Background:The global penetration of mobile phones has offered novel opportunities for communicating health-related information to individuals. A low-cost system that facilitates autonomous communication with individuals via mobile phones holds potential for expanding the reach of health messaging in settings with human resource and infrastructure limitations. Objective:We sought to design a flexible, low-code system using open-source software that could be adapted to different contexts and technical environments and accommodate a wide range of automation needs. We report on key details of the mobile phone-based appointment reminder and incentive system (mParis), document its use, review implementation challenges and adaptations to address these challenges in the context of a quasi-randomized trial of mobile phone-based reminders and incentives as means of increasing the timeliness of childhood vaccinations in Tanzania, and outline other use cases that highlight the versatility of the system. Methods:The mParis instance described in this paper, which is hosted in Tanzania, sent automated, individualized vaccination reminders in the form of SMS text messages to the mobile phones of mothers of young children. Process workflows, based on the national vaccination schedule of Tanzania, were programmed into mParis. Reminders for vaccinations due at ages 6, 10, and 14 weeks were sent 7 days and 1 day before and 14 days after each vaccination due date. A subset of messages included financial incentive offers to mothers for the timely vaccination of their children. We report on implementation outcomes, challenges, and adaptations to address these challenges. Results:Between August and December 2017, a total of 412 pregnant women were enrolled in the trial. After mothers reported the birth of their children, individualized vaccination reminder messages were sent for vaccination due dates between January and July 2018. From March 2018, messages contained financial incentive offers. Of 1397 messages sent, 1122 (80.3%) messages were recorded as delivered, 249 (18.8%) as expired and resent; 23 (1.6%) as failed, and 3 (0.2%) as sent but lacking a delivery confirmation. In total, 633 (45.3%) messages contained incentive offers. Of 173 women who received at least 1 message, 67 (38.7%) were sent reminders only; 106 (61.3%) women were sent at least 1 incentivized message. Numerous challenges were encountered during the system's implementation, despite its deliberate design to accommodate basic problems, such as intermittent internet access and power failures. Continuous adaptation to increase the resilience of the system resulted in a successful deployment. Conclusions:mParis' open-source nature, auditability, and ability to autonomously execute algorithms in a low-resource setting with frequent infrastructure challenges suggest favorable prospects to automate health communication in a wide range of settings. mParis' use in other applications, including enrollment and follow-up for health-related research studies, demonstrates its versatility and ability to accommodate diverse challenges that may be encountered.

Carbapenem-resistant Pseudomonas aeruginosa exacerbates the healing of chronic leg ulcer among patients. Further, production and dissemination of the carbapenemase genes are associated with P. aeruginosa high-risk sequence types. Hence, understanding the population structure of these organisms is essential for healthcare personnel to establish effective leg ulcers care management, prevention interventions and control strategies particularly in regions with poor diagnosis. A cross-sectional study included inpatients and outpatients with chronic leg ulcers was conducted from August 2022 to April 2023 in 2 hospitals in Kilimanjaro region. Antimicrobial susceptibility testing was done by using the disc diffusion method. Further, whole genome sequencing was performed to study the genotypic characteristics of the isolates. Ten of 92 participants were positive for genus Pseudomonas isolates upon culture during the study period. Ambler class D carbapenemase genes were carried in all 8 isolates, and class B ( bla VIM - 2 $$ {\mathrm{bla}}_{\mathrm{VIM}-2} $$ , bla DIM - 1 $$ {\mathrm{bla}}_{\mathrm{DIM}-1} $$ ) in 2 isolates. The tree topology showed that all 8 P. aeruginosa isolates that carried any of the Ambler carbapenemase genes were in one clade with the reference strain PAO1. This study sheds light on different carbapenemase gene types (VIM-2, DIM-1, and OXA-types) harboured in the denominated global high-risk and endemic sequence types in 2 tertiary hospitals in northern Tanzania, alarming the possibility of a prolonged healing process and a high risk of treatment failure among patients because of the increased spread of antimicrobial resistance. Further, the findings underscore the need for antimicrobial surveillance to guide healthcare personnel in managing chronic leg ulcers for better patient outcomes and the implementation of antimicrobial stewardship programs.

The Confidential Social Network Referrals for HIV Testing (CONSORT) intervention leverages the ubiquity of mobile phones and social networks to nudge at-risk populations to test for HIV. Pilot results suggest that confidential SMS testing invitations are acceptable among diverse populations and may reach those at above-average risk of HIV infection.

