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      Emerging epidemic of the Africa-type plasmid in penicillinase-producing Neisseria gonorrhoeae in Guangdong, China, 2013–2022

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          ABSTRACT

          The prevalence of penicillinase-producing Neisseria gonorrhoeae (PPNG) is a crucial public health concern because of its resistance to penicillin and cephalosporins. From 2013 to 2022, a total of 1748 N. gonorrhoeae isolates from Guangdong, China, were examined for their antibiotic susceptibility and molecular epidemiological characteristics. PPNG prevalence increased markedly from 37.25% to 63.87%. This increase was accompanied by a shift in predominant plasmid types carried by PPNG isolates: the rate of PPNG isolates carrying the Africa-type plasmid increased from 18.42% to 91.55%, whereas the rate of isolates carrying the Asia-type plasmid decreased from 81.58% to 7.58%. The prevalence of bla TEM-135, which is linked to cephalosporin resistance, declined from 52.63% to 4.37%, whereas that of bla TEM-1 increased from 47.37% to 86.88%, and new bla TEM variants emerged (10.99% by 2022). Most bla TEM-1 (88.26%) and new bla TEM alleles (83.70%) were associated with the Africa-type plasmid, whereas 86.79% of bla TEM-135 alleles were linked to the Asia-type plasmid. Resistance to ceftriaxone was higher in the Asia-type group (11.67%) than in the Africa-type, Toronto/Rio-type and non-PPNG groups. Genotyping identified diverse sequence types (STs) among PPNGs, in which MLST ST7363, NG-STAR ST2477, NG-MAST ST17748, and NG STAR CC1124 were predominant. This study underscores the rising prevalence of PPNG in Guangdong driven by clonal expansion and changing plasmid dynamics, affecting cephalosporin resistance and highlighting the need for continued surveillance and research into effective treatment strategies.

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          Fast and accurate short read alignment with Burrows–Wheeler transform

          Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk
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            RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

            Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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              Twelve years of SAMtools and BCFtools

              Abstract Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. Findings The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Conclusion Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.
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                Author and article information

                Journal
                Emerg Microbes Infect
                Emerg Microbes Infect
                Emerging Microbes & Infections
                Taylor & Francis
                2222-1751
                9 December 2024
                2025
                9 December 2024
                : 14
                : 1
                : 2440489
                Affiliations
                [a ]School of Pharmaceutical Sciences, Southern Medical University , Guangzhou, People’s Republic of China
                [b ]Dermatology Hospital, Southern Medical University , Guangzhou, People’s Republic of China
                [c ]Guangzhou Key Laboratory for Sexually Transmitted Disease Control , Guangzhou, People’s Republic of China
                Author notes
                [CONTACT ] Kui Cheng chengk@ 123456smu.edu.cn ;
                [*]

                Xiao-Lin Qin and Yang Chen contributed equally to this work.

                Supplemental data for this article can be accessed online at https://doi.org/10.1080/22221751.2024.2440489.

                Author information
                https://orcid.org/0000-0002-4062-3865
                Article
                2440489
                10.1080/22221751.2024.2440489
                11703304
                39648890
                470b97a8-de30-457d-a177-ae57eb55896e
                © 2024 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group, on behalf of Shanghai Shangyixun Cultural Communication Co., Ltd

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent.

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                Page count
                Figures: 4, Tables: 2, Equations: 0, References: 71, Pages: 13, Words: 6312
                Categories
                Drug Resistance and Novel Antimicrobial Agents
                Research Article

                penicillinase-producing neisseria gonorrhoeae,epidemiology,plasmid type,tem variant,genotype,whole-genome sequencing,antimicrobial resistance

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