Fiona Cresswell

Whole-genome sequencing to determine transmission of Neisseria gonorrhoeae: an observational study

BACKGROUND New approaches are urgently required to address increasing rates of gonorrhoea and the emergence and global spread of antibiotic-resistant Neisseria gonorrhoeae. We used whole-genome sequencing to study transmission and track resistance in N gonorrhoeae isolates. METHODS We did whole-genome sequencing of isolates obtained from samples collected from patients attending sexual health services in Brighton, UK, between Jan 1, 2011, and March 9, 2015. We also included isolates from other UK locations, historical isolates from Brighton, and previous data from a US study. Samples from symptomatic patients and asymptomatic sexual health screening underwent nucleic acid amplification testing; positive samples and all samples from symptomatic patients were cultured for N gonorrhoeae, and resulting isolates were whole-genome sequenced. Cefixime susceptibility testing was done in selected isolates by agar incorporation, and we used sequence data to determine multi-antigen sequence types and penA genotypes. We derived a transmission nomogram to determine the plausibility of direct or indirect transmission between any two cases depending on the time between samples: estimated mutation rates, plus diversity noted within patients across anatomical sites and probable transmission pairs, were used to fit a coalescent model to determine the number of single nucleotide polymorphisms expected. FINDINGS 1407 (98%) of 1437 Brighton isolates between Jan 1, 2011, and March 9, 2015 were successfully sequenced. We identified 1061 infections from 907 patients. 281 (26%) of these infections were indistinguishable (ie, differed by zero single nucleotide polymorphisms) from one or more previous cases, and 786 (74%) had evidence of a sampled direct or indirect Brighton source. We observed multiple related samples across geographical locations. Of 1273 infections in Brighton (including historical data), 225 (18%) were linked to another case elsewhere in the UK, and 115 (9%) to a case in the USA. Four lineages initially identified in Brighton could be linked to 70 USA sequences, including 61 from a lineage carrying the mosaic penA XXXIV allele, which is associated with reduced cefixime susceptibility. INTERPRETATION We present a whole-genome-sequencing-based tool for genomic contact tracing of N gonorrhoeae and demonstrate local, national, and international transmission. Whole-genome sequencing can be applied across geographical boundaries to investigate gonorrhoea transmission and to track antimicrobial resistance. FUNDING Oxford National Institute for Health Research Health Protection Research Unit and Biomedical Research Centre.

Hepatitis C Core Antigen Testing: A Reliable, Quick, and Potentially Cost-effective Alternative to Hepatitis C Polymerase Chain Reaction in Diagnosing Acute Hepatitis C Virus Infection

Hepatitis C virus (HCV) is increasingly common among human immunodeficiency virus (HIV)-infected men who have sex with men. We evaluated the efficacy of HCV core antigen in diagnosing acute HCV in an HIV-infected cohort. Compared with HCV polymerase chain reaction, core antigen proved sensitive (100%) and specific (97.9%). As a quick, simple, and cost-effective test, it has considerable utility in screening for acute HCV.

Diagnostic accuracy of Xpert MTB/RIF Ultra for tuberculous meningitis in HIV-infected adults: a prospective cohort study

