Judson SD, Torimiro J, Pigott DM, Maima A, Mostafa A, Samy A et al. COVID-19 data reporting systems in Africa reveal insights for pandemic preparedness. medRxiv. 2021;2021.10.01.21264385.

Egyir B, Obeng-Nkrumah N, Kyei GB. COVID-19 pandemic and antimicrobial resistance: another call to strengthen laboratory diagnostic capacity in Africa. Afr J Lab Med. 2012;9(1):4.

Google Scholar 

Antimicrobial resistance in. The age of COVID-19. Nat Microbiol. 2020;5(6):779.

Article  Google Scholar 

O’Neil J. Tackling drug-resistant infections globally: Final report and recommendations. Review on Antimicrobial Resistance. 2016.

Afari-Asiedu S, Oppong FB, Tostmann A, Ali Abdulai M, Boamah-Kaali E, Gyaase S, et al. Determinants of Inappropriate Antibiotics Use in Rural Central Ghana using a mixed methods Approach. Front Public Health. 2020;8(March):1–11.

Google Scholar 

Havers FP, Hicks LA, Chung JR, Gaglani M, Murthy K, Zimmerman RK, et al. Outpatient antibiotic prescribing for Acute Respiratory Infections during Influenza Seasons. JAMA Netw Open. 2018;1(2):1–13.

Article  Google Scholar 

Inzaule SC, Ondoa P, Loembe MM, Tebeje YK, Ogwell Ouma AE, Nkengasong JN. COVID-19 and indirect health implications in Africa: impact, mitigation measures, and lessons learned for improved disease control. PLoS Med. 2021;18(6):1–12.

Article  Google Scholar 

Elton L, Thomason MJ, Tembo J, Velavan TP, Pallerla SR, Arruda LB, et al. Antimicrobial resistance preparedness in sub-saharan african countries. Antimicrob Resist Infect Control. 2020;9(145):1–11.

Google Scholar 

World Health Organization. COVID-19 clinical management (living guidance). World Health Organization; 2021.

Feldman C, Anderson R. The role of co-infections and secondary infections in patients with COVID-19. Pneumonia. 2021;13(1).

Gutema G, Homa G. Cropping up Crisis at the Nexus between COVID-19 and AMR in Africa: A Scoping Review and Synthesis of Early Evidence. [Preprint] [Internet]. 2021;(May):1–13. Available from: https://www.preprints.org/manuscript/202105.0152/v1

Xu XW, Wu XX, Jiang XG, Xu KJ, Ying LJ, Ma CL, et al. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series. The BMJ. 2020;368(January):1–7.

CAS  Google Scholar 

Zhou F, Yu T, Du R, Fan G, Liu Y, Liu Z et al. Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study. The Lancet [Internet]. 2020;395(10229):1054–62. Available from: https://doi.org/10.1016/S0140-6736(20)30566-3

Rawson TM, Moore LS, Zhu N, Ranganathan N, Skolimowska K, Gilchrist M et al. Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing. Clinical Infectious Diseases. 2020;1–32.

Lai CC, Shih TP, Ko WC, Tang HJ, Hsueh PR. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges. Int J Antimicrob Agents [Internet]. 2020;55(3):105924. Available from: https://doi.org/10.1016/j.ijantimicag.2020.105924

Goyal P. Clinical characteristics of Covid-19 in New York City. N Engl J Med. 2020;100(1):1–3.

Google Scholar 

Martin AJ, Shulder S, Dobrzynski D, Quartuccio K, Pillinger KE. Rate of Antibiotic Use and Associated Risk Factors in COVID-19 Hospitalized Patients. medRxiv. 2020;2020.10.21.20217117.

Sharifipour E, Shams S, Esmkhani M, Khodadadi J, Fotouhi-Ardakani R, Koohpaei A et al. Evaluation of bacterial co-infections of the respiratory tract in COVID-19 patients admitted to ICU. BMC Infect Dis. 2020 Sep 1;20(1).

Shafran N, Shafran I, Ben-Zvi H, Sofer S, Sheena L, Krause I, et al. Secondary bacterial infection in COVID-19 patients is a stronger predictor for death compared to influenza patients. Sci Rep. 2021;11(1):1–8.

Article  Google Scholar 

Yap FHY, Gomersall CD, Fung KSC, Ho P, leung, Ho O man, Lam PKN et al. Increase in Methicillin-Resistant Staphylococcus aureus Acquisition Rate and Change in Pathogen Pattern Associated with an Outbreak of Severe Acute Respiratory Syndrome. Clinical Infectious Diseases. 2004;39:511–6.