The ongoing threat of antimicrobial resistance (AMR) demands capacity strengthening in Africa for improved pathogen surveillance. The high-resolution picture of AMR provided by pathogen whole genome sequencing (WGS) can help close data gaps and inform disease prevention strategies, interventions and public health actions. Here, we report on phase 1 of the Fleming Fund-supported SeqAfrica project (2019–2023), one of the first genomic AMR surveillance networks in Africa. SeqAfrica established five regional sequencing hubs across West, East, and Southern Africa, expanded infrastructure, and delivered hybrid training programs to strengthen workforce capacity. During phase 1, the network generated 29,269 pathogen genomes (18,264 bacterial, 300 fungal, and 10,705 SARS-CoV-2) from 21 African countries, contributing to 40 scientific publications and substantial genomic data for national and global surveillance efforts, supporting outbreak investigations and antimicrobial stewardship initiatives. The median turnaround time from sample receipt to data release was 12 weeks (range: 3–104 weeks), demonstrating the feasibility of genomic AMR surveillance despite logistical challenges. By nurturing a community of practice, expanding the workforce, and translating data into actionable insights, SeqAfrica has advanced the integration of pathogen genomics into national and regional surveillance frameworks. However, sustaining this capacity remains a challenge amid global funding constraints, procurement bottlenecks, and workforce retention issues. Lessons learned from implementation include successes in regional collaboration and persistent challenges in procurement, workforce retention, and metadata completeness, which informed the design of phase 2. As Africa continues to invest in genomic health infrastructure, SeqAfrica provides a proven model for embedding pathogen genomics into public health strategies and strengthening AMR surveillance across the continent.

PURPOSE:To understand the mechanisms of carbapenem-resistant Klebsiella pneumoniae (CRKP) from Tanzania and characterize the genomes carrying the carbapenemase genes. METHODS:Clinical CRKP isolates were selected from ongoing antimicrobial resistance surveillance at Muhimbili National Hospital, Dar es Salaam, Tanzania. Whole-genome sequencing was performed utilizing Illumina and Nanopore platforms. RESULTS:A total of twelve CRKP were analyzed in this study. Six different multilocus sequence types were detected, six isolates were sequence type ST437 and one belonged to a novel sequence type, ST6258. Resistance to carbapenems was multifactorial with co-existence of blaNDM-5 and blaOXA-181 in six CRKP, and blaNDM-5 and blaOXA-232 in one isolate, and chromosomal mutation of ompK36 and ompK37 in all twelve isolates. All the CRKP carried genes conferring resistance to 3rd generation cephalosporins, penicillin, aminoglycosides, fosfomycin, trimethoprim-sulfamethoxazole, and quinolones. The hybrid assemblies of 001BS and 002PS2 revealed that they harbored seven and six different plasmids, respectively. The 001BS carried two blaNDM-5 on distinct plasmids. The first blaNDM-5 gene was carried on an IncFIB(K) plasmid; and the second blaNDM-5 co-existed with blaOXA-181 on the ColPK3-IncX3 plasmid. In contrast, in 002PS2 the blaNDM-5 and blaOXA-181 were carried on the IncFIB(K)-IncFII(K) and ColPK3-IncX3 plasmids, respectively. The genetic environment of the blaNDM-5 gene on both plasmids was flanked by the same genetic core IS26-IS30-blaNDM-5 -ble-trpF-DsbD-ISCR1-sul1- QacE-IS3000. CONCLUSION:Clonally related CRKP ST437 with multiple co-existing carbapenemase genes were detected for the first time at the tertiary hospital in Tanzania. The existence of this high-risk clone poses a great risk for further spread at our facility.

