Contamination of the minnow Rastrineobola argenta, through handling at landing sites and retail markets around Lake Victoria

Background: The quality of fish could be a challenge both locally and internationally as microbial contaminants may result in infections of humans when seafood is handled unhygienically. This is because enteric bacteria such as Escherichia coli, Staphylococcus aureus, Salmonella spp. and Vibrio cholerae are likely to  accumulate in fish where low hygienic standards are maintained. Therefore, studies on fish contamination are critical for the acceptance of fish food locally and in international markets.Objective: To evaluate and compare the microbiological quality of R. argentea at the fish landing sites and local retail markets in Homa Bay County.Design: Purposive, cross-sectional study.Setting: Fish landing sites and retail markets in Homa Bay CountySubject: Studies on fish contamination are critical for the acceptance of fish food locally and in international markets. In this study, Rastrineobola argentea were examined for microbial loads.Results: Samples indicated high levels of coliforms and Escherichia coli in fish. At the landing sites, coliforms ranged from 1.6 x 103 to 4.0 x 103 while E. coli was between 0.8 x101 and 4.8 x 102. In water samples, coliforms ranged between 1.3 x 103 and 1.8x106 / ml whereas E. coli was 1.1x102 to 4.6x101. Personnel hands were found to be contaminated with Salmonella typhimurium and Shigella  dysenteriae. The samples from markets had coliform and E. coli at 5.0x104 to 9.0x105 and 2.0x102 to 4.0x102 respectively.Conclusion: The findings demonstrate that precaution should be taken to improve the hygiene levels along the value chains to ensure that the quality of fish is not compromised

Virulence and antimicrobial resistance genes are enriched in the plasmidome of clinical Escherichia coli isolates compared with wastewater isolates from western Kenya

Many low-middle income countries in Africa have poorly-developed infectious disease monitoring systems. Here, we employed whole genome sequencing (WGS) to investigate the presence/absence of antimicrobial resistance (AMR) and virulence-associated (VA) genes in a collection of clinical and municipal wastewater Escherichia coli isolates from Kakamega, west Kenya. We were particularly interested to see whether, given the association between infection and water quality, the isolates from these geographically-linked environments might display similar genomic signatures. Phylogenetic analysis based on the core genes common to all of the isolates revealed two broad divisions, corresponding to the commensal/enterotoxigenic E. coli on the one hand, and uropathogenic E. coli on the other. Although the clinical and wastewater isolates each contained a very similar mean number of antibiotic resistance-encoding genes, the clinical isolates were enriched in genes required for in-host survival. Furthermore, and although the chromosomally encoded repertoire of these genes was similar in all sequenced isolates, the genetic composition of the plasmids from clinical and wastewater E. coli was more habitat-specific, with the clinical isolate plasmidome enriched in AMR and VA genes. Intriguingly, the plasmid-borne VA genes were often duplicates of genes already present on the chromosome, whereas the plasmid-borne AMR determinants were more specific. This reinforces the notion that plasmids are a primary means by which infection-related AMR and VA-associated genes are acquired and disseminated among these strains.The Cambridge–Africa ALBORADA Research Fund, the Academy of Medical Sciences GCRF networking grant, a studentship from the NC3Rs and a studentship from the Cambridge Trust-CONACyT.http://www.elsevier.com/locate/meegid2022-02-26hj2021BiochemistryGeneticsMicrobiology and Plant Patholog

A comparison of all-cause and cause-specific mortality by household socioeconomic status across seven INDEPTH network health and demographic surveillance systems in sub-Saharan Africa

