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A global increase in the incidence of invasive group A Streptococcus (iGAS) infections was observed after lifting of COVID-19 related restrictions in 2022, and type M1 dominated in many countries. After seasonal declines in iGAS incidence during the summer of 2023, simultaneous, rapid expansion of a previously rare emm type 3.93 was seen beginning in November, increasing to 20% of all cases in England and 60% of all cases in the Netherlands within 4 months. emm3.93 was associated with iGAS in children 6-17 years of age and with increased risk for pneumonia or pleural empyema and meningitis in both countries. No excess risk of death was identified for emm3.93 compared with other types. Genomic analysis of historic and contemporary emm3.93 isolates revealed the emergence of 3 new clades with a potentially advantageous genomic configuration. Our findings demonstrate the value of molecular surveillance, including long-read sequencing, in identifying clinical and public health threats.

Identifying structure underlying high-dimensional data is a common challenge across scientific disciplines. We revisit correspondence analysis (CA), a classical method revealing such structures, from a network perspective. We present the poorly-known equivalence of CA to spectral clustering and graph-embedding techniques. We point out a number of complementary interpretations of CA results, other than its traditional interpretation as an ordination technique. These interpretations relate to the structure of the underlying networks. We then discuss an empirical example drawn from ecology, where we apply CA to the global distribution of Carnivora species to show how both the clustering and ordination interpretation can be used to find gradients in clustered data. In the second empirical example, we revisit the economic complexity index as an application of correspondence analysis, and use the different interpretations of the method to shed new light on the empirical results within this literature.

Mycoplasma genitalium (MG) is a sexually transmitted bacterium in which macrolide resistance is rapidly increasing, limiting treatment options. We validated a new assay to detect the presence of macrolide resistance-associated mutations in MG (MG-MRAM). In 2018, symptomatic and asymptomatic clients visiting sexually transmitted infections (STI) clinics in Amsterdam or The Hague were tested for MG using transcription mediated amplification (TMA) assays. The sensitivity to detect MG of the newly developed MG-MRAM qPCR was compared to the MgPa qPCR, both in relation to the TMA assay. For the sensitivity and specificity to detect relevant mutations the MG-MRAM qPCR was compared to 23SrRNA sequencing analysis. The qPCR was subsequently used to determine the presence of MG-MRAM at different anatomical locations and to identify risk factors for MG-MRAM. MG-positive clients (402) providing 493 MG-positive samples were included. In total 309/493 (62.7%) samples from 291 (72.4%) clients were successfully typed with the MG-MRAM qPCR. The MG-MRAM qPCR had a sensitivity of 98.6% (95%CI 91.1%-99.9%) and specificity of 94.1% (95%CI 78.9%-99.0%) to detect MG-MRAM compared to sequencing analysis. Infection with MG-MRAM was detected in 193/291 (66.3%) clients: in 129/178 (72.5%) men and 64/113 (56.6%) women (p = 0.005). Prevalence of MG-MRAM was significantly higher in men, clients with a higher education, HIV-positive clients and clients with >10 sexual partners in the previous six months, but in multivariable analysis no factor was significantly associated with MG-MRAM presence. Since MG-MRAM prevalence was very high, testing for MG-MRAM is essential if treatment for MG is considered, and can be performed with this sensitive and specific qPCR test in routine diagnostics.