BACKGROUND:Methicillin-resistant Staphylococcus aureus (MRSA) is a formidable public scourge causing worldwide mild to severe life-threatening infections. The ability of this strain to swiftly spread, evolve, and acquire resistance genes and virulence factors such as pvl genes has further rendered this strain difficult to treat. Of concern, is a recently recognized ability to resist antiseptic/disinfectant agents used as an essential part of treatment and infection control practices. This study aimed at detecting the presence of pvl genes and determining the distribution of antiseptic resistance genes in Methicillin-resistant Staphylococcus aureus isolates through whole genome sequencing technology. MATERIALS AND METHODS:A descriptive cross-sectional study was conducted across six regional referral hospitals-Dodoma, Songea, Kitete-Kigoma, Morogoro, and Tabora on the mainland, and Mnazi Mmoja from Zanzibar islands counterparts using the archived isolates of Staphylococcus aureus bacteria. The isolates were collected from Inpatients and Outpatients who attended these hospitals from January 2020 to Dec 2021. Bacterial analysis was carried out using classical microbiological techniques and whole genome sequencing (WGS) using the Illumina Nextseq 550 sequencer platform. Several bioinformatic tools were used, KmerFinder 3.2 was used for species identification, MLST 2.0 tool was used for Multilocus Sequence Typing and SCCmecFinder 1.2 was used for SCCmec typing. Virulence genes were detected using virulenceFinder 2.0, while resistance genes were detected by ResFinder 4.1, and phylogenetic relatedness was determined by CSI Phylogeny 1.4 tools. RESULTS:Out of the 80 MRSA isolates analyzed, 11 (14%) were found to harbor LukS-PV and LukF-PV, pvl-encoding genes in their genome; therefore pvl-positive MRSA. The majority (82%) of the MRSA isolates bearing pvl genes were also found to exhibit the antiseptic/disinfectant genes in their genome. Moreover, all (80) sequenced MRSA isolates were found to harbor SCCmec type IV subtype 2B&5. The isolates exhibited 4 different sequence types, ST8, ST88, ST789 and ST121. Notably, the predominant sequence type among the isolates was ST8 72 (90%). CONCLUSION:The notably high rate of antiseptic resistance particularly in the Methicillin-resistant S. aureus strains poses a significant challenge to infection control measures. The fact that some of these virulent strains harbor the LukS-PV and LukF-PV, the pvl encoding genes, highlight the importance of developing effective interventions to combat the spreading of these pathogenic bacterial strains. Certainly, strengthening antimicrobial resistance surveillance and stewardship will ultimately reduce the selection pressure, improve the patient's treatment outcome and public health in Tanzania.

BackgroundRabies remains a major public health problem in low- and middle-income countries. However, human rabies deaths are rarely laboratory-confirmed or sequenced, especially in Africa. Five human rabies deaths from Tanzania and Kenya were investigated and the causative rabies viruses sequenced, with the aim of identifying implications for rabies control at individual, healthcare and societal levels.Case presentationThe epidemiological context and care of these cases was contrasting. Four had a clear history of being bitten by dogs, while one had an unclear biting history. Two individuals sought medical attention within a day of being bitten, whereas three sought care only after developing rabies symptoms. Despite seeking medical care, none of the cases received complete post-exposure prophylaxis: one patient received only tetanus vaccination, one did not complete the post-exposure vaccination regimen, one followed an off-label vaccination schedule, and two did not receive any post-exposure vaccinations before the onset of symptoms. These cases highlight serious gaps in health-seeking behaviour, and in health systems providing appropriate care following risky exposures, including in the accessibility and effectiveness of post-exposure prophylaxis as it is administered in the region.ConclusionsThe viral genomic and epidemiological data confirms dog-mediated rabies as the cause of each of these deaths. The phylogenetic investigation highlights the transboundary circulation of rabies within domestic dog populations, revealing distinct rabies virus clades with evidence of regional spread. These findings underscore the importance of coordinated cross-border control efforts between the two countries. Urgent action is needed to improve awareness around the need for emergency post-exposure vaccines that should be accessible in local communities and administered appropriately, as well as investment in coordinated dog vaccination to control dog-mediated rabies, the underlying cause of these deaths.

Brucella abortus causes infections in humans and livestock. Bacterial isolates are challenging to obtain, and very little is known about the genomic epidemiology of this species in Africa. Here, we report the complete genome sequence of a Brucella abortus isolate cultured from a febrile human in northern Tanzania.

