Comparative analysis of clinical breakpoints, normalized resistance interpretation and epidemiological cut-offs in interpreting antimicrobial resistance of Escherichia coli isolates originating from poultry in different farm types in Tanzania

This research article was published in the Access Microbiology, an open research platform Volume 5, Issue 7Introduction. Existing breakpoint guidelines are not optimal for interpreting antimicrobial resistance (AMR) data from animal studies and low-income countries, and therefore their utility for analysing such data is limited. There is a need to integrate diverse data sets, such as those from low-income populations and animals, to improve data interpretation. Gap statement. There is very limited research on the relative merits of clinical breakpoints, epidemiological cut-offs (ECOFFs) and normalized resistance interpretation (NRI) breakpoints in interpreting microbiological data, particularly in animal studies and studies from low-income countries. Aim. The aim of this study was to compare antimicrobial resistance in Escherichia coli isolates using ECOFFs, CLSI and NRI breakpoints. Methodology. A total of 59 non-repetitive poultry isolates were selected for investigation based on lactose fermentation on MacConkey agar and subsequent identification and confirmation as E. coli using chromogenic agar and uidA PCR. Kirby Bauer disc diffusion was used for susceptibility testing. For each antimicrobial agent, inhibition zone diameters were measured, and ECOFFs, CLSI and NRI bespoke breakpoints were used for resistance interpretation. Results. According to the interpretation of all breakpoints except ECOFFs, tetracycline resistance was significantly higher (TET) (67.8 –69.5 %), than those for ciprofloxacin (CIPRO) (18.6 –32.2 %), imipenem (IMI) (3.4 –35 %) and ceftazidime (CEF) (1.7 –45.8 %). Prevalence estimates of AMR using CLSI and NRI bespoke breakpoints did not differ for CEF (1.7 % CB and 1.7 % COWT ), IMI (3.4 % CB and 4.0 % COWT ) and TET (67.8 % CB and 69.5 % COWT ). However, with ECOFFs, AMR estimates for CEF, IMI and CIP were sig- nificantly higher (45.8, 35.6 and 64.4 %, respectively; P<0.05). Across all the three breakpoints, resistance to ciprofloxacin varied significantly (32.2 % CB, 64.4 % ECOFFs and 18.6 % COWT , P<0.05). Conclusion. AMR interpretation is influenced by the breakpoint used, necessitating further standardization, especially for microbiological breakpoints, in order to harmonize outputs. The AMR ECOFF estimates in the present study were significantly higher compared to CLSI and NRI

Antimicrobial resistant coliforms across four poultry production systems in Arusha and Moshi, Tanzania

This research article was published in the PAMJ One Health, Volume 7, Article 4, 11 Jan 2022Introduction: resistance to antimicrobials poses a threat to human and animal health. This study aimed to determine the prevalence of resistant coliforms in poultry cloacal samples collected from different poultry systems in Arusha and Moshi districts, Tanzania. Methods: ten administrative wards were randomly chosen in Moshi and Arusha urban districts, with a random selection of one representative farm in each ward per production system (extensive, semi-intensive, intensive, and broiler systems). Per farm, 10 chickens were sampled using cloacal swabs. Samples were tested for the presence of coliforms using MacConkey agar without or with tetracycline, ciprofloxacin, ceftazidime, and Imipenem. R software was used for data analysis. Results: of the 80 farms targeted, samples were collected from 79 farms representing a total of 746 samples, of which 648 (86.8%) had coliforms corresponding to 74 of the 79 sampled farms. There was no significant difference in the overall prevalence of coliforms between Moshi (86%) and Arusha districts (87%) (p=0.81). The overall proportions of resistant coliforms in Arusha and Moshi varied depending on each antimicrobial type. The prevalence of coliforms resistant to tetracycline (95%) across all farm types in both districts was higher compared to ciprofloxacin (72%), imipenem (71%), and ceftazidime (84%) (p<0.0001). The median counts of coliform resistance (in log cfu) ranged from 4 to 10, with no significant distinctions between antimicrobial types. Conclusion: there is a widespread presence of antimicrobial resistant coliforms in poultry production systems. High tetracycline resistance was observed across all farm types in both districts

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Assessment of hepatitis B vaccination status and hepatitis B surface antibody titres among health care workers in selected public health hospitals in Kenya.