Chai LYA, Ng TM, Habib AG, Singh K, Kumarasinghe G, Tambyah PA. Paradoxical increase in Methicillin-Resistant Staphylococcus aureus Acquisition Rates despite Barrier Precautions and increased hand washing compliance during an outbreak of severe Acute Repiratory Syndrome. Clin Infect Dis. 2005;40:632–3.

Article  PubMed  Google Scholar 

Tomczyk S, Twyman A, de Kraker MEA, Coutinho Rehse AP, Tartari E, Toledo JP, et al. The first WHO global survey on infection prevention and control in health-care facilities. Lancet Infect Dis. 2022;3099(21):1–12.

Google Scholar 

Haider N, Osman AY, Gadzekpo A, Akipede GO, Asogun D, Ansumana R, et al. Lockdown measures in response to Saharan COVID-19 in nine sub-african countries. BMJ Glob Health. 2020;5:1–10.

Article  Google Scholar 

World Health Organization. Prevention of Hospital-Acquired Infections. 2002.

Stubblefield H. What Are Nosocomial Infections? 2017.

Kalil AC, Metersky ML, Klompas M, Muscedere J, Sweeney DA, Palmer LB, et al. Management of adults with hospital-acquired and ventilator-associated Pneumonia: 2016 clinical practice guidelines by the infectious Diseases Society of America and the american thoracic society. Clin Infect Dis. 2016;63(5):e61–111.

Article  PubMed  PubMed Central  Google Scholar 

Ahmed MI. Prevalence of nosocomial wound infection among postoperative patients and antibiotics patterns at Teaching Hospital in Sudan. N Am J Med Sci. 2012;4(1):29–34.

Article  PubMed  PubMed Central  Google Scholar 

Chanda DO. Nosocomial infections among Burns patients at the University Teaching Hospital, Lusaka, Zambia. Med J Zambia. 2007;34(4):150–3.

Google Scholar 

Sample Size Calculator [Internet]. [cited 2023 Mar 21]. Available from: https://clincalc.com/stats/samplesize.aspx

Rosner B. Fundementals of Biostatistics. 7th Edition. Boston, MA: Brooks/Cole; 2011.

World Health Organization (WHO). COVID-19 dashboard - Sudan [Internet]. [cited 2022 Sep 15]. Available from: https://covid19.who.int/region/emro/country/sd

World Health Organization (WHO). COVID-19 dashboard - Zambia [Internet]. [cited 2022 Sep 15]. Available from: https://covid19.who.int/region/afro/country/zm

BioMérieux. API 20 E. 2002.

Oxoid Limited. Antimicrobial Susceptibility Discs In Cartridges [Internet]. 2022 [cited 2022 Jan 14]. Available from: http://www.oxoid.com/UK/blue/prod_detail/prod_detail.asp?pr=CT0003&c=UK&lang

Clinical and Laboratory Standards Institute. Performance Standards for Antimicrobial Susceptibility Testing. In: CLSI supplement M100. 31st ed. 2021.

Magiorakos A, Srinivasan A, Carey RB, Carmeli Y, Falagas ME, Giske CG, et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect. 2012;18:268–81.

Article  CAS  PubMed  Google Scholar 

Lee PY, Costumbrado J, Hsu CY, Kim YH. Agarose gel electrophoresis for the separation of DNA fragments. Journal of Visualized Experiments. 2012;(62):1–5.

Oxford Nanopore Technologies. Rapid Barcoding kit protocol (SQK-RBK004). 2019. p. 1–4.

Babraham Bioinformatics. FastQC [Internet]. 2019 [cited 2021 Jun 28]. Available from: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Ewels P, Magnusson M, Lundin S, Käller M, MultiQC. Summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32(19):3047–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34(18):3094–100.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Oxford Nanopore Technologies. Medaka [Internet]. 2018 [cited 2021 Jun 28]. Available from: https://nanoporetech.github.io/medaka/

Clausen PTLC, Aarestrup FM, Lund O. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics. 2018;19(1):1–8.

Article  Google Scholar 

Clausen PTLC, Zankari E, Aarestrup FM, Lund O. Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data. J Antimicrob Chemother. 2016;71(9):2484–8.

Article  CAS  PubMed  Google Scholar 

Carattoli A, Zankari E, Garciá-Fernández A, Larsen MV, Lund O, Villa L, et al. In Silico detection and typing of plasmids using plasmidfinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014;58(7):3895–903.

Article  PubMed  PubMed Central  Google Scholar 

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: Architecture and applications. BMC Bioinformatics. 2009;10:1–9.

Article  Google Scholar 

Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, et al. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol. 2012;50(4):1355–61.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bartual SG, Seifert H, Hippler C, Luzon MAD, Wisplinghoff H, Rodríguez-Valera F. Development of a multilocus sequence typing scheme for characterization of clinical isolates of Acinetobacter baumannii. J Clin Microbiol. 2005;43(9):4382–90.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Griffiths D, Fawley W, Kachrimanidou M, Bowden R, Crook DW, Fung R, et al. Multilocus sequence typing of Clostridium difficile. J Clin Microbiol. 2010;48(3):770–8.