BackgroundCritical to efforts to end the HIV epidemic is the identification of persons living with HIV who have yet to be diagnosed and engaged in care. Expanded HIV testing outreach efforts need to be both efficient and ambitious, targeting the social networks of persons living with HIV and those at above-average risk of undiagnosed HIV infection. The ubiquity of mobile phones across many high HIV prevalence settings has created opportunities to leverage mobile health (mHealth) technologies to engage social networks for HIV testing outreach, prevention, and treatment. ObjectiveThe purpose of this study is to evaluate the acceptability and efficacy of a novel mHealth intervention, “Confidential Social Network Referrals for HIV Testing (CONSORT),” to nudge at-risk individuals to test for HIV using SMS text messages. MethodsWe will conduct the CONSORT study in Moshi, Tanzania, the commercial center and administrative capital of the Kilimanjaro Region in northern Tanzania. After qualitative formative work and pilot testing, we will enroll 400 clients presenting for HIV counseling and testing and 200 persons living with HIV and receiving care at HIV care and treatment centers as “inviters” into a randomized controlled trial. Eligible participants will be aged 18 years or older and live, work, or regularly receive care in Moshi. We will randomize inviters into 1 of 2 study arms. All inviters will be asked to complete a survey of their HIV testing and risk behaviors and to think of social network contacts who would benefit from HIV testing. They will then be asked to whom they would prefer to extend an HIV testing invitation in the form of a physical invitation card. Arm 1 participants will also be given the opportunity to extend CONSORT invitations in the form of automated confidential SMS text messages to any of their social network contacts or “invitees.” Arm 2 participants will be offered physical invitation cards alone. The primary outcome will be counselor-documented uptake of HIV testing by invitees within 30 days of inviter enrollment. Secondary outcomes will include the acceptability of CONSORT among inviters, the number of new HIV diagnoses, and the HIV risk of invitees who present for testing. ResultsEnrollment in the randomized controlled trial is expected to start in September 2024. The findings will be disseminated to stakeholders and published in peer-reviewed journals. ConclusionsIf CONSORT is acceptable and effective for increasing the uptake of HIV testing, given the minimal costs of SMS text reminders and the potential for exponential but targeted growth using chain referrals, it may shift current practices for HIV testing programs in the area. Trial RegistrationClincalTrials.gov NCT05967208; https://clinicaltrials.gov/study/NCT05967208 International Registered Report Identifier (IRRID)PRR1-10.2196/55068

BackgroundThe emergence of multidrug-resistant termed Methicillin-resistant Staphylococcus aureus (MRSA) strain, driven by the acquisition of resistance gene mecA imposes a substantial challenge in the treatment and control of their related infections. Although quinolones have historically been effective against both MRSA and methicillin-susceptible S. aureus (MSSA) strains, the rising resistance to quinolones among S. aureus isolates, particularly in MRSA, has severely curtailed their potency and further narrowed down the therapeutic options. This study aimed to determine the burden of MRSA among isolates, as well as their resistance profile, genotypic characterization, and molecular relatedness through the construction of a phylogenetic tree.Materials and methodsArchived clinical S. aureus isolates from a descriptive, cross-sectional study involving six regional referral hospitals in Dodoma, Songea, Kigoma, Kitete, and Morogoro in the mainland Tanzania and Mnazi Mmoja in Zanzibar were analyzed. Bacterial identification was performed using both classical microbiology and whole genome sequencing on Illumina Nextseq 550 Sequencer. Species identification was done using KmerFinder 3.2, Multilocus Sequence Typing using MLST 2.0, SCCmec typing using SCCmecFinder 1.2, resistance genes using ResFinder 4.1, and phylogenetic relatedness using CSI Phylogeny 1.4.ResultsOut of the 140 isolates analyzed, 69 (49.3%) were identified as MRSA, with 57 (82.6%) exhibiting quinolone resistance. Conversely, 71 isolates were identified as MSSA, and none of them exhibited resistance to quinolones. Spa-typing revealed six spa types, with t355, t1476, and t498 being the most common. Moreover, all (69) MRSA were found to carry SCCmec type IV. The isolates exhibited 14 different sequence types (STs). Notably, ST152 was prevalent among MSSA (50 isolates, 70%), while ST8 was the predominant sequence type among MRSA (58 isolates, 84%). The antimicrobial resistance profile revealed at least three horizontally acquired resistance genes, with blaZ, dfrG, tet(K), and aac (6')-aph (2'') genes being highly prevalent.ConclusionThere is a high genetic diversity among the S. aureus isolates existing in Tanzania regional hospitals, with a concerning burden of quinolone resistance among MRSA isolates. The diversity in resistance genes among MRSA lineages emphasizes the necessity for the development of sustainable antimicrobial stewardship and surveillance to support evidence-based guidelines for managing and controlling MRSA infections in both community and hospital settings.