Summary Background WHO recommends Xpert MTB/RIF as initial diagnostic testing for tuberculous meningitis. However, diagnosis remains difficult, with Xpert sensitivity of about 50–70% and culture sensitivity of about 60%. We evaluated the diagnostic performance of the new Xpert MTB/RIF Ultra (Xpert Ultra) for tuberculous meningitis. Methods We prospectively obtained diagnostic cerebrospinal fluid (CSF) specimens during screening for a trial on the treatment of HIV-associated cryptococcal meningitis in Mbarara, Uganda. HIV-infected adults with suspected meningitis (eg, headache, nuchal rigidity, altered mental status) were screened consecutively at Mbarara Regional Referral Hospital. We centrifuged CSF, resuspended the pellet in 2 mL of CSF, and tested 0·5 mL with mycobacteria growth indicator tube culture, 1 mL with Xpert, and cryopreserved 0·5 mL, later tested with Xpert Ultra. We assessed diagnostic performance against uniform clinical case definition or a composite reference standard of any positive CSF tuberculous test. Findings From Feb 27, 2015, to Nov 7, 2016, we prospectively evaluated 129 HIV-infected adults with suspected meningitis for tuberculosis. 23 participants were classified as probable or definite tuberculous meningitis by uniform case definition, excluding Xpert Ultra results. Xpert Ultra sensitivity was 70% (95% CI 47–87; 16 of 23 cases) for probable or definite tuberculous meningitis compared with 43% (23–66; 10/23) for Xpert and 43% (23–66; 10/23) for culture. With composite standard, we detected tuberculous meningitis in 22 (17%) of 129 participants. Xpert Ultra had 95% sensitivity (95% CI 77–99; 21 of 22 cases) for tuberculous meningitis, which was higher than either Xpert (45% [24–68]; 10/22; p=0·0010) or culture (45% [24–68]; 10/22; p=0·0034). Of 21 participants positive by Xpert Ultra, 13 were positive by culture, Xpert, or both, and eight were only positive by Xpert Ultra. Of those eight, three were categorised as probable tuberculous meningitis, three as possible tuberculous meningitis, and two as not tuberculous meningitis. Testing 6 mL or more of CSF was associated with more frequent detection of tuberculosis than with less than 6 mL (26% vs 7%; p=0·014). Interpretation Xpert Ultra detected significantly more tuberculous meningitis than did either Xpert or culture. WHO now recommends the use of Xpert Ultra as the initial diagnostic test for suspected tuberculous meningitis. Funding National Institute of Neurologic Diseases and Stroke, Fogarty International Center, National Institute of Allergy and Infectious Disease, UK Medical Research Council/DfID/Wellcome Trust Global Health Trials, Doris Duke Charitable Foundation.

UK guideline for the use of HIV Post-Exposure Prophylaxis Following Sexual Exposure, 2015

We present the updated British Association for Sexual Health and HIV guidelines for HIV post-exposure prophylaxis following sexual exposure (PEPSE). This document includes a review of the current data to support the use of PEPSE, considers how to calculate the risks of infection after a potential exposure, and provides recommendations on when PEPSE should and should not be considered. We also review which medications to use for PEPSE, provide a checklist for initial assessment, and make recommendations for monitoring individuals receiving PEPSE. Special scenarios, cost-effectiveness of PEPSE, and issues relating to service provision are also discussed. Throughout the document, the place of PEPSE within the broader context of other HIV prevention strategies is considered.

Syphilis treatment in the presence of HIV: the debate goes on.

Purpose of review Benzathine Penicillin G has been used to treat syphilis for over 50 years; however, the precise regimen of penicillin for treatment of syphilis in HIV-positive individuals remains a hot topic of debate. Although international guidelines recommend the same treatment for syphilis, regardless of HIV status, there are inconsistencies in prescribing practices among clinicians. Recent findings Two previous systematic reviews have found limited evidence for enhanced treatment of syphilis in the presence of HIV. However, a growing body of literature indicates that the rate of asymptomatic neurosyphilis may be higher in HIV, and that syphilis infection is associated with poorer long-term neurocognitive outcomes. A number of retrospective studies propose that serological response may be slower, or serological failure may be higher, among HIV-positive individuals, but these studies are limited by high loss to follow-up, high reinfection rates and a focus on serological rather than clinical response. Beyond penicillin, some evidence suggests equivalence of macrolides, cephalosporins and doxycycline, although macrolide resistance is an increasing concern. Summary Until a prospective, randomized study is conducted, inconsistency with treatment will continue. We offer a pragmatic approach to recognizing patients who may require further investigation or neuropenetrative antibiotic treatment.

Systematic Review of Prevalence and Predictors of Frailty in Individuals with Human Immunodeficiency Virus.

To describe the prevalence and predictors of frailty in individuals with the human immunodeficiency virus (HIV) using systematic review methodology.

Diagnosis and treatment strategies of tuberculous intestinal perforations: a case series.