Background: Understanding socioeconomic disparities in all-cause and cause-specific mortality can help inform prevention and treatment strategies. Objectives: To quantify cause-specific mortality rates by socioeconomic status across seven health and demographic surveillance systems (HDSS) in five countries (Ethiopia, Kenya, Malawi, Mozambique, and Nigeria) in the INDEPTH Network in sub-Saharan Africa. Methods: We linked demographic residence data with household survey data containing living standards and education information we used to create a poverty index. Person-years lived and deaths between 2003 and 2016 (periods varied by HDSS) were stratified in each HDSS by age, sex, year, and number of deprivations on the poverty index (0–8). Causes of death were assigned to each death using the InterVA-4 model based on responses to verbal autopsy questionnaires. We estimated rate ratios between socioeconomic groups (2–4 and 5–8 deprivations on our poverty index compared to 0–2 deprivations) for specific causes of death and calculated life expectancy for the deprivation groups. Results: Our pooled data contained almost 3.5 million person-years of observation and 25,038 deaths. All-cause mortality rates were higher among people in households with 5–8 deprivations on our poverty index compared to 0–2 deprivations, controlling for age, sex, and year (rate ratios ranged 1.42 to 2.06 across HDSS sites). The poorest group had consistently higher death rates in communicable, maternal, neonatal, and nutritional conditions (rate ratios ranged 1.34–4.05) and for non-communicable diseases in several sites (1.14–1.93). The disparities in mortality between 5–8 deprivation groups and 0–2 deprivation groups led to lower life expectancy in the higher-deprivation groups by six years in all sites and more than 10 years in five sites. Conclusions: We show large disparities in mortality on the basis of socioeconomic status across seven HDSS in sub-Saharan Africa due to disparities in communicable disease mortality and from non-communicable diseases in some sites. Life expectancy gaps between socioeconomic groups within sites were similar to the gaps between high-income and lower-middle-income countries. Prevention and treatment efforts can benefit from understanding subpopulations facing higher mortality from specific conditions

Virulence and antimicrobial resistance genes are enriched in the plasmidome of clinical Escherichia coli isolates compared with wastewater isolates from western Kenya.

Many low-middle income countries in Africa have poorly-developed infectious disease monitoring systems. Here, we employed whole genome sequencing (WGS) to investigate the presence/absence of antimicrobial resistance (AMR) and virulence-associated (VA) genes in a collection of clinical and municipal wastewater Escherichia coli isolates from Kakamega, west Kenya. We were particularly interested to see whether, given the association between infection and water quality, the isolates from these geographically-linked environments might display similar genomic signatures. Phylogenetic analysis based on the core genes common to all of the isolates revealed two broad divisions, corresponding to the commensal/enterotoxigenic E. coli on the one hand, and uropathogenic E. coli on the other. Although the clinical and wastewater isolates each contained a very similar mean number of antibiotic resistance-encoding genes, the clinical isolates were enriched in genes required for in-host survival. Furthermore, and although the chromosomally encoded repertoire of these genes was similar in all sequenced isolates, the genetic composition of the plasmids from clinical and wastewater E. coli was more habitat-specific, with the clinical isolate plasmidome enriched in AMR and VA genes. Intriguingly, the plasmid-borne VA genes were often duplicates of genes already present on the chromosome, whereas the plasmid-borne AMR determinants were more specific. This reinforces the notion that plasmids are a primary means by which infection-related AMR and VA-associated genes are acquired and disseminated among these strains

Community suicide rates and related factors within a surveillance platform in Western Kenya

Background Suicide is an important contributor to the burden of mental health disorders, but community-based suicide data are scarce in many low- and middle-income countries (LMIC) including Kenya. Available data on suicide underestimates the true burden due to underreporting related to stigma and legal restrictions, and under-representation of those not utilizing health facilities. Methods We estimated the cumulative incidence of suicide via verbal autopsies from the Health and Demographic Surveillance System (HDSS) in Kisumu County, Kenya. We then used content analysis of open history forms among deaths coded as accidents to identify those who likely died by suicide but were not coded as suicide deaths. We finally conducted a case-control study of suicides (both verbal autopsy confirmed and likely suicides) compared to accident-caused deaths to assess factors associated with suicide in this HDSS. Results A total of 33 out of 4306 verbal autopsies confirmed suicide as the cause of death. Content analysis of a further 228 deaths originally attributed to accidents identified 39 additional likely suicides. The best estimate of suicide-specific mortality rate was 14.7 per 100,000 population per year (credibility window = 11.3 – 18.0). The most common reported method of death was self-poisoning (54%). From the case-control study interpersonal difficulties and stressful life events were associated with increased odds of suicide in both confirmed suicides and confirmed combined with suspected suicides. Other pertinent factors such as age and being male differed depending upon which outcome was used. Conclusion Suicide is common in this area, and interventions are needed to address drivers. The twofold increase in the suicide-specific mortality rate following incorporation of misattributed suicide deaths exemplify underreporting and misclassification of suicide cases at community level. Further, verbal autopsies may underreport suicide specifically among older and female populations