cluster of three cases), a cluster of 11 patients with GES-5-positive K. oxytoca was identified over 18 weeks in the same hospital.METHODS: Bacteria were identified by MALDI-TOF, antimicrobial susceptibility testing followed EUCAST guidelines. Ertapenem-resistant isolates were referred to Public Health England for characterization using PCR detection of GES, pulse-field gel electrophoresis (PFGE) and WGS for the second cluster.RESULTS: The identification of the first GES-5 K. oxytoca isolate was delayed, being identified on WGS. A GES-gene PCR informed the occurrence of the second cluster in real-time. In contrast to PFGE, WGS phylogenetic analysis refuted an epidemiological link between the two clusters; it also suggested a cascade of patient-to-patient transmission in the later cluster. A novel GES-5-encoding plasmid was present in K. oxytoca,E. coli and E. cloacae isolates from unlinked patients within the same hospital group and in human and wastewater isolates from three hospitals elsewhere in the UK.CONCLUSIONS: Genomic sequencing revolutionized the epidemiological understanding of the clusters, it also underlined the risk of covert plasmid propagation in healthcare settings and revealed the national distribution of the resistance-encoding plasmid. Sequencing results also informed and led to the ongoing use of enhanced diagnostic tests for detecting carbapenemases locally and nationally.
Aliabadi S, Honeyford K, Jauneikaite E, et al., 2019, Risk factors for E. coli Susceptibility in Bloods Stream Infections in England Between 2013-2017, Publisher: OXFORD UNIV PRESS, Pages: 111-111, ISSN: 1101-1262
Lynskey NN, Jauneikaite E, Li H-K, et al., 2019, Emergence of dominant toxigenic M1T1 Streptococcus pyogenes clone during increased scarlet fever activity in England: a population-based molecular epidemiological study, Lancet Infectious Diseases, Vol: 19, Pages: 1209-1218, ISSN: 1473-3099
BackgroundEngland is experiencing scarlet fever activity unprecedented in modern times. In 2016, England’s scarlet fever seasonal rise coincided with an unexpected elevation in invasive Streptococcus pyogenes infections. We describe the molecular-epidemiological investigation of these events and emergence of a new emm1 lineage.Methods We analysed changes in S. pyogenes emm-genotypes, and notifications of scarlet fever and invasive disease 2014-2016 using regional (North-West London) and national (England and Wales) data. We analysed genomes of 135 non-invasive and 552 invasive emm1 isolates from 2009-2016, and compared 2800 global emm1 sequences. Expression of Streptococcal pyrogenic exotoxin (Spe)A by sequenced non-invasive emm1 isolates was quantified.FindingsCoincident with national increases in scarlet fever and invasive disease notifications, emm1 S. pyogenes increased significantly, from 19% (28/147) of upper respiratory tract isolates in MarchMay 2015, to 32·6% (47/144) in the same period 2016 in North-West London (χ2 (1df)=7·024, p=0·008), and from 31% (183/587) of invasive isolates in March-May 2015, to 41·9% (267/637)in the same period 2016 nationally (χ2 (1df)=15·16, p=0·0001). Sequences of emm1 isolates from 2009-2016 demonstrated emergence of a new emm1 lineage (M1UK), with overlap of pharyngitis, scarlet fever, and invasive M1UK strains, that could be genotypically distinguished from pandemic emm1 isolates (M1global). Compared with M1global, median expression of SpeA increased 9-fold in M1UK isolates (M1global, median=20·9 ng/ml, IQ range=21.3; (M1UK, median=190·2 ng/ml, IQ3 range 31.5; Mann-Whitney p<0·001). M1UK expanded nationally to represent 84% (252/299) of all emm1 genomes in 2016; phylogenetic analysis of published datasets identified single M1UK isolates in Denmark and USA.
