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2AbstractThe antimicrobial resistance ofNeisseria gonorrhoeato all classes of current available antibiotics is a global concern. National surveillance programmes monitoring the susceptibility profiles ofNeisseria gonorrhoeaehardly exist in resource constraint settings. Therefore, little is known about the antimicrobial susceptibility profile and associated genetic resistance mechanisms ofN. gonorrhoeaein Madagascar. We report susceptibility data ofN. gonorrhoeaeisolates obtained by the medical laboratory of the Institut Pasteur de Madagascar, from 2014 -2020. In addition, we present data on the antimicrobial resistance mechanisms and antimicrobial resistance profile of a subset of isolates (N=46), including all isolates available of 2020. Over the study period, ceftriaxone resistant isolates exceeding the threshold of 5% in 2017 and 2020, were reported. Of the subset of re-tested isolates, all were found susceptible to ceftriaxone, azithromycin, and spectinomycin. Conversely, all isolates were resistant to ciprofloxacin and the majority was also resistant to penicillin and tetracycline. None of the isolates carried the mosaicpenAgene and chromosomal mutations associated to the antibiotic resistance ingyrA, parC, penA, ponA, porBandmtrRgenes were detected. The high rate of resistance to Penicillin and Tetracycline is explained by the presence of β-lactamaseblaTEMandtetMgenes, respectively, a plasmid mediated resistance. We found a high number of circulating multilocus sequence types. Almost half of them were new types, and one of them was among the four most predominant sequence types. Our report provides a detailed dataset obtained through phenotypic and genotypic methods which will serve as baseline for future surveillance ofN. gonorrhoeaein our setting, and Madagascar.1.5RepositoriesThis Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the Accession BioProject PRJNA929018.3Impact statementNeisseria gonorrhoeaeis becoming increasingly resistant to all classes of antibiotics available for infections treatment.Resource constraint settings encounter difficulties in implementing surveillance of the antimicrobial susceptibility ofN. gonorrhoeae. We report here antimicrobial susceptibility results from gonorrhoea among patients consulting a medical laboratory in Antananarivo, Madagascar in 2014–2020. We used whole-genome sequencing to identify resistance mechanisms in a subset of isolates including all viable isolates of 2020.We report multilocus sequence types and discuss phenotypes and genotypes according to the phylogenetic analysis of the isolates. The susceptibility results are the first in a decade to be reported. We set the baseline to study further the evolution and transmission ofN. gonorrhoeaeresistance mechanisms and genotypes in general. Our report will enable improving surveillance ofNeisseria gonorrhoeaein Madagascar and Africa.Overall, it will contribute to the global, regional, and national surveillance ofN. gonorrhoeae. In addition, it may set a benchmark for implementation in other settings facing barriers implementing phenotypic resistance surveillance ofN. gonorrhoeae.4Data summaryThe source code of the Tormes pipeline used in this study is also available on Github:https://github.com/nmquijada/tormes.The SRA sequences have been deposited in the NCBI SRA database under accession numbers SRR23260223 and SRR23260193.The genome assemblies can be accessed using the accession numbers: SAMN32949360 - SAMN32949405.The MLST genes of all isolates can be accessed through this link:https://doi.org/10.5281/zenodo.7581537The Perl scripts used for a quality filtering of the assemblies which is to remove small contigs can be accessed through the following link:https://github.com/Alainnoah/Remove-Small-Contigs-Draft-Assemblies.Genomic analysis with metadata in Pathogenwatch could be accessed with this link:https://pathogen.watch/collection/f7t4wjtjlybh-mdgwhofaA visualization of genomic epidemiology of our isolates with Microreact can be accessed with this link:https://microreact.org/project/7FADQYwhm5h1zJyJTynM6R-unnamed-projectA supplementary material in an Excel sheet summarizing the lists of plasmids used for alignment (Table S1), the statistics of the sequences (Table S2), and the minimum inhibitory concentration values ofN. gonorrhoeaeisolates and their antimicrobial resistance genetic mechanisms (Table S3) is available through this link:https://doi.org/10.6084/m9.figshare.21973511

2.AbstractSalmonella Enteritidis is one of the most commonly reported serovars of non-typhoidal Salmonella causing human disease and is responsible for both gastroenteritis and invasive non-typhoidal Salmonella (iNTS) disease worldwide. Whole-genome sequence (WGS) comparison of Salmonella Enteritidis isolates from across the world have identified three distinct clades, named Global Epidemic, Central/East African and West African, all of which have been implicated in epidemics: the Global Epidemic clade was linked to poultry-associated gastroenteritis, while the two African clades were related to iNTS disease. However, the distribution and epidemiology of these clades across Africa is poorly understood because identification of these clades currently requires whole genome sequencing capacity. Here, we report a sensitive, time- and cost-effective real-time PCR assay capable of differentiating between the Salmonella Enteritidis clades to facilitate surveillance and to inform public health responses.3.Impact statementChallenges in the diagnosis and treatment of invasive Salmonella Enteritidis (S. Enteritidis) bloodstream infections in sub–Saharan Africa are responsible for a case fatality rate of approximately 15% (12). It is important to identify distinct clades of S. Enteritidis in diagnostic laboratories in the African setting to determine whether particular outbreaks are associated with different health outcomes. Here, we have described the development of a high-quality molecular classification assay for the clade-typing of S. Enteritidis that is ideal for use in public health laboratories in resource-limited settings.