Abstract Background Escherichia coli is known to cause about 2 million deaths annually of which diarrhea infection is leading and typically occurs in children under 5 years old. Although Africa is the most affected region there is little information on their pathotypes diversity and their antimicrobial resistance. Objective To determine the pathotype diversity and antimicrobial resistance among E. coli from patients attending regional referral hospitals in Tanzania. Materials and methods A retrospective cross-section laboratory-based study where a total of 138 archived E. coli isolates collected from 2020 to 2021 from selected regional referral hospitals in Tanzania were sequenced using the Illumina Nextseq550 sequencer platform. Analysis of the sequences was done in the CGE tool for the identification of resistance genes and virulence genes. SPSS version 20 was used to summarize data using frequency and proportion. Results Among all 138 sequenced E. coli isolates, the most prevalent observed pathotype virulence genes were of extraintestinal E. coli UPEC fyuA gene 82.6% (114/138) and NMEC irp gene 81.9% (113/138). Most of the E. coli pathotypes observed exist as a hybrid due to gene overlapping, the most prevalent pathotypes observed were NMEC/UPEC hybrid 29.7% (41/138), NMEC/UPEC/EAEC hybrid 26.1% (36/138), NMEC/UPEC/DAEC hybrid 18.1% (25/138) and EAEC 15.2% (21/138). Overall most E. coli carried resistance gene to ampicillin 90.6% (125/138), trimethoprim 85.5% (118/138), tetracycline 79.9% (110/138), ciprofloxacin 76.1% (105/138) and 72.5% (100/138) Nalidixic acid. Hybrid pathotypes were more resistant than non-hybrid pathotypes. Conclusion Whole genome sequencing reveals the presence of hybrid pathotypes with increased drug resistance among E. coli isolated from regional referral hospitals in Tanzania.

Background Methicillin-resistant Staphylococcus aureus (MRSA) colonization increases the risk of subsequent infection by MRSA strain complex interlinking between hospital and community-acquired MRSA which increases the chance of drug resistance and severity of the disease. Objective Genomic characterization of Staphylococcus aures strains isolated from patients attending regional referral hospitals in Tanzania. Methodology A laboratory-based cross-sectional study using short read-based sequencing technology, (Nextseq550,Illumina, Inc. San diego, California, USA). The samples used were collected from patients attending selected regional referral hospitals in Tanzania under the SeqAfrica project. Sequences were analyzed using tools available in the center for genomic and epidemiology server, and visualization of the phylogenetic tree was performed in ITOL 6.0. SPSS 28.0 was used for statistical analysis. Results Among 103 sequences of S. aureus, 48.5% (50/103) carry the mecA gene for MRSA. High proportions of MRSA were observed among participants aged between 18 and 34 years (52.4%), in females (54.3%), and among outpatients (60.5%). The majority of observed MRSA carried plasmids rep5a (92.0%), rep16 (90.0%), rep7c (90.0%), rep15 (82.0%), rep19 (80.0%) and rep10 (72.0%). Among all plasmids observed rep5a, rep16, rep20, and repUS70 carried the blaZ gene, rep10 carried the erm(C) gene and rep7a carried the tet(K) gene. MLST and phylogeny analysis reveal high diversity among MRSA. Six different clones were observed circulating at selected regional hospitals and MRSA with ST8 was dominant. Conclusion The study reveals a significant presence of MRSA in Staphylococcus aureus strains from Tanzanian regional hospitals, with nearly half carrying the mecA gene. MRSA is notably prevalent among young adults, females, and outpatients, showing high genetic diversity and dominance of ST8. Various plasmids carrying resistance genes indicate a complex resistance profile, highlighting the need for targeted interventions to manage MRSA infections in Tanzania.

Background: Chronic leg ulcers are hard to treat and can be a burden, particularly in resource-limited settings where diagnosis is a challenge. Staphylococcus aureus is among the common bacteria isolated from chronic wounds with a great impact on wound healing, particularly in patients with co-morbidities. Antimicrobial resistance genes and virulence factors in Staphylococcus aureus isolates were assessed to support healthcare professionals to make better therapeutic choices, and importantly to curb the development and spread of antibiotic resistance. Methods: A cross-sectional study involved both inpatients and outpatients with chronic leg ulcers was conducted from August 2022 to April 2023 in 2 health facilities in Kilimanjaro region in Tanzania. Antimicrobial susceptibility testing was done using the disk diffusion method. Further, whole genome sequencing was performed to study the genotypic characteristics of the isolates. Results: A total of 92 participants were recruited in which 9 participants were only positive for 10 Staphylococcus aureus isolates upon culture. Five STs among 9 isolates were identified. Most of them belonged to ST8 (44%), with 1 isolate does not belong to any ST. Additionally, 50% of the isolates were methicillin-resistant Staphylococcus aureus (MRSA). All S. aureus isolates had almost similar virulence factors such as hemolysin, proteases and evasions that promote toxin production, protease production and host immune evasion respectively. Moreover, all mecA positive S. aureus isolates were phenotypically susceptible to cefoxitin. Conclusion: Presence of mecA positive S. aureus isolates which are also phenotypically susceptible to cefoxitin implies the possibility of classifying MRSA as MSSA. This may result in the possible emergence of highly cefoxitin - resistant strains in health care and community settings when subsequently exposed to beta-lactam agents. Therefore, combination of whole genome sequencing and conventional methods is important in assessing bacterial resistance and virulence to improve management of patients.