Martinez-Vega R, Jauneikaite E, Thoon KC, et al., 2019, Risk factor profiles and clinical outcomes for children and adults with pneumococcal infections in Singapore: a need to expand vaccination policy?, PLoS ONE, Vol: 14, ISSN: 1932-6203
Invasive pneumococcal infection is a major cause of morbidity and mortality worldwide despite the availability of pneumococcal vaccines. The aim of this study was to re-evaluate the clinical syndromes, prognostic factors and outcomes for pneumococcal disease in adults and children in Singapore during the period before and after the introduction of the pneumococcal vaccine. We retrospectively analyzed a large cohort of patients admitted to the four main public hospitals in Singapore with S. pneumoniae infection between 1997 and 2013. A total of 889 (64% of all isolates identified in the clinical laboratories) cases were included in the analysis; 561 (63.1%) were adult (≥16 years) cases with a median age of 62 years and 328 (36.9%) were paediatric cases with a median age of 3 years. Bacteraemic pneumonia was the most common syndrome in both groups (69.3% vs. 44.2%), followed by primary bacteraemia without pneumonia (14.3% vs. 13.4%), meningitis (6.4% vs. 7.6%) and non-bacteraemic pneumonia (5.2% vs. 21%). The major serotypes in adults were 3, 4, 6B, 14, 19F and 23F whereas in children they were 14, 6B and 19F, accounting both for nearly half of pneumococcal disease cases. No particular serotype was associated with mortality or severity of the pneumococcal disease. Overall mortality rate was 18.5% in adults and 3% in children. Risk factors for mortality included acute cardiac events in adults, meningitis in children and critical illness and bilateral pulmonary infiltrates in both adults and children. Penicillin resistance was not associated with increased mortality. Our results agree with global reports that the course of pneumococcal disease and its clinical outcome were more severe in adults than in children. The main serotypes causing invasive disease were all covered by the vaccines in use. The high mortality rates reflect an urgent need to increase vaccination coverage in both adults and children to tackle this vaccine-preventable infection.
Mosavie M, Blandy O, Jauneikaite E, et al., 2019, Sampling and diversity of Escherichia coli from the enteric microbiota in patients with Escherichia coli bacteraemia, BMC Research Notes, Vol: 12, ISSN: 1756-0500
ObjectiveThe increase in Escherichia coli bloodstream infections mandates better characterisation of the relationship between commensal and invasive isolates. This study adopted a simple approach to characterize E. coli in the gut reservoir from patients with either E. coli or other Gram-negative bacteraemia, or those without bacteraemia, establishing strain collections suitable for genomic investigation. Enteric samples from patients in the three groups were cultured on selective chromogenic agar. Genetic diversity of prevailing E. coli strains in gut microbiota was estimated by RAPD-PCR.ResultsEnteric samples from E. coli bacteraemia patients yielded a median of one E. coli RAPD pattern (range 1–4) compared with two (range 1–5) from groups without E. coli bacteraemia. Of relevance to large-scale clinical studies, observed diversity of E. coli among hospitalised patients was not altered by sample type (rectal swab or stool), nor by increasing the colonies tested from 10 to 20. Hospitalised patients demonstrated an apparently limited diversity of E. coli in the enteric microbiota and this was further reduced in those with E. coli bacteraemia. The reduced diversity of E. coli within the gut during E. coli bacteraemia raises the possibility that dominant strains may outcompete other lineages in patients with bloodstream infection.
To K, Cornwell E, Daniel R, et al., 2019, Evaluation of matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of group B streptococcus, BMC Research Notes, Vol: 12, ISSN: 1756-0500
ObjectiveGroup B Streptococcus (GBS) is a leading cause of neonatal meningitis and sepsis worldwide. Intrapartum antibiotics given to women carrying GBS are an effective means of reducing disease in the first week of life. Rapid and reliable tests are needed to accurately identify GBS from these women for timely intrapartum antibiotic administration to prevent neonatal disease. Many laboratories now use matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) by direct plating or cell lysis for the identification of GBS isolates. The cell lysis step increases time to results for clinical samples and is more complex to perform. Therefore, we seek to evaluate the sensitivity and specificity of the quicker and more rapid direct plating method in identifying GBS.ResultsWe directly compared swab isolates analysed by both direct plating and cell lysis method and demonstrated that direct plating has a sensitivity and specificity of 0.97 and 1, respectively, compared to an additional cell lysis step. We demonstrated that MALDI-TOF MS can be successfully used for batch processing by the direct plating method which saves time. These results are reassuring for laboratories worldwide who seek to identify GBS from swabs samples as quickly as possible.