Gastrointestinal tuberculosis (TB) may result in intestinal obstruction and perforation, even after antituberculous therapy has been initiated. Despite surgical intervention tuberculous perforation has a high complication and mortality rate, and it is difficult to predict the subgroup of patients with abdominal TB who progress to perforation. In this study, we retrospectively investigated the clinical features that may predict disease progression in patients in our institution who presented abdominal TB over a 5-year period between January 2006 and August 2011, as well as describe an unreported method of managing tuberculous intestinal perforations when resection with end-to-end anastomosis is unfeasible. Six out of 91 patients (6.6%) with abdominal TB developed perforations. Factors linked with increased complications and mortality were age, comorbidities, multiple perforations and length of time between onset of abdominal symptoms and perforation. Four patients (66.7%) had long histories of abdominal symptoms before perforation. Three patients were receiving or had completed antituberculous therapy before developing perforation. Five patients were managed surgically, two underwent laparostomy as both primary closure and end-to-end anastomosis were deemed too risky. Mortality following perforation was 17%. Patients with prolonged abdominal symptoms, even after antituberculous therapy, should raise suspicion for subacute intestinal obstruction. This should be recognized early and surgical intervention considered in order to prevent mortality secondary to perforation. Laparostomy may be an alternative when resection and end-to-end anastomosis is not possible.

Genomic analysis of urogenital and rectal Neisseria meningitidis isolates reveals encapsulated hyperinvasive meningococci and coincident multidrug-resistant gonococci

Objective Invasive meningococcal disease (IMD) outbreaks in men who have sex with men (MSM) have been associated with meningococcal colonisation of the urethra and rectum, but little is known about this colonisation or co-colonisation with the closely related gonococcus. Whole genome sequencing (WGS) was employed to explore these phenomena. Methods Meningococci isolated from the urogenital tract and rectum (n=23) and coincident gonococci (n=14) were analysed by WGS along with contemporary meningococci from IMD (n=11). All isolates were obtained from hospital admissions in Brighton, UK, 2011–2013. Assembled WGS were deposited in the PubMLST/neisseria database (http://pubmlst.org/neisseria) and compared at genomic loci common to gonococci or meningococci. Results As expected, most meningococci from IMD were encapsulated and belonged to hyperinvasive lineages. So too were meningococci found in the urogenital tract and rectum, contrasting to those asymptomatically carried in the nasopharynx where such meningococci are rare. Five hyperinvasive meningococcal lineages and four distinct gonococcal genotypes were recovered, including multiresistant ST-1901 (NG MAST-1407) gonococci. Conclusions These data were consistent with a predisposition for potentially virulent encapsulated hyperinvasive meningococci to colonise the urethra and rectum, which suggests their involvement in MSM IMD outbreaks. The coincidence of multiresistant gonococci raises wider public health concerns.

Shigella flexneri: A Cause of Significant Morbidity and Associated With Sexually Transmitted Infections in Men Who Have Sex With Men.

S exually transmitted Shigella flexneri has been reported in men who have sex 1–8 with men (MSM). S flexneri is an infectious enterobacteria causing a self-limited diarrheal illness that has been associated with HIV-infection, unsafe-sexual behavior, sexually transmitted infections (STIs), and more recently recreational drug use. Brighton & Hove is a city in the United Kingdom with a large population of MSM who have an estimated HIV prevalence of 14%. We describe a local analysis of cases of S flexneri in MSM in 2013 using both clinical and laboratory data. Through 2013, 24 cases of S flexneri were identified in MSM with no associated travel history. The median age was 43 years (range, 16–77 years). Cases occurred every month; 5 cases occurred in May and August. Twenty-one of 24 reported condom-less anal sex, and 18 of 24 reported sexualized drug use in the past 3 months. Serotype was identified in 10 cases, 3a being the most common (5 cases). Antibiotic sensitivities were available in 4 cases with no cases of ciprofloxacin resistance. Twelve (50%) of 24 required hospital admission, with an average length of hospital stay of 4.3 days (range, 2–7 days). Four (17%) of 24 had an acute kidney injury requiring renal support, and 1 of 24 required 3 days of treatment in the intensive care unit. C-reactive protein was elevated in all 12 patients tested with a median of 153.1 mg/L (range, 43–287 mg/L). Four of (17%) 24 underwent lower gastrointestinal tract endoscopy as investigation of diarrhea. Thirteen of the (54%) 24 MSM were HIV positive including one who was diagnosed during the episode. Ten (77%) of 13 patients were on antiretroviral therapy at the time of Shigella, all with undetectable HIV viral loads (<40 copies/mL). Median CD4 count was 586 10 cells/L (range, 285–964 10 cells/L). The HIV-MSM with S flexneri were not

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

Objectives Prevention 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. Methods During 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. Results 104/149 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. Conclusions We 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.