New Vibrio cholerae sequences from Eastern and Southern Africa alter our understanding of regional cholera transmission.

Despite ongoing containment and vaccination efforts, cholera remains prevalent in many countries in sub-Saharan Africa. Part of the difficulty in containing cholera comes from our lack of understanding of how it circulates throughout the region. To better characterize regional transmission, we generated and analyzed 118 Vibrio cholerae genomes collected between 2007-2019 from five different countries in Southern and Eastern Africa. We showed that V. cholerae sequencing can be successful from a variety of sample types and filled in spatial and temporal gaps in our understanding of circulating lineages, including providing some of the first sequences from the 2018-2019 outbreaks in Uganda, Kenya, Tanzania, Zambia, and Malawi. Our results present a complex picture of cholera transmission in the region, with multiple lineages found to be co-circulating within several countries. We also find evidence that previously identified sporadic cases may be from larger, undersampled outbreaks, highlighting the need for careful examination of sampling biases and underscoring the need for continued and expanded cholera surveillance across the African continent.

Omicron B.1.1.529 variant infections associated with severe disease are uncommon in a COVID-19 under-vaccinated, high SARS-CoV-2 seroprevalence population in Malawi.

Background: The B.1.1.529 (Omicron) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the fourth COVID-19 pandemic wave across the southern African region, including Malawi. The seroprevalence of SARS-CoV-2 antibodies and their association with epidemiological trends of hospitalisations and deaths are needed to aid locally relevant public health policy decisions. Methods: We conducted a population-based serosurvey from December 27, 2021 to January 17, 2022, in 7 districts across Malawi to determine the seroprevalence of SARS-CoV-2 antibodies. Serum samples were tested for antibodies against SARS-CoV-2 receptor binding domain using WANTAI SARS-CoV-2 Receptor Binding Domain total antibody commercial enzyme-linked immunosorbent assay (ELISA). We also evaluated COVID-19 epidemiologic trends in Malawi, including cases, hospitalisations and deaths from April 1, 2021 through April 30, 2022, collected using the routine national COVID-19 reporting system. A multivariable logistic regression model was developed to investigate the factors associated with SARS-CoV-2 seropositivity. Findings: Serum samples were analysed from 4619 participants (57% female; 60% aged 18-50 years), of whom 878/3794 (23%) of vaccine eligible adults had received a single dose of any COVID-19 vaccine. The overall assay-adjusted seroprevalence was 83.7% (95% confidence interval (CI), 79.3%-93.4%). Seroprevalence was lowest among children <13 years of age (66%) and highest among adults 18-50 years of age (82%). Seroprevalence was higher among vaccinated compared to unvaccinated participants (1 dose, 94% vs. 77%, adjusted odds ratio 4.89 [95% CI, 3.43-7.22]; 2 doses, 97% vs. 77%, aOR 6.62 [95% CI, 4.14-11.3]). Urban residents were more likely to be seropositive than those from rural settings (91% vs. 78%, aOR 2.76 [95% CI, 2.16-3.55]). There was at least a two-fold reduction in the proportion of hospitalisations and deaths among the reported cases in the fourth wave compared to the third wave (hospitalisations, 10.7% (95% CI, 10.2-11.3) vs. 4.86% (95% CI, 4.52-5.23), p < 0.0001; deaths, 3.48% (95% CI, 3.18-3.81) vs. 1.15% (95% CI, 1.00-1.34), p < 0.0001). Interpretation: We report reduction in proportion of hospitalisations and deaths from SARS-CoV-2 infections during the Omicron variant dominated wave in Malawi, in the context of high SARS-CoV-2 seroprevalence and low COVID-19 vaccination coverage. These findings suggest that COVID-19 vaccination policy in high seroprevalence settings may need to be amended from mass campaigns to targeted vaccination of reported at-risk populations. Funding: Supported by the Bill and Melinda Gates Foundation (INV-039481).

National action plan on antimicrobial resistance: An evaluation of implementation in the World Health Organization Africa region.