Article  CAS  PubMed  Google Scholar 

Lemee L, Dhalluin A, Pestel-Caron M, Lemeland JF, Pons JL. Multilocus sequence typing analysis of human and animal Clostridium difficile isolates of various toxigenic types. J Clin Microbiol. 2004;42(6):2609–17.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lalis A, Wirth T. Mice and Men: an Evolutionary History of Lassa Fever. In: Biodiversity and Evolution. 2017.

Jaureguy F, Landraud L, Passet V, Diancourt L, Frapy E, Guigon G, et al. Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains. BMC Genomics. 2008;9:1–14.

Article  Google Scholar 

Republic of Sudan Federal Ministry of Health. National Infection Prevention and Control Manual, Second edition. 2015. p. 1–268.

Zambian Ministry of Health. Infection Prevention and Control Water Sanitation and Hygiene in Health Care Facilities the Minimum Standards. 2018. p. 1–66.

Zambian Ministry of Health. Interim Clinical Guidance for Management of Patients with Confirmed Coronavirus Disease (COVID-19). Vol. April. 2020. p. 1–41.

Soba University Hospital (Sudan). COVID-19 protocol of isolation guidelines. 2020. p. 1–5.

Republic of Sudan Federal Ministry of Health. Case Treatment Protocol For COVID-19 Patients. 2020. p. 1–9.

University Teaching Hospital Zambia. Health Facility Infection Prevention and Control Monitoring Tool. 2021. p. 1–17.

Soba University Hospital (Sudan). Infection Prevention Committee Manual Operation Guideline Table of Contents. 2021. p. 1–60.

Alhumaid S, Al Mutair A, Al Alawi Z, Alsuliman M, Ahmed GY, Rabaan AA, et al. Knowledge of infection prevention and control among healthcare workers and factors influencing compliance: a systematic review. Antimicrob Resist Infect Control. 2021;10(1):1–32.

Article  Google Scholar 

Amanya SB, Nyeko R, Obura B, Acen J, Nabasirye C, Nakaziba R, et al. Knowledge and compliance with Covid-19 infection prevention and control measures among health workers in regional referral hospitals in northern Uganda: a cross-sectional online survey. F1000Res. 2021;10:136.

Article  CAS  Google Scholar 

World Health Organization. Improving infection prevention and control at the health facility: Interim practical manual supporting implementation of the WHO Guidelines on Core Components of Infection Prevention and Control Programmes. Vol. 7. 2018. p. S6–15.

Xu Q, Liu Y, Cepulis D, Jerde A, Sheppard RA, Reichle W et al. Hand hygiene behaviours monitored by an electronic system in the intensive care unit – a prospective observational study. Journal of Hospital Infection. 2022 Feb

Treadway G, Pontani D, Reisman A. The safety of azithromycin in the treatment of adults with community-acquired respiratory tract infections. Int J Antimicrob Agents. 2002;19(3):189–94.

Article  CAS  PubMed  Google Scholar 

Schwartz RA, Suskind RM. Azithromycin and COVID-19: prompt early use at first signs of this infection in adults and children, an approach worthy of consideration. Dermatol Ther. 2020;33(e13785):1–3.

Google Scholar 

Adebisi YA, Jimoh ND, Ogunkola IO, Uwizeyimana T, Olayemi AH, Ukor NA et al. The use of antibiotics in COVID-19 management: a rapid review of national treatment guidelines in 10 African countries. Trop Med Health. 2021;49(1).

Bizot E, Cointe A, Bidet P, Mriani-Kurkdjian P, Amaris Hobson C, Courroux C et al. Azithromycin resistance in Shiga-toxin Producing Escherichia coli in France between 2004 and 2020 and detection of mef(C)-mph(G) genes. Antimicrob Agents Chemother. 2021

Gomes C, Ruiz-Roldán L, Mateu J, Ochoa TJ, Ruiz J. Azithromycin resistance levels and mechanisms in Escherichia coli. Sci Rep. 2019;9(1):1–10.

Article  Google Scholar 

Elton L, PANDORA-ID-NET. TGHN hub: Sequencing tutorials [Internet]. 2020 [cited 2022 Sep 21]. Available from: https://pandora.tghn.org/sequencing/sequencing-tutorials/

Knight GM, Glover RE, McQuaid CF, Olaru ID, Gallandat K, Leclerc QJ, et al. Antimicrobial resistance and covid-19: intersections and implications. Elife. 2021;10:1–27.

Article  Google Scholar