scholarly journals Risk factors associated with large clusters of tuberculosis patients determined by whole-genome sequencing in a high-tuberculosis-burden country

Tuberculosis ◽  
2020 ◽  
Vol 125 ◽  
pp. 101991
Author(s):  
Reiko Miyahara ◽  
Nat Smittipat ◽  
Tada Juthayothin ◽  
Hideki Yanai ◽  
Areeya Disratthakit ◽  
...  
Keyword(s):  
Risk Factors ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Tuberculosis Patients ◽  
Factors Associated ◽  
Large Clusters

scholarly journals Prospective Surveillance and Rapid Whole-Genome Sequencing Detects Two Unsuspected Outbreaks of Carbapenemase-Producing Klebsiella pneumoniae in a UK Teaching Hospital

2017 ◽  
Vol 4 (suppl_1) ◽  
pp. S43-S44
Author(s):  
Estee Torok ◽  
Hayley Brodrick ◽  
Fahad Khokhar ◽  
Beth Blane ◽  
Petra Polgarova ◽  
...  
Keyword(s):  
Risk Factors ◽  
High Risk ◽  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Teaching Hospital ◽  
Multidrug Resistant ◽  
Health Concern ◽  
Whole Genome ◽  
Prospective Surveillance

Abstract Background The increasing incidence of carbapenemase-producing Enterobacteriaceae (CPE) is a global health concern, as treatment options are extremely limited. The prevalence of CPE in UK hospitals is unknown, as national screening guidelines only recommend screening in patients considered to be at high-risk of CPE. Patients in intensive care units (ICU) are at high-risk of healthcare-associated infections caused by multidrug-resistant organisms (MDRO). Methods We conducted a six-month prospective surveillance study to determine the prevalence of MDRO in a UK teaching hospital ICU. Between June and December 2016, all adult patients admitted to ICU were screened for MDRO on admission, on discharge, and weekly during their ICU stay. Surveillance samples included stool or rectal swabs, urine, sputum or tracheal aspirates, and wound swabs (if wounds were present). Isolates were characterized phenotypically before undergoing whole-genome sequencing (WGS), epidemiological, and phylogenetic analyses. Results During the first week of the study we identified stool carriage of a multidrug-resistant Klebsiella pneumoniae strain in two patients neither of whom had recognized risk factors for CPE. Both isolates were resistant to all antibiotics tested, apart from colistin, and were PCR-positive for the blaNDM-1 gene. Enhanced surveillance by the infection control team identified four additional patients in several wards who had stool carriage (n = 3) or bloodstream infection (n = 1) with a blaNDM-1K. pneumoniae isolate. Epidemiological links were identified between these six patients. Five months later, a second outbreak of multidrug-resistant K. pneumoniae was detected, involving stool carriage by four patients on two different wards. Environmental screening identified environmental contamination with multidrug-resistant K. pneumoniae on one ward. DNA sequence analysis confirmed that a novel blaNDM-1K. pneumoniaelineage (ST78) was responsible for both outbreaks in the hospital. Conclusion We identified two unsuspected blaNDM-1K. pneumoniae outbreaks in patients with no recognized risk factors for CPE. This highlights the importance of prospective surveillance for MDRO in high-risk settings, such as ICUs, and supports the use of rapid WGS to support outbreak investigations in real-time. Disclosures All authors: No reported disclosures.

scholarly journals Whole genome sequencing of Neisseria gonorrhoeae reveals transmission clusters involving patients of mixed HIV serostatus

2017 ◽  
Vol 94 (2) ◽  
pp. 138-143 ◽  
Author(s):  
Joanna Peters ◽  
Fiona Cresswell ◽  
Lauren Amor ◽  
Kevin Cole ◽  
Gillian Dean ◽  
...  
Keyword(s):  
Risk Factors ◽  
Neisseria Gonorrhoeae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Hiv Positive ◽  
Sexual Networks ◽  
Whole Genome ◽  
Questionnaire Data ◽  
Hiv Serostatus ◽  
Geosocial Networking

ObjectivesPrevention and control of gonorrhoea depends on understanding the nature of sexual networks and risk factors for infection. We aimed to use high-resolution typing (whole genome sequencing (WGS)) of Neisseria gonorrhoeae isolates plus patient questionnaire data to gain insights into transmission patterns in a high prevalence setting.MethodsDuring a 9-month period (July 2014–March 2015), patients diagnosed with gonorrhoea attending sexual health service in Brighton, UK, were invited to provide anonymised detailed information by questionnaire about risk factors for infection. Questionnaire data plus WGS data from cultured isolates were analysed to yield information about sexual networks and risk factors for infection.Results104/149 individuals who consented to participate in the study were culture positive. 97/104 (93%) were male. 80 self-reported to be men who have sex with men (MSM). 35/104 (34%) of patients were HIV positive. 51/104 (49%) individuals reported using geosocial networking applications to facilitate contact. Sex under the influence of drugs was reported by 16/34 (46%) of HIV-positive MSM, 17/41 (41%) of HIV-negative MSM and 5/15 (31%) of heterosexuals. WGS data were available for 100 isolates from 83 patients. 55 isolates (66%) belonged to genetically related subtypes involving one or more patients, who could be plausibly linked through recent direct or indirect transmission. Four transmission clusters containing 3–12 individuals were composed of MSM of mixed HIV serostatus.ConclusionsWe show that data obtained from WGS of N. gonorrhoeae and enhanced epidemiological data obtained from patient questionnaires are mutually supportive and reveal insights into sexual networks. Our findings suggest that serosorting may have declined as a practice and indicate the importance of designing public health interventions that target infection risks associated with recreational drug use and contact made using geosocial networking applications.