Background Diagnosis of infected individuals with Mycoplasma genitalium (MG) is often performed by real-time PCR or transcription-mediated amplification (TMA). A limitation of the MG-TMA assay is the relatively short time span of 24 h in which the collected urine is required to be transferred into a Urine Specimen Transport Tube, according to the manufacturer’s guidelines. If not transferred within 24 h, the manufacturer’s claimed sensitivity cannot be guaranteed anymore, and samples may instead be tested with an in-house validated real-time PCR, despite its recognized lower sensitivity. This study aimed to validate an exception to the sample transport and storage conditions of the MG-TMA assay as set by the manufacturer, being the prolongation of the acceptable testing time limit of 24 h. Methods From June to December 2022, first-void urines were collected from clients attending the clinic for sexual health in Amsterdam, the Netherlands. Urine samples that tested positive for MG by TMA assay at the day of collection were concomitantly stored at room (18–24 °C) and refrigerator temperature (4–8 °C) for 15 days. The stored urine samples were tested with both an in-house validated real-time PCR and MG-TMA assay after transfer of the original urine samples to the respective test tubes at 3, 7, 12 and 15 days post collection. Results In total, 47 MG-positive urine samples were collected, stored and tested for MG by real-time PCR and TMA assays. After storage at room temperature, the MG-detection rate by TMA was significantly higher compared to real-time PCR, at days 0 ( p  ≤ 0.001), 7 ( p  ≤ 0.001) and 12 ( p  < 0.05). After storage at refrigerator temperature, the MG-detection rate determined by TMA assay was significantly enhanced in comparison with real-time PCR at days 3 ( p  < 0.01), 7 ( p  ≤ 0.001) and 15 ( p  < 0.01). Conclusions This validation study showed that the MG - TMA assay has a superior detection rate in urine compared to real-time PCR, up to 15 days post sample collection and irrespective of storage temperature. Accepting urines older than 24 h to be tested by TMA will improve clinical diagnosis of MG infections.

Background It is important to gain insight into the burden of COVID-19 at city district level to develop targeted prevention strategies. We examined COVID-19 related hospitalisations by city district and migration background in the municipality of Amsterdam, the Netherlands. Methods We used surveillance data on all PCR-confirmed SARS-CoV-2 hospitalisations in Amsterdam until 31 May 2020, matched to municipal registration data on migration background. We calculated directly standardised (age, sex) rates (DSR) of hospitalisations, as a proxy of COVID-19 burden, per 100,000 population by city district and migration background. We calculated standardised rate differences (RD) and rate ratios (RR) to compare hospitalisations between city districts of varying socio-economic and health status and between migration backgrounds. We evaluated the effects of city district and migration background on hospitalisation after adjusting for age and sex using Poisson regression. Results Between 29 February and 31 May 2020, 2326 cases (median age 57 years [IQR = 37–74]) were notified in Amsterdam, of which 596 (25.6%) hospitalisations and 287 (12.3%) deaths. 526/596 (88.2%) hospitalisations could be matched to the registration database. DSR were higher in individuals living in peripheral (South-East/New-West/North) city districts with lower economic and health status, compared to central districts (Centre/West/South/East) (RD = 36.87,95%CI = 25.79–47.96;RR = 1.82,95%CI = 1.65–1.99), and among individuals with a non-Western migration background compared to ethnic-Dutch individuals (RD = 57.05,95%CI = 43.34–70.75; RR = 2.36,95%CI = 2.17–2.54). City district and migration background were independently associated with hospitalisation. Conclusion City districts with lower economic and health status and those with a non-Western migration background had the highest burden of COVID-19 during the first wave of COVID-19 in Amsterdam.