In line with global instruments, within the last five years, two-thirds of all countries in the WHO Africa Region (WHO AFR) have developed a National Action Plan (NAP) on Antimicrobial Resistance (AMR). We sought to evaluate progress made across the countries implementing NAP for effective response to AMR. A semi-structured survey tool was administered to obtain information from national focal persons on the implementation of strategic elements of NAP on AMR. This was followed by a Lessons Learnt Workshop in June 2019 at Douala, Cameroon, where focal persons made presentations on the country's progress. Later, a desktop review of the LLW report and other key documents was conducted. Countries in WHO AFR that have set up a national surveillance system and are enrolled into the WHO global antimicrobial resistance surveillance system have progressively increased to 30 (of 47 countries), of which 15 are already submitting surveillance data. Of the 20 countries at the Lessons Learnt Workshop, 14 have infection prevention and control (IPC) policies and functional healthcare facility IPC programs, 15 participate in the commemoration of the annual world hand hygiene days. Although almost all countries surveyed have national standard treatment guidelines, only five have incorporated the WHO AWaRe classification into the national essential medicines list. Fourteen of 20 countries have established an active/functional national secretariat/coordinating center for AMR. Discernible progress is being made on the implementation of NAP in WHO AFR region. Gaps identified in the strategic elements of action plans need to be filled for effective AMR control.

Global Antimicrobial Resistance and Use Surveillance System on the African continent: Early implementation 2017-2019.

Background: Antimicrobial resistance (AMR) is becoming a critical public health issue globally. The World Health Organization launched the Global Antimicrobial Resistance and Use Surveillance System (GLASS) to support the strengthening of the AMR evidence base. Objective: The article describes the evolution of national AMR surveillance systems and AMR data reporting of countries in the African continent between 2017 and 2019, and the constraints, perceived impact and value of the participation in GLASS. Methods: Data on implementation of national surveillance systems and AMR rates were submitted to GLASS between 2017 and 2019 and summarised though descriptive statistics. The information on constraints and perceived impact and value in GLASS participation was collected though a set of questionnaires. Results: Between 2017 and 2019, Egypt, Ethiopia, Madagascar, Malawi, Mali, Mozambique, Nigeria, South Africa, Sudan, Tunisia, Uganda and Zambia submitted data to GLASS. The main constraints listed are linked to scarce laboratory capacity and capability, limited staffing, budget issues, and data management. Moreover, while the data are not yet nationally representative, high resistance rates were reported to commonly-used antibiotics, as the emerging resistance to last treatment options. Conclusion: Despite the limitations, more and more countries in the African continent are working towards reaching a status that will enable them to report AMR data in a complete and systematic manner. Future improvements involve the expansion of routine surveillance capacity for several countries and the implementation of surveys that allow to effectively define the magnitude of AMR in the continent.

A multidrug-resistant Stenotrophomonas maltophilia clinical isolate from Kamuzu Central Hospital, Malawi.

Background: Stenotrophomonas maltophilia is a significant opportunistic pathogen that is associated with high mortality in immunocompromised individuals. In this study, we describe a multidrug-resistant (MDR) S. maltophilia clinical isolate from Kamuzu Central Hospital (KCH), Lilongwe, Malawi. Methods: A ceftriaxone and meropenem nonsusceptible isolate (Sm-MW08), recovered in December 2017 at KCH, was referred to the National Microbiology Reference Laboratory for identification. In April 2018, we identified the isolate using MALDI Biotyper mass spectrometry and determined its antimicrobial susceptibility profile using microdilution methods. Sm-MW08 was analysed by S1-PFGE, PCR, and Sanger sequencing, in order to ascertain the genotypes that were responsible for the isolate's multidrug-resistance (MDR) phenotype. Results: Sm-MW08 was identified as S. maltophilia and exhibited resistance to a range of antibiotics, including all ß-lactams, aminoglycosides (except arbekacin), chloramphenicol, minocycline, fosfomycin and fluoroquinolones, but remained susceptible to colistin and trimethoprim-sulfamethoxazole. The isolate did not harbour any plasmid but did carry chromosomally-encoded blaL1 metallo-ß-lactamase and blaL2 ß-lactamase genes; this was consistent with the isolate's resistance profile. No other resistance determinants were detected, suggesting that the MDR phenotype exhibited by Sm-MW08 was innate. Conclusion: Herein, we have described an MDR S. maltophilia from KCH in Malawi, that was resistant to almost all locally available antibiotics. We therefore recommend the practice of effective infection prevention measures to curtail spread of this organism.