Healthcare workers (HCWs) have a significant occupational risk of hepatitis B virus (HBV) infection. Vaccination remains the most effective measure recommended to avert the risk. However, there's limited information on hepatitis B vaccine uptake rates and the seroprotection status of HCWs, especially in sub-Saharan Africa. This study aimed to assess hepatitis B vaccination status and also seroprotection status of HCWs in three selected public hospitals in Kenya. This was a cross-sectional study carried out among HCWs at Kenyatta National Hospital (KNH), Naivasha and Mbagathi County hospitals. Data on participants' demographics and hepatitis B vaccination status was collected using an interviewer-guided questionnaire. Blood samples were collected and tested for hepatitis B surface antigen (HBsAg), hepatitis B surface antibodies (anti-HBs), and hepatitis B core antibodies (anti-HBc) using Enzyme Linked Immuno Sorbent Assay technique. Data were analyzed using Statistical Package for the Social Sciences (SPSS) and Graph pad prism. Of the 145 eligible HCWs, 120 (82.8%) were vaccinated, with 77 (53.1%) having received the recommended three doses. Three quarters (108/145) of the vaccinated HCWs were seroprotected (titres ≥10 mIU/ml) against HBV infection, while 16.6% were non-responders (titres <10 mIU/ml). Vaccination with more than two doses and HBV exposure were significantly associated with anti-HBs titre levels (P<0.05). HCWs who received less than 2 doses of the vaccine were 70% less likely to have high anti-HBs titre levels (aOR, 0.3; 95% CI, 0.1-0.8; P = 0.013). Nearly all HCWs were vaccinated against hepatitis B virus. The majority of all HCWs were seroprotected against hepatitis B virus but a number of them had an insufficient immunity to the virus despite vaccination or prior exposure. There's need to sensitize HCWs and enforce mandatory full vaccination as per the recommended vaccination schedule

Interviewer-guided questionnaire.

Healthcare workers (HCWs) have a significant occupational risk of hepatitis B virus (HBV) infection. Vaccination remains the most effective measure recommended to avert the risk. However, there’s limited information on hepatitis B vaccine uptake rates and the seroprotection status of HCWs, especially in sub-Saharan Africa. This study aimed to assess hepatitis B vaccination status and also seroprotection status of HCWs in three selected public hospitals in Kenya. This was a cross-sectional study carried out among HCWs at Kenyatta National Hospital (KNH), Naivasha and Mbagathi County hospitals. Data on participants’ demographics and hepatitis B vaccination status was collected using an interviewer-guided questionnaire. Blood samples were collected and tested for hepatitis B surface antigen (HBsAg), hepatitis B surface antibodies (anti–HBs), and hepatitis B core antibodies (anti–HBc) using Enzyme Linked Immuno Sorbent Assay technique. Data were analyzed using Statistical Package for the Social Sciences (SPSS) and Graph pad prism. Of the 145 eligible HCWs, 120 (82.8%) were vaccinated, with 77 (53.1%) having received the recommended three doses. Three quarters (108/145) of the vaccinated HCWs were seroprotected (titres ≥10 mIU/ml) against HBV infection, while 16.6% were non–responders (titres PP = 0.013). Nearly all HCWs were vaccinated against hepatitis B virus. The majority of all HCWs were seroprotected against hepatitis B virus but a number of them had an insufficient immunity to the virus despite vaccination or prior exposure. There’s need to sensitize HCWs and enforce mandatory full vaccination as per the recommended vaccination schedule.</div

Anti–HBs response based on vaccination and HBV exposure status among HCW at KNH, Mbagathi County and Naivasha sub-county hospitals.

Anti–HBs response based on vaccination and HBV exposure status among HCW at KNH, Mbagathi County and Naivasha sub-county hospitals.</p

Demographic characteristics and hepatitis B vaccination status of participating HCW at KNH, Mbagathi County and Naivasha sub-county hospitals (N = 145).

Demographic characteristics and hepatitis B vaccination status of participating HCW at KNH, Mbagathi County and Naivasha sub-county hospitals (N = 145).</p

Classification of immune responses based on anti-HBs titres, vaccination and HBV exposure status among HCW at KNH, Mbagathi County and Naivasha sub-county hospitals.

Classification of immune responses based on anti-HBs titres, vaccination and HBV exposure status among HCW at KNH, Mbagathi County and Naivasha sub-county hospitals.</p

Odds ratio for covariates that impact anti-HBs production among HCW.

ORs and 95% CI with significant associations indicated at P<0.05 Abbreviations: OR, odds ratio; cOR, crude odds ratio; aOR, adjusted odds ratio; CI, confidence interval.</p