Traditional methods for molecular epidemiology of Neisseria gonorrhoeae are suboptimal. Whole-genome sequencing (WGS) offers ideal resolution to describe population dynamics and to predict and infer transmission of antimicrobial resistance, and can enhance infection control through linkage with epidemiological data. We used WGS, in conjunction with linked epidemiological and phenotypic data, to describe the gonococcal population in 20 European countries. We aimed to detail changes in phenotypic antimicrobial resistance levels (and the reasons for these changes) and strain distribution (with a focus on antimicrobial resistance strains in risk groups), and to predict antimicrobial resistance from WGS data. We carried out an observational study, in which we sequenced isolates taken from patients with gonorrhoea from the European Gonococcal Antimicrobial Surveillance Programme in 20 countries from September to November, 2013. We also developed a web platform that we used for automated antimicrobial resistance prediction, molecular typing (N gonorrhoeae multi-antigen sequence typing [NG-MAST] and multilocus sequence typing), and phylogenetic clustering in conjunction with epidemiological and phenotypic data. The multidrug-resistant NG-MAST genogroup G1407 was predominant and accounted for the most cephalosporin resistance, but the prevalence of this genogroup decreased from 248 (23%) of 1066 isolates in a previous study from 2009–10 to 174 (17%) of 1054 isolates in this survey in 2013. This genogroup previously showed an association with men who have sex with men, but changed to an association with heterosexual people (odds ratio=4·29). WGS provided substantially improved resolution and accuracy over NG-MAST and multilocus sequence typing, predicted antimicrobial resistance relatively well, and identified discrepant isolates, mixed infections or contaminants, and multidrug-resistant clades linked to risk groups. To our knowledge, we provide the first use of joint analysis of WGS and epidemiological data in an international programme for regional surveillance of sexually transmitted infections. WGS provided enhanced understanding of the distribution of antimicrobial resistance clones, including replacement with clones that were more susceptible to antimicrobials, in several risk groups nationally and regionally. We provide a framework for genomic surveillance of gonococci through standardised sampling, use of WGS, and a shared information architecture for interpretation and dissemination by use of open access software. The European Centre for Disease Prevention and Control, The Centre for Genomic Pathogen Surveillance, Örebro University Hospital, and Wellcome.

People experiencing homelessness (PEH) may be at increased risk of SARS-CoV-2 infection and severe COVID-19. The Dutch government established emergency shelters and introduced preventive measures for homelessness services. There were no major SARS-CoV-2 outbreaks noticed among PEH during the first two waves of infections. This study aimed to assess the prevalence of current and past infections among PEH and staff by conducting an on-site COVID-19 screening project at homelessness services in Amsterdam, the Netherlands. We assessed the proportion of visitors and staff members of four homelessness services at two locations in Amsterdam with positive SARS-CoV-2 qPCR and antibody results (IgG/IgM Rapid Test/Biozek) in May 2021. We also assessed sociodemographic, clinical and lifestyle characteristics, compliance with basic prevention measures and intention to vaccinate against COVID-19 among PEH and staff. A total of 138 visitors and 53 staff members filled out a questionnaire and were tested. Among PEH, the SARS-CoV-2 positivity rate was 0% (0/133;95%CI = 0-1.9) and the antibody positivity rate was 1.6% (2/131;95%CI = 0.8-7.5) among those without prior COVID-19 vaccination. Among staff, these percentages were 3% (1/32;95%CI = 0.1-16.2) and 11% (5/53;95%CI = 3.6-23.6), respectively. Most participants were often compliant with the basic preventive measures 'not shaking hands', 'wearing a face mask' and 'washing hands', but not with 'physical distancing'. High vaccination intent was more common among staff members (55%) than among visitors (42%), while high trust in the governmental COVID-19 policies was more common among visitors (41%) than among staff (30%). We observed a low prevalence of past and current SARS-CoV-2 infections among PEH, which may be explained by instated shelter policies, limited daily activities of PEH and compliance with prevention measures. Vaccine hesitancy and mistrust among visitors and staff could hinder vaccination uptake, suggesting that interventions towards homelessness services are needed.

The use of a nucleic acid amplification test (NAAT) as a test of cure after treatment is subject to discussion, as the presence of C. trachomatis nucleic acids after treatment may be prolonged and intermittent without presence of infectious bacteria. We used cell culture to assess if a positive RNA- or DNA-based NAAT after treatment indicates the presence of viable C. trachomatis. We included women with asymptomatic urogenital C. trachomatis infection visiting the Amsterdam STI clinic from September 2015 through June 2016. Endocervical swabs were collected prior to treatment with azithromycin, and during three follow-up visits 7, 21 and 49 days after treatment. Collected swabs were subjected to C. trachomatis culture and a RNA- and DNA-based NAAT. High-resolution multilocus sequence typing (hr-MLST) was used to further differentiate potential re-infections. We included 90 women with a positive RNA-test prior to receiving treatment of whom 81 (90%) were also DNA-positive, and 69 (76.7%) culture-positive. Prolonged and intermittent positive RNA and DNA results over time were observed. Three women had culture positive results at the second visit, but all were negative at the third visit. Five women had NAAT-positive results at the fourth visit of whom three women were also culture-positive indicating a viable infection. All five women reported unprotected sexual contact since the first visit. From 2, hr-MLST sequence types were obtained. One had a different sequence type indicating a new infection the other was identical to the previously found indicating a potentially persisting infection. Most RNA- or DNA-positive results after treatment of urogenital C. trachomatis may be caused by non-viable molecular remnants since they cannot be confirmed by culture. In a minority viable C. trachomatis was found in culture at the second visit, indicating that patients may remain infectious at least 7 days after treatment.