scholarly journals Whole genome sequencing to identify host genetic risk factors for severe outcomes of hepatitis a virus infection

2014 ◽  
Vol 86 (10) ◽  
pp. 1661-1668 ◽  
Author(s):  
Dustin Long ◽  
Oren K. Fix ◽  
Xutao Deng ◽  
Mark Seielstad ◽  
Adam S. Lauring ◽  
...  
Keyword(s):  
Risk Factors ◽  
Virus Infection ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Risk ◽  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Genetic Risk Factors ◽  
Whole Genome ◽  
Host Genetic

scholarly journals 1530. A Cluster of Disseminated Gonococcal Infections in a Non-Immunocompromised Veteran Population

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S765-S766
Author(s):  
Nicole C Vissichelli ◽  
Emily Hill ◽  
Linda E Anderson ◽  
Angela Eckert ◽  
Cynthia M Fagan ◽  
...  
Keyword(s):  
Risk Factors ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Medical Center ◽  
Tertiary Care ◽  
Case Series ◽  
Clinical History ◽  
Nucleic Acid Amplification ◽  
Whole Genome ◽  
Gonococcal Infection

Abstract Background Disseminated gonococcal infection (DGI) is an uncommon manifestation of N. gonorrhoeae that is estimated to occur in 0.5-3% of cases, with a decreasing incidence that has been attributed to changes in circulating serotypes. At a Veterans Affairs Medical Center (VAMC), 3 cases were identified within 4 months in 2019. Methods A case series of patients with DGI between March and July 2019 was conducted at a 399-bed tertiary care VAMC that serves central Virginia. Clinical case data was abstracted from the medical record, and data regarding prior gonorrhea cases at the facility was obtained from the laboratory information system. Results In 2019, the rate of DGI was 4.9%, with 3 cases out of 61 reported. All occurred in immunocompetent, African-American males with a mean age of 59 years, and all had female sexual partners (Table 1). All presented with joint symptoms, 2 had skin manifestations, and none had genital symptoms. Two patients had positive synovial fluid cultures and the third had a positive blood culture. All isolates were beta-lactamase negative. Orogenital testing by nucleic acid amplification was only positive in 1 patient. No other sexually transmitted infections were identified. One patient underwent surgical washout of the involved shoulder joint, but the others were managed non-operatively. All received a single dose of azithromycin and a 14-day course of ceftriaxone with full symptom resolution. These were the first positive N. gonorrhoeae isolates from invasive specimens at this VAMC since at least 2016. Table 1. Clinical History and Laboratory Results at Presentation for Patients with Disseminated Gonococcal Infection Conclusion This cluster of DGI cases was unusual given the recent rarity at this VAMC, the age of the patients, and lack of overt risk factors. In Virginia, DGI is reported to the health department no differently than uncomplicated infections, so the actual rate of DGI regionally is unknown. One isolate was preserved and sent to the Centers for Disease Control and Prevention for deidentified whole genome sequencing. More refined reporting is necessary to improve understanding of local gonorrhea epidemiology, as well as coupling with additional methodologies such as serotyping or whole genome sequencing. Clinicians should be aware of the possibility of DGI, even in older patients without classic risk factors. Disclosures All Authors: No reported disclosures

scholarly journals Whole genome sequencing data used for surveillance of Campylobacter infections: detection of a large continuous outbreak, Denmark, 2019

2021 ◽  
Vol 26 (22) ◽  
Author(s):  
Katrine Grimstrup Joensen ◽  
Susanne Schjørring ◽  
Mette Rørbæk Gantzhorn ◽  
Camilla Thougaard Vester ◽  
Hans Linde Nielsen ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Chicken Meat ◽  
Clinical Isolates ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Bacterial Gastroenteritis ◽  
Large Clusters ◽  
Small Clusters

Background Campylobacter is one of the most frequent causes of bacterial gastroenteritis. Campylobacter outbreaks are rarely reported, which could be a reflection of a surveillance without routine molecular typing. We have previously shown that numerous small outbreak-like clusters can be detected when whole genome sequencing (WGS) data of clinical Campylobacter isolates was applied. Aim Typing-based surveillance of Campylobacter infections was initiated in 2019 to enable detection of large clusters of clinical isolates and to match them to concurrent retail chicken isolates in order to react on ongoing outbreaks. Methods We performed WGS continuously on isolates from cases (n = 701) and chicken meat (n = 164) throughout 2019. Core genome multilocus sequence typing was used to detect clusters of clinical isolates and match them to isolates from chicken meat. Results Seventy-two clusters were detected, 58 small clusters (2–4 cases) and 14 large clusters (5–91 cases). One third of the clinical isolates matched isolates from chicken meat. One large cluster persisted throughout the whole year and represented 12% of all studied Campylobacter cases. This cluster type was detected in several chicken samples and was traced back to one slaughterhouse, where interventions were implemented to control the outbreak. Conclusion Our WGS-based surveillance has contributed to an improved understanding of the dynamics of the occurrence of Campylobacter strains in chicken meat and the correlation to clusters of human cases.

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