Background: Rabies remains a major public health problem in low- and middle-income countries. However, human rabies deaths are rarely laboratory-confirmed, especially in Africa. Here, we use rabies virus sequence data to enhance investigations for a series of 5 human rabies deaths in East Africa and discuss the implications of these at individual, healthcare, and societal-level. Case presentation: The epidemiological context and care of these cases is contrasting: three of the bite victims did not receive any post-exposure vaccinations to prevent the fatal onset of disease, despite one attending a health facility on the day of exposure; one received only their first post-exposure vaccination; while the last received timely post-exposure vaccination but following a vaccination timeline that is not recommended by WHO. These differences raise concerns about health-seeking behaviour, competency of healthcare professionals in handling rabies exposures and accessibility and effectiveness of post-exposure prophylaxis as it is administered in these settings. Result and conclusion: Our investigation confirms dog-mediated rabies as the cause of each of these deaths. The viral genomic data highlight the transboundary circulation of rabies within domestic dog populations across the region. We conclude that urgent action is needed to improve awareness around the need for emergency post-exposure prophylaxis that should be accessible in local communities and administered appropriately, as well as investment in coordinated dog vaccination to control dog-mediated rabies, the underlying cause of these deaths.

BackgroundTanzania is 1 of 20 countries where the majority of unvaccinated and undervaccinated children reside. Prior research identified substantial rural-urban disparities in the coverage and timeliness of childhood vaccinations in Tanzania, with children in rural settings being more likely to receive delayed or no vaccinations. Further research is necessary to identify effective and scalable interventions that can bridge rural-urban gaps in childhood vaccination while accounting for multifaceted barriers to vaccination. ObjectiveThis protocol describes a type 1 effectiveness-implementation hybrid study to evaluate Chanjo Kwa Wakati (timely vaccination in Kiswahili), a community-based digital health intervention to improve vaccination timeliness. The intervention combines human resources (community health workers), low-cost digital strategies (electronic communication, digital case management, and task automation), a vaccination knowledge intervention, and insights from behavioral economics (reminders and incentives) to promote timely childhood vaccinations. MethodsThe study will be conducted in 2 predominantly rural regions in Tanzania with large numbers of unvaccinated or undervaccinated children: Shinyanga and Mwanza. Forty rural health facilities and their catchment areas (clusters) will be randomized to an early or delayed onset study arm. From each cluster, 3 cohorts of mother-child dyads (1 retrospective cohort and 2 prospective cohorts) will be enrolled in the study. The timeliness and coverage of all vaccinations recommended during the first year of life will be observed for 1200 children (n=600, 50% intervention group children and n=600, 50% nonintervention group children). The primary effectiveness outcome will be the timeliness of the third dose of the pentavalent vaccine (Penta3). Quantitative surveys, vaccination records, study logs, fidelity checklists, and qualitative interviews with mothers and key informants will inform the 5 constructs of the reach, effectiveness, adoption, implementation, and maintenance (RE-AIM) framework. The results will be used to develop an implementation blueprint to guide future adaptations and scale-up of Chanjo Kwa Wakati. ResultsThe study was funded in August 2022. Data collection is expected to last from February 2024 to July 2027. ConclusionsThis study will address the lack of rigorous evidence on the effectiveness of community-based digital health interventions for promoting vaccination coverage and timeliness among children from sub-Saharan Africa and identify potential implementation strategies to facilitate the deployment of vaccination promotion interventions in low- and middle-income countries. Trial RegistrationClinicalTrials.gov NCT06024317; https://www.clinicaltrials.gov/study/NCT06024317 International Registered Report Identifier (IRRID)PRR1-10.2196/52523