A multidrug-resistant Stenotrophomonas maltophilia clinical isolate from Kamuzu Central Hospital, Malawi

Background Stenotrophomonas maltophilia is a significant opportunistic pathogen that is associated with high mortality in immunocompromised individuals. In this study, we describe a multidrug-resistant (MDR) S. maltophilia clinical isolate from Kamuzu Central Hospital (KCH), Lilongwe, Malawi. Methods: A ceftriaxone and meropenem nonsusceptible isolate (Sm-MW08), recovered in December 2017 at KCH, was referred to theNational Microbiology Reference Laboratory for identification. In April 2018, we identified the isolate using MALDI Biotyper mass spectrometry and determined its antimicrobial susceptibility profile using microdilution methods. Sm-MW08 was analysed by S1-PFGE, PCR, and Sanger sequencing, in order to ascertain the genotypes that were responsible for the isolate`s multidrug-resistance (MDR) phenotype. Results Sm-MW08 was identified as S. maltophilia and exhibited resistance to a range of antibiotics, including all ß-lactams, aminoglycosides (except arbekacin), chloramphenicol, minocycline, fosfomycin and fluoroquinolones, but remained susceptible to colistin and trimethoprim-sulfamethoxazole. The isolate did not harbour any plasmid but did carry chromosomally-encoded blaL1 metallo-ßlactamase and blaL2 ß-lactamase genes; this was consistent with the isolate's resistance profile. No other resistance determinants were detected, suggesting that the MDR phenotype exhibited by Sm-MW08 was innate. Conclusion : Herein, we have described an MDR S. maltophilia from KCH in Malawi, that was resistant to almost all locally available antibiotics. We therefore recommend the practice of effective infection prevention measures to curtail spread of this organism

Field Evaluation of Cholkit Rapid Diagnostic Test for Vibrio Cholerae O1 During a Cholera Outbreak in Malawi, 2018.

Rapid diagnostic tests (RDTs) for cholera are an important emerging tool for surveillance, yet the currently available tests have several limitations. We assess the performance of a new RDT, Cholkit, during a cholera outbreak in Malawi compared with culture and find a sensitivity of 93.0% (95% CI, 83.0%-98.1%) and a specificity of 95.7% (95% CI, 78.1%-100.0%).

Feasibility Study of the World Health Organization Health Care Facility-Based Antimicrobial Stewardship Toolkit for Low- and Middle-Income Countries.

Antimicrobial stewardship (AMS) has emerged as a systematic approach to optimize antimicrobial use and reduce antimicrobial resistance. To support the implementation of AMS programs, the World Health Organization developed a draft toolkit for health care facility AMS programs in low- and middle-income countries. A feasibility study was conducted in Bhutan, the Federated States of Micronesia, Malawi, and Nepal to obtain local input on toolkit content and implementation of AMS programs. This descriptive qualitative study included semi-structured interviews with national- and facility-level stakeholders. Respondents identified AMS as a priority and perceived the draft toolkit as a much-needed document to further AMS program implementation. Facilitators for implementing AMS included strong national and facility leadership and clinical staff engagement. Barriers included lack of human and financial resources, inadequate regulations for prescription antibiotic sales, and insufficient AMS training. Action items for AMS implementation included improved laboratory surveillance, establishment of a stepwise approach for implementation, and mechanisms for reporting and feedback. Recommendations to improve the AMS toolkit's content included additional guidance on defining the responsibilities of the committees and how to prioritize AMS programming based on local context. The AMS toolkit was perceived to be an important asset as countries and health care facilities move forward to implement AMS programs.

First Identification and genomic characterization of multidrug-resistant carbapenemase-producing Enterobacteriaceae clinical isolates in Malawi, Africa.

