Antimicrobial resistance and molecular characteristics of N. gonorrhoea isolates in Ghana

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to strain UU1008 to yield 390 bp . nt 1118 Software and Algorithms Ltd , South Africa using Sanger sequencing technology on an ABI Genetic Analyser 3500XL ( Thermo Fisher Scientific® , UK) . Thermo Fisher Scientific® Suggestion: (Thermo Fisher Scientific, RRID:SCR_008452)( link) MEGA XMEGA X software was employed to align sequences using ClustalW and to draw the phylogenetic tree using the maximum composite likelihood model while employing 1000 bootstrap replications to test the confidence of the tree. ClustalW Suggestion: (ClustalW, RRID:SCR_017277)( link) SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore also checks for the presence and correctness of several unique identifiers, including RRIDs (research resource identifiers) in the manuscript, detects sentences that appear to be missing RRIDs, and can even suggest RRIDs under certain circumstances. All RRID suggestions should be verified; only the author can know whether the suggestions are correct. For a full description of scored criteria and tips for improving your score, please see https:// www.scicrunch.com/sciscorereport-faq

Materials

Design Analysis Reporting (MDAR) Checklist for Authors The MDAR framework establishes a minimum set of requirements in transparent reporting applicable to studies in the life sciences (see Statement of Task: doi:10.31222/osf.oio/9sm4x.). The MDAR checklist is a tool for authors, editors and others seeking to adopt the MDAR framework for transparent reporting in manuscripts and other outputs. Please refer to the MDAR Elaboration Document for additional context for the MDAR framework. Report provided by SciScore | August 12, 2023 | Based on DocumentID 2281_64d790b6422720.49447682

