BackgroundAn outbreak of pneumococcal meningitis among non-infant children and adults occurred in the Brong-Ahafo region of Ghana between December 2015 and April 2016 despite the recent nationwide implementation of a vaccination programme for infants with the 13-valent pneumococcal conjugate vaccine (PCV13).MethodsCerebrospinal fluid (CSF) specimens were collected from patients with suspected meningitis in the Brong-Ahafo region. CSF specimens were subjected to Gram staining, culture and rapid antigen testing. Quantitative PCR was performed to identify pneumococcus, meningococcus and Haemophilus influenzae. Latex agglutination and molecular serotyping were performed on samples. Antibiogram and whole genome sequencing were performed on pneumococcal isolates.ResultsEight hundred eighty six patients were reported with suspected meningitis in the Brong-Ahafo region during the period of the outbreak. In the epicenter district, the prevalence was as high as 363 suspected cases per 100,000 people. Over 95 % of suspected cases occurred in non-infant children and adults, with a median age of 20 years. Bacterial meningitis was confirmed in just under a quarter of CSF specimens tested. Pneumococcus, meningococcus and Group B Streptococcus accounted for 77 %, 22 % and 1 % of confirmed cases respectively. The vast majority of serotyped pneumococci (80 %) belonged to serotype 1. Most of the pneumococcal isolates tested were susceptible to a broad range of antibiotics, with the exception of two pneumococcal serotype 1 strains that were resistant to both penicillin and trimethoprim-sulfamethoxazole. All sequenced pneumococcal serotype 1 strains belong to Sequence Type (ST) 303 in the hypervirulent ST217 clonal complex.ConclusionThe occurrence of a pneumococcal serotype 1 meningitis outbreak three years after the introduction of PCV13 is alarming and calls for strengthening of meningitis surveillance and a re-evaluation of the current vaccination programme in high risk countries.Electronic supplementary materialThe online version of this article (doi:10.1186/s12879-016-1914-3) contains supplementary material, which is available to authorized users.

medRxiv preprint 2The ongoing pandemic of SARS-CoV-2, a novel coronavirus, caused over 3 million reported cases of coronavirus disease 2019 (COVID-19) and 200,000 reported deaths between December 2019 and April 2020 1 . Cases and deaths will increase as the virus continues its global march outward. In the absence of effective pharmaceutical interventions or a vaccine, wide-spread virological screening is required to inform where restrictive isolation measures should be targeted and when they can be lifted 2-6 . However, limitations on testing capacity have restricted the ability of governments and institutions to identify individual clinical cases, appropriately measure community prevalence, and mitigate transmission. Group testing offers a way to increase efficiency, by combining samples and testing a small number of pools 7-9 . Here, we evaluate the effectiveness of group testing designs for individual identification or prevalence estimation of SARS-CoV-2 infection when testing capacity is limited. To do this, we developed mathematical models for epidemic spread, incorporating empirically measured individual-level viral kinetics to simulate changing viral loads in a large population over the course of an epidemic. We used these to construct representative populations and assess pooling strategies for community screening, accounting for variability in viral load samples, dilution effects, changing prevalence and resource constraints. We confirmed our group testing framework through pooled tests on de-identified human nasopharyngeal specimens with viral loads representative of the larger population. We show that group testing designs can both accurately estimate overall prevalence using a small number of measurements and substantially increase the identification rate of infected individuals in resource-limited settings. : medRxiv preprint 3 We aimed to evaluate the effectiveness of group testing for overall prevalence estimation and individual case identification. In the classical version of the identification problem 7 , samples from multiple individuals are combined and tested as a single pool ( Fig. 1a). If the test is negative (which might be likely if the prevalence is low and the pool is not too large), then each of the individuals is assumed to have been negative. If the test is positive, it is assumed that at least one individual in the pool was positive; each of the pooled samples is then tested individually. This strategy leverages the low frequency of cases which would otherwise cause substantial inefficiency, as the majority of pools will test negative when prevalence is low. The simple pooling method can be expanded to combinatorial pooling (each sample represented in multiple pools) for direct sample identification 8,9 ( Fig. 1b) and to pooled testing for prevalence estimation 10,11 ( Fig. 1c).To deploy group testing in the current pandemic, we need designs that can account for the (i) prevalence of infection within the population, (ii) position along the epidemic curve , and (iii) within-host kin...

Serotype 1 Streptococcus pneumoniae is a leading cause of invasive pneumococcal disease (IPD) worldwide, with the highest burden in developing countries. We report the whole-genome sequencing analysis of 448 serotype 1 isolates from 27 countries worldwide (including 11 in Africa). The global serotype 1 population shows a strong phylogeographic structure at the continental level, and within Africa there is further region-specific structure. Our results demonstrate that regionspecific diversification within Africa has been driven by limited cross-region transfer events, genetic recombination and antimicrobial selective pressure. Clonal replacement of the dominant serotype 1 clones circulating within regions is uncommon; however, here we report on the accessory gene content that has contributed to a rare clonal replacement event of ST3081 with ST618 as the dominant cause of IPD in the Gambia.

The coronavirus disease 2019 response in many African countries has been swift, progressive, and adaptable, despite resource limitations. 1 As the novel coronavirus infection spread through Wuhan (China) in January, 2020, African countries rapidly acquired de novo severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing capacity so that by March, most could confirm COVID-19. Airport screening began early and efforts to mitigate the spread of COVID-19 have typically emphasised case identification, contact tracing and isolation, handwashing and hand hygiene, and several social distancing and stay-at-home measures with, in some cases, lockdowns of exceedingly high risk areas (appendix). These strategies are likely to remain integral to disease mitigation until an effective vaccine is deployed or population immunity is sufficient to slow transmission. However, the application of COVID-19 mitigation strategies in sub-Saharan Africa needs careful and continued deliberation because of the unique socioeconomic dynamics in this region. In this Comment, we discuss some of these challenges and suggest potential, non-resource-intensive solutions.Rapid urbanisation has led to an informal sector surge and consequent increase in people living in informal settlements and slums within African cities. 2 These communities are particularly susceptible to economic shock resulting from stay-at-home orders and lockdowns, which need to be tempered with food and basic necessity provisions. 2,3 Water tanks can be set up for handwashing and sanitation in these susceptible communities, as well as public toilets which could potentially serve as sentinel COVID-19 surveillance sites through periodic faecal matter sampling and testing. 4 An added layer of complexity is the multigenerational structure and large size of typical African households. 5 Household transmission is a substantial driver of SARS-CoV-2 spread in the community and multigenerational households might be prone to higher fatality. 6 Interrupting COVID-19 transmission is challenging because a substantial proportion of transmission occurs in the presymptomatic stage. 7 Effective contact tracing, testing in the community, and targeted door-to-door surveillance in high-risk