Background Antimicrobial resistance (AMR) of Neisseria gonorrhoeae is a threat to public health as strains have developed resistance to antimicrobials available for the treatment of gonorrhea. Whole genome sequencing (WGS) can detect and predict antimicrobial resistance to enhance the control and prevention of gonorrhea. Data on the molecular epidemiology of N. gonorrhoeae is sparse in Zambia. This study aimed to determine the genetic diversity of N. gonorrhoeae isolated from patients attending sexually transmitted infection (STI) clinics in Lusaka, Zambia. Methods A cross-sectional study that sequenced 38 N. gonorrhoeae isolated from 122 patients with gonorrhea from 2019 to 2020 was conducted. The AMR profiles were determined by the E-test, and the DNA was extracted using the NucliSens easyMaG magnetic device. Whole genome sequencing was performed on the Illumina NextSeq550 platform. The Bacterial analysis pipeline (BAP) that is readily available at: https://cge.cbs.dtu.dk/services/CGEpipeline-1.1 was used for the identification of the species, assembling the genome, multi-locus sequence typing (MLST), detection of plasmids and AMR genes. Phylogeny by single nucleotide polymorphisms (SNPs) was determined with the CCphylo dataset. Results The most frequent STs with 18.4% of isolates each were ST 7363 , ST 1921 and ST 1582 , followed by ST 1583 (13%), novel ST 17026 (7.9%), ST 1588 (7.9%), ST 1596 (5.3%), ST 11181 (5.3%), ST 11750 (2.6/%) and ST 11241 (2.6%) among the 38 genotyped isolates. The blaTeM-1B and tetM (55%) was the most prevalent combination of AMR genes, followed by blaTeM-1B (18.4%), tetM (15.8%), and the combination of blaTeM-1B , ermT , and tetL was 2.6% of the isolates. The AMR phenotypes were predicted in ciprofloxacin, penicillin, tetracycline, azithromycin, and cefixime. The combination of mutations 23.7% was gryA (S91F), parC (E91G), ponA (L421) and rpsJ (V57M), followed by 18.4% in gyrA (S91F), ponA (L421P), rpsJ (V57M), and 18.4% in gyrA (D95G, S91F), ponA (L421P), and rpsJ (V57M). The combinations in gyrA (D95G, S91F) and rpsJ (V57M), and gyrA (D95G, S91F), parC (E91F), ponA (L421P) and rpsJ (V57M) were 13.2% each of the isolates. Plasmid TEM-1 (84.2%), tetM ( 15.8%), and gonococcal genetic island (GGI) was detected in all isolates. Conclusion This study revealed remarkable heterogeneity of N. gonorrhoeae with bla TEM−1 , tetM, ponA, gyrA , and parC genes associated with high resistance to penicillin, tetracycline, and ciprofloxacin demanding revision of the standard treatment guidelines and improved antimicrobial stewardship in Zambia.

Staphylococcus aureus is a common cause of infection in humans and animals, including bovine mastitis, globally. The objective of this study was to genetically characterize a collection of S. aureus isolates recovered from milk and nasal swabs from humans with and without animal contact (bovine = 43, human = 12). Using whole genome sequencing (NextSeq550), isolates were sequence typed, screened for antimicrobial resistance and virulence genes and examined for possible inter-species host transmission. Multi locus sequence typing (MLST) and single nucleotide polymorphism (SNP)-based phylogeny revealed 14 different sequence types, including the following six novel sequence types: ST7840, 7841, 7845, 7846, 7847, and 7848. The SNP tree confirmed that MLST clustering occurred most commonly within CC97, CC5477, and CC152. ResFinder analysis revealed five common antibiotic resistance genes, namely tet(K), blaZ, dfrG, erm©, and str, encoding for different antibiotics. mecA was discovered in one human isolate only. Multidrug resistance was observed in 25% of the isolates, predominantly in CC152 (7/8) and CC121 (3/4). Known bovine S. aureus (CC97) were collected in humans and known human S. aureus lineages (CC152) were collected in cattle; additionally, when these were compared to bovine-isolated CC97 and human-isolated CC152, respectively, no genetic distinction could be observed. This is suggestive of inter-host transmission and supports the need for surveillance of the human–animal interface.