Materials

Antibodies Yes (indicate where provided: page no/section/legend) n/a For commercial reagents, provide supplier name, catalogue number and RRID, if available No antibodes detected. Please add identifiers for all resources where possible Cell Materials Yes (indicate where provided: page no/section/legend) n/a Cell lines: Provide species information, strain. Provide accession number in repository OR supplier name, catalog number, clone number, OR RRID No cell lines detected Please add identifiers for all resources where possible Primary cultures: Provide species, strain, sex of origin, genetic modification status. Not currently checked by SciScore Experimental Animals Yes (indicate where provided: page no/section/legend) n/a Laboratory animals: Provide species, strain, sex, age, genetic modification status. Provide accession number in repository OR supplier name, catalog number, clone number, OR RRID Yes, 1 organism detected, 0 RRID provided : nt 1118 Please add identifiers for all resources where possible Animal observed in or captured from the field: Provide species, sex and age where possible Not currently checked by SciScore Model organisms: Provide Accession number in repository (where relevant) OR RRID See laboratory animals section for information. Plants and microbes Yes (indicate where provided: page no/section/legend) n/a Plants: provide species and strain, unique accession number if available, and source (including location for collected wild specimens) Not currently checked by SciScore Microbes: provide species and strain, unique accession number if available, and source Not currently checked by SciScore Human research participants Yes (indicate where provided: page no/section/legend) n/a Identify authority granting ethics approval (IRB or equivalent committee(s), provide reference number for approval. Not detected. Provide statement confirming informed consent obtained from study participants. Not detected. Report on age and sex for all study participants. Age:not detected. Sex:not detected. Report provided by SciScore | August 12, 2023 | Based on DocumentID 2281_64d790b6422720.49447682 Design Study protocol Yes (indicate where provided: page no/section/legend) n/a For clinical trials, provide the trial registration number OR cite DOI in manuscript. Not detected. Laboratory protocol Yes (indicate where provided: page no/section/legend) n/a Provide DOI or other citation details if detailed step- by-step protocols are available. Not detected. Experimental study design (statistics details) Yes (indicate where provided: page no/section/legend) n/a State whether and how the following have been done, or if they were not carried out Sample size determination not detected. Randomization not detected. Blinding not detected. inclusion/exclusion criteria not required. Sample definition and in-laboratory replication Yes (indicate where provided: page no/section/legend) n/a State number of times the experiment was replicated in laboratory Not detected. Define whether data describe technical or biological replicates Not detected. Ethics Yes (indicate where provided: page no/section/legend) n/a Studies involving human participants: State details of authority granting ethics approval (IRB or equivalent committee(s), provide reference number for approval. Not detected. Studies involving experimental animals: State details of authority granting ethics approval (IRB or equivalent committee(s), provide reference number for approval. Not detected. Studies involving specimen and field samples: State if relevant permits obtained, provide details of authority approving study; if none were required, explain why. Not detected. Dual Use Research of Concern (DURC) Yes (indicate where provided: page no/section/legend) n/a If study is subject to dual use research of concern, state the authority granting approval and reference number for the regulatory approval Not currently checked by SciScore Report provided by SciScore | August 12, 2023 | Based on DocumentID 2281_64d790b6422720.49447682 Analysis Attrition Yes (indicate where provided: page no/section/legend) n/a State if sample or data point from the analysis is excluded, and whether the criteria for exclusion were determined and specified in advance. not required. Statistics Yes (indicate where provided: page no/section/legend) n/a Describe statistical tests used and justify choice of tests. Not detected. Data availability Yes (indicate where provided: page no/section/legend) n/a State whether newly created datasets are available, including protocols for access or restriction on access. Data Availability statement: Molecular data has been deposited on Genbank with accompanying accession numbers as stated earlier. If data are publicly available, provide accession number in repository or DOI or URL. Not detected. If publicly available data are reused, provide accession number in repository or DOI or URL, where possible. Not detected. Code availability Yes (indicate where provided: page no/section/legend) n/a For all newly generated code and software essential for replicating the main findings of the study: State whether the code or software is available. Not detected. If code is publicly available, provide accession number in repository, or DOI or URL. Not detected. Report provided by SciScore | August 12, 2023 | Based on DocumentID 2281_64d790b6422720.49447682 Analysis Adherence to community standards Yes (indicate where provided: page no/section/legend) n/a MDAR framework recommends adoption of discipline-specific guidelines, established and endorsed through community initiatives. Journals have their own policy about requiring specific guidelines and recommendations to complement MDAR. State if relevant guidelines (eg., ICMJE, MIBBI, ARRIVE) have been followed, and whether a checklist (eg., CONSORT, PRISMA, ARRIVE) is provided with the manuscript. Not currently checked by SciScore Report provided by SciScore | August 12, 2023 | Based on DocumentID 2281_64d790b6422720.49447682 ACMI-S-23-00255.pdf By Haris Musah WORD COUNT 5745 TIME SUBMITTED 12-AUG-2023 03:00PM PAPER ID 101945729 5 4 5 1 4 1 4 1 5 1 2 2 0 2 6 2 8 1 8 8 8 1 5 3 0 1 1 1 1 2 1 5 1 1 1 2 9 1 1 1 6 1 0 1 9 9 1 3 2 2 2 7 3 7 7 7 2 1 2 9 3 1 1 7 1 8 2 5 2 3 1 1 1 1 2 2 4 1 6 3 2 19% SIMILARITY INDEX 1 2 3 4 5 6 7 ACMI-S-23-00255.pdf ORIGINALITY REPORT PRIMARY SOURCES www.researchsquare.com Internet assets.researchsquare.com Internet www.tandfonline.com Internet Iddrisu Baba Yabasin, Mohammed Mohammed Ibrahim, Abass Adam, Sam-Awortwi Wilfred et al. "Anticancer effects of vecuronium bromide and cisatracurium besylate on lung cancer cells (A549), in vitro", Biomedicine & Aging Pathology, 2014 Crossref www.science.gov Internet diagnostics.roche.com Internet Ana Paula Ramalho da Costa-Lourenço, A. Jeanine Abrams, Késia Thaís Barros dos Santos, Isabella Campelo Vilardi Argentino et al. "Phylogeny and antimicrobial resistance in Neisseria gonorrhoeae isolates from Rio de Janeiro, Brazil", Infection, Genetics and Evolution, 2018 Crossref 309 words — 7% 84 words — 2% 48 words — 1% 31 words — 1% 24 words — 1% 23 words — 1% 21 words — < 1% 8 9 10 11 12 13 14 José Luis Rodrigues Martins, Emerith Mayra Hungria Pinto, Salomão Antonio Oliveira, Fernanda Almeida Costa Gomes et al. "Treatment of Sexually Transmitted Infections (STIs) Caused by Neisseria gonorrhoeae and the Global Shortage of Antibiotics", Venereology, 2022 Crossref docksci.com Internet www.aloki.hu Internet jvm.vam.org.my Internet A.C Fluit, F.J Schmitz, J Verhoef. "Multi-resistance to antimicrobial agents for the ten most frequently isolated bacterial pathogens", International Journal of Antimicrobial Agents, 2001 Crossref Helmy Mohamed El-Bahar, Nadia Gabr Ali, Ibrahim Mohamed Aboyadak, Samy Abd El Salam Khalil, Madiha Salah Ibrahim. "Virulence genes contributing to Aeromonas hydrophila pathogenicity in Oreochromis niloticus", International Microbiology, 2019 Crossref Sunil Sethi, Daniel Golparian, Manju Bala, Dorji Dorji, Muhammad Ibrahim, Kausar Jabeen, Magnus Unemo. "Antimicrobial susceptibility and genetic characteristics of Neisseria gonorrhoeae isolates from India, Pakistan and Bhutan in 2007–2011", BMC Infectious Diseases, 2013 Crossref 21 words — < 1% 20 words — < 1% 17 words — < 1% 16 words — < 1% 14 words — < 1% 13 words — < 1% 13 words — < 1% 15 16 17 18 19 20 21 22 23 Haris Sualah Musah, Francis Addy, Osman Adamu Dufailu. "Surveillance of N. gonorrhoea in Tamale, Northern Region of Ghana", Research Square Platform LLC, 2022 Crossref Posted Content www.biorxiv.org Internet studyres.com Internet repo.lib.semmelweis.hu Internet D. M. Whiley. "Neisseria gonorrhoeae multi- antigen sequence typing using non-cultured clinical specimens", Sexually Transmitted Infections, 02/01/2010 Crossref Rita Tinoco Torres, Mónica V. Cunha, Helena Ferreira, Carlos Fonseca, Josman Dantas Palmeira. "A high-risk carbapenem-resistant Pseudomonas aeruginosa clone detected in red deer (Cervus elaphus) from Portugal", Science of The Total Environment, 2022 Crossref journals.plos.org Internet www.ijpir.com Internet L. Monfort, V. Caro, Z. Devaux, A.-S. Delannoy, S. Brisse, P. Sednaoui. "First Neisseria gonorrhoeae Genotyping Analysis in France: Identification of a Strain Cluster 12 words — < 1% 12 words — < 1% 11 words — < 1% 10 words — < 1% 9 words — < 1% 9 words — < 1% 9 words — < 1% 9 words — < 1% 8 words — < 1% 24 25 26 27 28 29 30 with Reduced Susceptibility to Ceftriaxone", Journal of Clinical Microbiology, 2009 Crossref T. A. Ogunnusi, O. Olorunfemi. "Isolation and Identification of Proteolytic and Lipolytic Bacteria in Cow Dung and Abattoir Effluent from Ekiti General Abattoir, Ekiti State, Nigeria", Journal of Advances in Microbiology, 2018 Crossref ir.jkuat.ac.ke Internet mdpi-res.com Internet theses.ncl.ac.uk Internet www.mjhid.org Internet M. Unemo. "High-level cefixime- and ceftriaxone- resistant N. gonorrhoeae in Europe (France): novel penA mosaic allele in a successful international clone causes treatment failure", Antimicrobial Agents and Chemotherapy, 12/12/2011 Crossref Beata Mlynarczyk-Bonikowska, Cezary Kowalewski, Aneta Krolak-Ulinska, Wojciech Marusza. "Molecular Mechanisms of Drug Resistance and Epidemiology of Multidrug-Resistant Variants of Neisseria gonorrhoeae", International Journal of Molecular Sciences, 2022 Crossref 8 words — < 1% 8 words — < 1% 8 words — < 1% 8 words — < 1% 8 words — < 1% 7 words — < 1% 6 words — < 1% 31 32 EXCLUDE QUOTES OFF EXCLUDE BIBLIOGRAPHY ON EXCLUDE SOURCES OFF EXCLUDE MATCHES OFF Irene Martin. "Emergence and Characterization of Neisseria gonorrhoeae Isolates With Decreased Susceptibilities to Ceftriaxone and Cefixime in Canada: 2001– 2010 :", Sexually Transmitted Diseases, 12/2011 Crossref wrap.warwick.ac.uk Internet 6 words — < 1% 4 words — < 1%

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