Jauneikaite E, Kapatai G, Davies F, et al., 2018, Serial clustering of late onset group B streptococcal infections in the neonatal unit - a genomic re-evaluation of causality, Clinical Infectious Diseases, Vol: 67, Pages: 854-860, ISSN: 1058-4838
Background. Invasive Group B streptococcus (GBS) is a major cause of serious neonatal infection. Current strategies to reduce early onset GBS disease have no impact on late onset disease (LOD). Although GBS is a normal part of the enteric microbiota in healthy term infants, LOD cases arising in the neonatal intensive care unit setting raise questions about mode of acquisition.Methods. Enhanced surveillance for any case of late onset GBS sepsis admitted to a level 3, 24-bed neonatal intensive care unit over a 2 year period was instituted following a cluster of four cases. All late onset GBS isolates were serotyped and genomes sequenced. Rectal screening of neonates for GBS was undertaken weekly. Healthcare workers and parents were not screened.Results. Over 24 months, a total of 12 late onset invasive GBS episodes were identified (incidence 0.6/1000 live births). Genomic analysis revealed that 11/12 GBS isolates (92%) were linked to at least one other LOD isolate. Four isolates from the first cluster were serotype V, resistant to macrolides and lincosamides, providing early evidence of a common source. Sequencing confirmed isolates were indistinguishable, or distinguishable by 1 SNP, from each other, and distinct from contemporary serotype V GBS. Although a common environmental source was not identified, prompt infection prevention interventions were instituted and no further serotype V GBS infections arose. Prospective surveillance identified three further clusters of LOD due to serotypes Ia, Ib, and III, leading to re-evaluation of interventions required for preventing GBS LOD. Conclusion. Acquisition routes for LOD GBS in the neonatal unit are poorly understood; such cases may not necessarily be sporadic. Within this neonatal unit, our data suggest that a single case of LOD GBS sepsis should be considered a potential nosocomial transmission event warranting prompt investigation, heightened infection prevention vigilance and action where required.
Jauneikaite E, Khan-Orakzai Z, Kapatai G, et al., 2016, Nosocomial outbreak of drug resistant Streptococcus pneumoniae serotype 9V in an adult respiratory medicine ward, Journal of Clinical Microbiology, Vol: 55, Pages: 776-782, ISSN: 1098-660X
Streptococcus pneumoniae infections arising in hospitalized patients are often assumed to be sporadic, and linked to community carriage. Here, whole genome sequencing was used to demonstrate nosocomial acquisition of antimicrobially-resistant ST156-9V S. pneumoniae in 3 respiratory patients resulting in two bacteremias and one lower respiratory tract infection. Two of the cases arose in patients who had recently been discharged from hospital and were re-admitted from the community. Nosocomial spread was suspected solely because of a highly unusual resistance pattern and case presentations within 24h of one another. The outbreak highlights a potential for rapid transmission and short incubation period in the respiratory ward setting.
Jauneikaite E, Tocheva AS, Jefferies JMC, et al., 2015, Current methods for capsular typing of Streptococcus pneumoniae, JOURNAL OF MICROBIOLOGICAL METHODS, Vol: 113, Pages: 41-49, ISSN: 0167-7012
Jauneikaite E, Jefferies JMC, Churton NWV, et al., 2014, Genetic diversity of Streptococcus pneumoniae causing meningitis and sepsis in Singapore during the first year of PCV7 implementation, EMERGING MICROBES & INFECTIONS, Vol: 3
Litt DJ, Jauneikaite E, Tchipeva D, et al., 2012, Direct molecular typing of Bordetella pertussis from clinical specimens submitted for diagnostic quantitative (real-time) PCR, JOURNAL OF MEDICAL MICROBIOLOGY, Vol: 61, Pages: 1662-1668, ISSN: 0022-2615
Jauneikaite E, Churton N, Lin R, et al., 2012, Prevalence of serotypes and molecular types among Streptococcus pneumoniae isolates causing invasive disease in Singapore between June 2009 and August 2010, Publisher: ELSEVIER SCI LTD, Pages: E223-E223, ISSN: 1201-9712
Jauneikaite E, Jefferies JM, Hibberd ML, et al., 2012, Prevalence of Streptococcus pneumoniae serotypes causing invasive and non-invasive disease in South East Asia: A review, VACCINE, Vol: 30, Pages: 3503-3514, ISSN: 0264-410X
<jats:title>Abstract</jats:title><jats:p>A hospital outbreak of carbapenem-resistant Enterobacteriales was detected by routine surveillance. Whole genome sequencing and subsequent analysis revealed a conserved promiscuous OXA-48 carrying plasmid as the defining factor within this outbreak. Four different species of Enterobacteriales were involved in the outbreak. <jats:italic>Escherichia coli</jats:italic> ST399 accounted for 20/55 of all the isolates. Comparative genomics with publicly available <jats:italic>E. coli</jats:italic> ST399 sequence data showed that the outbreak isolates formed a unique clade. The OXA-48 plasmid identified in the outbreak differed from other known plasmids by an estimated five homologous recombination events. We estimated a lower bound to the plasmid conjugation rate to be 0.23 conjugation events per lineage per year. Our analysis suggests co-evolution between the plasmid and its main bacterial host to be a key driver of the outbreak. This is the first study to report carbapenem-resistant <jats:italic>E. coli</jats:italic> ST399 carrying OXA48 as the main cause of a plasmid-borne outbreak within a hospital setting. This study supports complementary roles for both plasmid conjugation and clonal expansion in the emergence of this outbreak.</jats:p>
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