Globally, zoonoses have serious consequences due to their socioeconomic impacts. Ngorongoro District is home to a diverse range of wildlife and domestic animals, including rodents and dogs, which often coexist in close proximity with humans. The aim of the study was to identify the zoonotic bacteria present in wild rodents, domestic dogs, and humans using metagenomics next-generation sequencing technology. A cross-sectional study was conducted in 2022. This study used both Illumina and Oxford Nanopore sequencing technologies to identify bacteria in 530 blood samples collected from humans (n = 200), wild rodents (n = 230), and dogs (n = 100). Several zoonotic airborne/contagious bacteria, including Mycobacterium spp., Mycoplasma spp., Bordetella spp., and Legionella spp., were detected in wild rodents, domestic dogs, and humans. Arthropod-borne zoonotic bacteria such as Bartonella spp., Borrelia spp., and Rickettsia spp. were detected in all three hosts, while Orientia spp. was found in wild rodents and domestic dogs. Yersinia pestis, Streptobacillus spp. and Anaplasma spp. were found only in wild rodents. Other zoonotic bacteria found shared among wild rodents, domestic dogs, and humans are Leptospira spp., Brucella spp., and Salmonella spp. Generally, wild rodents had the highest prevalence of zoonotic bacterial species when compared to domestic dogs and humans. The detection of zoonotic bacteria in rodents, dogs, and humans supports the hypothesis that infections can spread between animals and humans sharing the same environment.

BackgroundCoronavirus Disease-2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) accounts for considerable morbidity and mortality globally. Paucity of SARS-CoV-2 genetic data from Tanzania challenges in-country tracking of the pandemic. We sequenced SARS-CoV-2 isolated in the country to determine circulating strains, mutations and phylogenies and finally enrich international genetic databases especially with sequences from Africa.MethodsThis cross-sectional study utilized nasopharyngeal swabs of symptomatic and asymptomatic adults with positive polymerase chain reaction tests for COVID-19 from January to May 2021. Viral genomic libraries were prepared using ARTIC nCoV-2019 sequencing protocol version three. Whole-genome sequencing (WGS) was performed using Oxford Nanopore Technologies MinION device. In silico genomic data analysis was done on ARTIC pipeline version 1.2.1 using ARTIC nCoV-2019 bioinformatics protocol version 1.1.0.ResultsTwenty-nine (42%) out of 69 samples qualified for sequencing based on gel electrophoretic band intensity of multiplex PCR amplicons. Out of 29 isolates, 26 were variants of concern [Beta (n = 22); and Delta (n = 4)]. Other variants included Eta (n = 2) and B.1.530 (n = 1). We found combination of mutations (S: D80A, S: D215G, S: K417N, ORF3a: Q57H, E: P71L) in all Beta variants and absent in other lineages. The B.1.530 lineage carried mutations with very low cumulative global prevalence, these were nsp13:M233I, nsp14:S434G, ORF3a:A99S, S: T22I and S: N164H. The B.1.530 lineage clustered phylogenetically with isolates first reported in south-east Kenya, suggesting regional evolution of SARS-CoV-2.ConclusionWe provide evidence of existence of Beta, Delta, Eta variants and a locally evolving lineage (B.1.530) from samples collected in early 2021 in Tanzania. This work provides a model for ongoing WGS surveillance that will be required to inform on emerging and circulating SARS-CoV-2 diversity in Tanzania and East Africa.

Plasmids are infectious double stranded DNA molecules that are found within bacteria. Horizontal gene transfer promotes successful spread of different types of plasmids within or among bacteria species, making their detection an important task for guiding clinical treatment. We used whole genome sequenced data to determine the prevalence of plasmid replicons in clinical bacterial isolates, the presence of resistance and virulence genes in plasmids, and the relationship between resistance and virulence genes within each plasmid. All bacterial sequences were de novo assembled using Unicycler before extraction of plasmids. Assembly graphs were submitted to Gplas+plasflow for plasmid prediction. The predicted plasmid components were validated using PlasmidFinder. A total of 159 (56.2%) out of 283 bacterial isolates were found to carry plasmids, with E. coli, K. pneumoniae and S. aureus being the most prevalent plasmid carriers. A total of 27 (87.1%) combined plasmids were found to carry both resistance and virulence genes compared to 4 (12.9%) single plasmids. No statistically significant correlation was found between the number of antimicrobial resistance and virulence genes in plasmids (r =-0.25, p > 0.05). Our findings show a relatively high proportion of plasmid-carrying isolates suggesting selection pressure due to antibiotic use in the hospital. Co-occurrence of antibiotic resistance and virulence genes in clinical isolates is a public health relevant problem needing attention.