IntroductionSpontaneous clearance of asymptomatic Neisseria gonorrhoeae (NG) does occur, but data are scarce. We aimed to assess spontaneous clearance among patients with asymptomatic anal, pharyngeal, vaginal and urethral NG infections who participated in the New AntiBiotic treatment Options for uncomplicated GOnorrhoea (NABOGO) trial. In addition, we assessed the determinants associated with spontaneous clearance.MethodsThe NABOGO trial (Trial registration number: NCT03294395) was a randomised controlled, double-blind, single-centre trial assessing non-inferiority of ertapenem, gentamicin and fosfomycin to ceftriaxone for treatment of uncomplicated gonorrhoea. For asymptomatic NABOGO participants, we collected pre-enrolment and enrolment visit samples before trial medication was given. Spontaneous clearance was defined as a positive pre-enrolment nucleic acid amplification test (NAAT) result, followed by a negative NAAT at enrolment. We compared the median time between pre-enrolment and enrolment visits for patients who cleared spontaneously and for those who did not. Determinants of spontaneous clearance were assessed using logistic regression.ResultsThirty-two of 221 (14.5%) anal NG infections cleared spontaneously, 17 of 91 (18.7%) pharyngeal, 3 of 13 (23.1%) vaginal and 9 of 28 (32.1%) urethral NG infections. The median time between the pre-enrolment and enrolment visit was longer for patients who cleared their pharyngeal infection spontaneously compared with those who did not (median 8 days (IQR=7–11) vs 6 days (IQR=4–8), p=0.012); no determinants of clearance at other sites were identified. Overall, patients with more days between the pre-enrolment and enrolment visit were more likely to clear spontaneously (adjusted OR=1.06 per additional day, 95% CI 1.01 to 1.12). No association between location of NG infection and spontaneous clearance was found.ConclusionsA significant proportion of asymptomatic patients cleared their NG infections spontaneously. Given these results, treatment of all NG infections after a one-time NAAT may be excessive, and more research on the natural history of NG is needed to improve antibiotic stewardship.

Yet, in the universal screening group, pharyngeal C trachomatis infections represented 22·9 % of all C trachomatis infections, and isolated pharyngeal infections were found in only 3·3% of all C trachomatis. [...]only 0·5% of all women had an isolated pharyngeal C trachomatis infection. [...]the authors concluded that “the probably limited clinical and public health effect and risk of overtreatment do not support routine universal testing as the recommended testing strategy”.4 However, since no increased prevalence of pharyngeal C trachomatis infections was found in any proposed risk group, selective screening does not provide any advantage over universal screening, and the conclusion of this paper might rather be that there is no place for pharyngeal screening of C trachomatis in women to begin with. Whereas the incidence of N gonorrhoeae and C trachomatis in heterosexual couples who had anogenital contact only could be similar,1 detection and treatment of pharyngeal N gonorrhoeae might be more important because of the difficulties to treat pharyngeal N gonorrhoeae infections, especially those caused by strains with decreased susceptibility to cephalosporins.7–9 Whereas screening strategies for N gonorrhoeae and C trachomatis often differ, many laboratory-developed and commercial test systems test for both microorganisms automatically.