Purpose. Carbapenemase-producing Enterobacteriaceae (CPE) have become a global concern and a serious threat to human health due to their resistance to multiple antibiotics. In this study, we identified and characterized CPE for the first time in Malawi, southeastern Africa.Methodology. We investigated the possible presence of carbapenemases among a collection of 200 ceftriaxone-nonsusceptible Gram-negative clinical isolates obtained from five Malawian hospitals between January 2016 and December 2017, using both phenotypic and genotypic tests. Molecular typing of CPE was done by PFGE, multilocus sequence typing (ST) or phylogenetic grouping. Resistant plasmids were characterized by S1 PFGE, Southern blotting and conjugation assays.Results. Out of 200 isolates, we detected 16 (8 %) CPE of which all originated from one referral hospital, Kamuzu Central Hospital, in the Central part of Malawi. Of 16 isolates, seven Klebsiella pneumoniae ST340/CC258 carried bla KPC-2, two Escherichia coli ST636 (phylogroup B2) carried bla NDM-5, six E. coli ST617 (phylogroup A) and one Klebsiella variicola carried bla OXA-48. All carbapenemases were plasmid-encoded, but only bla NDM-5-carrying plasmids could be conjugated. Most isolates co-harboured other ß-lactamases and consequently exhibited a wider spectrum of resistance to commonly used antibiotics. We observed indistinguishable genetic profiles between strain types, despite originating from different wards, suggesting acquisition during admission and intra-hospital spread.Conclusion. This report strongly suggests a probable existence of highly resistant various types of CPE organisms in Malawi including KPC-2-producing K. pneumoniae ST340/CC258, a known high-risk epidemic lineage.

Whole genome sequence of Vibrio cholerae directly from dried spotted filter paper.

BACKGROUND: Global estimates for cholera annually approximate 4 million cases worldwide with 95,000 deaths. Recent outbreaks, including Haiti and Yemen, are reminders that cholera is still a global health concern. Cholera outbreaks can rapidly induce high death tolls by overwhelming the capacity of health facilities, especially in remote areas or areas of civil unrest. Recent studies demonstrated that stool specimens preserved on filter paper facilitate molecular analysis of Vibrio cholerae in resource limited settings. Specimens preserved in a rapid, low-cost, safe and sustainable manner for sequencing provides previously unavailable data about circulating cholera strains. This may ultimately contribute new information to shape public policy response on cholera control and elimination. METHODOLOGY/PRINCIPAL FINDINGS: Whole genome sequencing (WGS) recovered close to a complete sequence of the V. cholerae O1 genome with satisfactory genome coverage from stool specimens enriched in alkaline peptone water (APW) and V. cholerae culture isolates, both spotted on filter paper. The minimum concentration of V. cholerae DNA sufficient to produce quality genomic information was 0.02 ng/µL. The genomic data confirmed the presence or absence of genes of epidemiological interest, including cholera toxin and pilus loci. WGS identified a variety of diarrheal pathogens from APW-enriched specimen spotted filter paper, highlighting the potential for this technique to explore the gut microbiome, potentially identifying co-infections, which may impact the severity of disease. WGS demonstrated that these specimens fit within the current global cholera phylogenetic tree, identifying the strains as the 7th pandemic El Tor. CONCLUSIONS: WGS results allowed for mapping of short reads from APW-enriched specimen and culture isolate spotted filter papers. This provided valuable molecular epidemiological sequence information on V. cholerae strains from remote, low-resource settings. These results identified the presence of co-infecting pathogens while providing rare insight into the specific V. cholerae strains causing outbreaks in cholera-endemic areas.

Effectiveness of oral cholera vaccine in preventing cholera among fishermen in Lake Chilwa, Malawi: A case-control study.

BACKGROUND: In response to a cholera outbreak among mobile, difficult-to-reach fishermen on Lake Chilwa, Malawi in 2016, a novel vaccine distribution strategy exploited the proven vaccine thermostability. Fishermen, while taking the first vaccine dose under supervision, received the second dose in a sealed bag, and were told to drink it two weeks later. This study assessed short-term vaccine protection of this strategy. METHODS: Patients with diarrhoea admitted to health facilities around lake were interviewed and a stool sample collected for PCR testing. Vaccine effectiveness was assessed in a case-control test-negative design by comparing cases (PCR-positive for V. cholerae O1) and controls (patients with diarrhoea but PCR-negative) and with the screening method that compared the proportions of vaccinated among cholera cases versus the general fishermen population. RESULTS: Of 145 study participants, 120 were fishermen living on the lake. Vaccine effectiveness at three-months was 90.0% [95%CI:38.8;98.4] among fishermen and 83.3% [95%CI: 20.8; 96.5] among all participants in the case-control test-negative design, and 97.5% [95%CI: 90.9;99.3] with the screening method. CONCLUSION: This strategy was effective in providing short-term protection in fishermen against cholera. Further research is needed to determine the adding value of the second dose and to identify the optimal vaccination strategies for different contexts.