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9 hojas, 4 figuras, 1 tabla. Demographic data of the participants are available in the appendix (pp 40–42). Genome sequences are publicly available on GISAID. All scripts used for the analysis, and beta and delta subtree files are publicly available at https://gitlab.com/tbgenomicsunit/mozcovid. The study protocol (appendix pp 1–35) and clinical questionnaire (appendix pp 36–39) will be available with publication, Background: From the start of the SARS-CoV-2 outbreak, global sequencing efforts have generated an unprecedented amount of genomic data. Nonetheless, unequal sampling between high-income and low-income countries hinders the implementation of genomic surveillance systems at the global and local level. Filling the knowledge gaps of genomic information and understanding pandemic dynamics in low-income countries is essential for public health decision making and to prepare for future pandemics. In this context, we aimed to discover the timing and origin of SARS-CoV-2 variant introductions in Mozambique, taking advantage of pandemic-scale phylogenies. Methods: We did a retrospective, observational study in southern Mozambique. Patients from Manhiça presenting with respiratory symptoms were recruited, and those enrolled in clinical trials were excluded. Data were included from three sources: (1) a prospective hospital-based surveillance study (MozCOVID), recruiting patients living in Manhiça, attending the Manhiça district hospital, and fulfilling the criteria of suspected COVID-19 case according to WHO; (2) symptomatic and asymptomatic individuals with SARS-CoV-2 infection recruited by the National Surveillance system; and (3) sequences from SARS-CoV-2-infected Mozambican cases deposited on the Global Initiative on Sharing Avian Influenza Data database. Positive samples amenable for sequencing were analysed. We used Ultrafast Sample placement on Existing tRees to understand the dynamics of beta and delta waves, using available genomic data. This tool can reconstruct a phylogeny with millions of sequences by efficient sample placement in a tree. We reconstructed a phylogeny (~7·6 million sequences) adding new and publicly available beta and delta sequences. Findings: A total of 5793 patients were recruited between Nov 1, 2020, and Aug 31, 2021. During this time, 133 328 COVID-19 cases were reported in Mozambique. 280 good quality new SARS-CoV-2 sequences were obtained after the inclusion criteria were applied and an additional 652 beta (B.1.351) and delta (B.1.617.2) public sequences were included from Mozambique. We evaluated 373 beta and 559 delta sequences. We identified 187 beta introductions (including 295 sequences), divided in 42 transmission groups and 145 unique introductions, mostly from South Africa, between August, 2020 and July, 2021. For delta, we identified 220 introductions (including 494 sequences), with 49 transmission groups and 171 unique introductions, mostly from the UK, India, and South Africa, between April and November, 2021. Interpretation: The timing and origin of introductions suggests that movement restrictions effectively avoided introductions from non-African countries, but not from surrounding countries. Our results raise questions about the imbalance between the consequences of restrictions and health benefits. This new understanding of pandemic dynamics in Mozambique can be used to inform public health interventions to control the spread of new variants. Funding: European and Developing Countries Clinical Trials, European Research Council, Bill & Melinda Gates Foundation, and Agència de Gestió d'Ajuts Universitaris i de Recerca., This publication was produced by MozCovid which is part of the EDCTP2 programme supported by the EU (grant number RIA2020EF-3005-MozCOVID). The COVID-19 testing was supported by Emory Global Health Institute, University of Emory, through the CHAMPS Program funded by the Bill & Melinda Gates Foundation (under the grant OPP1126780 to Robert Breiman, subcontract SC00003286). This work was also supported by the European Research Council under the EU’s Horizon 2020 Research and Innovation Program grant (101001038; TB-RECONNECT), the European Commission–NextGenerationEU (Regulation EU 2020/2094), through CSIC’s Global Health Platform (PTI Salud Global), the Departament d’Universitats i Recerca de la Generalitat de Catalunya (AGAUR; 2021 SGR 01517), and the Ministerio de Ciencia e Innovación (Spanish Government) Project PID2019–104477RB-I00. CISM is supported by the Government of Mozambique and the Spanish Agency for International Development. ISGlobal is a member of the CERCA Programme, Generalitat de Catalunya (http://cerca.cat/en/suma/). We also acknowledge support from the Spanish Ministry of Science and Innovation and State Research Agency through the Centro de Excelencia Severo Ochoa 2019–2023 Program (CEX2018–000806-S).

Commensal/ooportunistic bacteria pathogens have been implicated severally in bacteremia and knee-joint infection. Methods & Materials: Fresh samples of feces (n =65) were obtained from a group of invading cattle egrets (≈ 1000) on trees in Vom, Nigeria. These egrets were not deterred by efforts at tree-trimming. Samples were enriched in tryptone-soy broth and plated on MacConkey agar using standard procedures. All positive cultures were sub-cultured on cefixime-rhamnose-sorbitol MacConkey agar (selective medium) and antibiogram was carried out using diffusion disc with 7 different antibiotics. Results: E. coli (n =58) and Micrococcus spp. (n =13) were isolated from the faecal material following enrichment. The pooled E. coli colonieswere sensitive toCiprofloxacin (+++), Chloramphenicol (+++), Streptomycin (+), Clindamycin (+) andTetracycline (+) but was resistant to Vancomycin VA (30) and Vancomycin VA (5).The Micrococcus spp was sensitive to Ciprofloxacin (+++), Vancomycin VA (30) (++) and Vancomycin VA (5) (+) but resistant to Streptomycin, Clindamycin, Tetracycline and Chloramphenicol. Conclusion: Food animal production processes in Africa is particularly opened to abuse of antibiotics with stockmen often treating their cattle without recourse to veterinarians. Since the ecology of cattle egrets and trans-humance cattle are similar with shared environment, food sources, watering points andmovement patterns, it is highly likely that drugs and medicaments are also shared by these species inadvertently. While this work has shown evidence of resistant organisms in fecal materials in cattle egret, more studies will become necessary to identify the potential epidemiologic role these species pose in spreading resistant organisms to poultry and other livestock.

The aim of this study was to determine the prevalence of extended-spectrum b-lactamase (ESBL)- producing Klebsiella pneumoniae isolated from urinary tract and bloodstream infections in a rural hospital in Manhic¸a, Mozambique. ESBLs were investigated among ceftriaxone-non-susceptible K. pneumoniae clinical isolates recovered between 2004 and 2009. Characterisation of blaCTX-M, blaSHV, blaOXA and blaTEM genes was performed by PCR and sequencing. Epidemiological relationships were established by phylogenetic analysis, repetitive extragenic palindromic PCR (REP-PCR), pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST), whilst plasmid transferability was evaluated by conjugation. In addition,the presence of class 1 and 2 integrons was studied.A total of 19 K. pneumoniae were analysed. The blaCTX-M-15 gene was found in all strains. Other ESBL genes were found concomitantly, including blaSHV-5, blaSHV-2, blaSHV-2A, blaSHV-12 and blaSHV-38. In addition, other b-lactamases such as blaTEM-1 and blaOXA-30 were also detected. REP-PCR identified 15 different epidemiological profiles. MLST analysis also showed great variability of sequence types. The blaCTX-M-15 gene showed a high transfer capacity. The presence of class 1 integrons was high. High levels of multidrug resistance were also found. In conclusion, these data show the dominance of the CTX-M-type ESBL, particularly CTX-M-15, supporting its worldwide dissemination, including in areas with limited access to third-generation cephalosporins. This finding is a matter of concern for clinical management as third-generation cephalosporins are an alternative for treating severe cases of multidrug-resistant infections in this community. Revisión por pares