Pathogenic and commensal Escherichia coli from irrigation water show potential in transmission of extended spectrum and AmpC β-lactamases determinants to isolates from lettuce

There are few studies on the presence of extendedspectrum β-lactamases and AmpC β-lactamases (ESBL/AmpC) in bacteria that contaminate vegetables. The role of the production environment in ESBL/ AmpC gene transmission is poorly understood. The occurrence of ESBL/AmpC in Escherichia coli (n = 46) from lettuce and irrigation water and the role of irrigation water in the transmission of resistant E. coli were studied. The presence of ESBL/AmpC, genetic similarity and phylogeny were typed using genotypic and phenotypic techniques. The frequency of β-lactamase gene transfer was studied in vitro. ESBLs/AmpC were detected in 35 isolates (76%). Fourteen isolates (30%) produced both ESBLs/AmpC. Prevalence was highest in E. coli from lettuce (90%). Twenty-two isolates (48%) were multi-resistant with between two and five ESBL/AmpC genes. The major ESBL determinant was the CTX-M type (34 isolates). DHA (33% of isolates) were the dominant AmpC β lactamases. There was a high conjugation efficiency among the isolates, ranging from 3.5 × 10−2 to 1 × 10−2 ± 1.4 × 10−1 transconjugants per recipient. Water isolates showed a significantly higher conjugation frequency than those from lettuce. A high degree of genetic relatedness between E. coli from irrigation water and lettuce indicated possible common ancestry and pathway of transmission.We acknowledge the TWAS Fellowship for Research and Advanced Training, National Research Foundation and Vice-Chancellor Postdoctoral Fellowship Programme at the University of Pretoria for financing P. M. K. Njage during the research work. The sequence analysis facility was funded by the National Research Foundation of South Africa.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1751-7915am201

Extended-spectrum β-lactamase, shigatoxin and haemolysis capacity of O157 and non-O157 E. coli serotypes from producer-distributor bulk milk

We investigated for virulence genes (stx1, stx2 and hlyA), serotypes and extended-spectrum β-lactamases (ESBLs) producing capacity in O157 and non-O157 Escherichia coli isolated from producer-distributor bulk milk (PDBM). Fifteen different E. coli O-serogroups were observed from the isolates (n=121). The prevalence of stx1 and stx2 genes among the E. coli isolates was 8.3% and 11.6% (n=121), respectively, while 5.8% harboured both stx1 and stx2. Four E. coli isolates (3.3%) had ESBLs producing capacity, resisted multiple cephalosporins and aztreonam, and carried stx genes. Cluster analysis using GTG5 finger printing revealed a diversity of E. coli seropathotypes in PDBM which are known to be associated with human diarrhoeal diseases. These results highlight a potential risk posed on human health by the consumption of PDBM contaminated with pathogenic E. coli. A further quantitative risk assessment of the impact of pathogenic E. coli contamination in PDBM on human health is therefore recommended.Milk South Africahttp://www.elsevier.com/locate/idairyj2018-03-31hb2017Food Scienc

Association of health, nutrition, and socioeconomic variables with global antimicrobial resistance: a modelling study

Background: Although antimicrobial use is a key selector for antimicrobial resistance, recent studies have suggested that the ecological context in which antimicrobials are used might provide important factors for the prediction of the emergence and spread of antimicrobial resistance. Methods: We used 1547 variables from the World Bank dataset consisting of socioeconomic, developmental, health, and nutritional indicators; data from a global sewage-based study on antimicrobial resistance (abundance of antimicrobial resistance genes [ARGs]); and data on antimicrobial usage computed from the ECDC database and the IQVIA database. We characterised and built models predicting the global resistome at an antimicrobial class level. We used a generalised linear mixed-effects model to estimate the association between antimicrobial usage and ARG abundance in the sewage samples; a multivariate random forest model to build predictive models for each antimicrobial resistance class and to select the most important variables for ARG abundance; logistic regression models to test the association between the predicted country-level antimicrobial resistance abundance and the country-level proportion of clinical resistant bacterial isolates; finite mixture models to investigate geographical heterogeneities in the abundance of ARGs; and multivariate finite mixture models with covariates to investigate the effect of heterogeneity in the association between the most important variables and the observed ARG abundance across the different country subgroups. We compared our predictions with available clinical phenotypic data from the SENTRY Antimicrobial Surveillance Program from eight antimicrobial classes and 12 genera from 56 countries. Findings: Using antimicrobial use data from between Jan 1, 2016, and Dec 31, 2019, we found that antimicrobial usage was not significantly associated with the global ARG abundance in sewage (p=0·72; incidence rate ratio 1·02 [95% CI 0·92-1·13]), whereas country-specific World Bank's variables explained a large amount of variation. The importance of the World Bank variables differed between antimicrobial classes and countries. Generally, the estimated global ARG abundance was positively associated with the prevalence of clinical phenotypic resistance, with a strong association for bacterial groups in the human gut. The associations between bacterial groups and ARG abundance were positive and significantly different from zero for the aminoglycosides (three of the four of the taxa tested), β-lactam (all the six microbial groups), fluoroquinolones (seven of nine of the microbial groups), glycopeptide (one microbial group tested), folate pathway antagonists (four of five microbial groups), and tetracycline (two of nine microbial groups). Interpretation: Metagenomic analysis of sewage is a robust approach for the surveillance of antimicrobial resistance in pathogens, especially for bacterial groups associated with the human gut. Additional studies on the associations between important socioeconomic, nutritional, and health factors and antimicrobial resistance should consider the variation in these associations between countries and antimicrobial classes.</b

Draft Genome Sequences of Enterococcus mundtii Strains Isolated from Beef Slaughterhouses in Kenya

We present here draft genome sequences of Enterococcus mundtii strains K7-EM, P2-EM, C11-EM, and H18-EM, which were isolated from slaughterhouse equipment, carcasses, and personnel of small- and medium-sized beef slaughterhouses in Kenya

Systematic review and meta‐analysis of the impact of decontamination interventions on the prevalence and concentration of Salmonella in broiler chickens during primary processing

SummarySystematic review and meta‐analysis aggregate quantitative data from different studies into unified effect size estimates with better statistical power in risk assessment model parameterisation. This study uses systematic review and meta‐analysis to estimate Salmonella decontamination during broiler slaughter from scalding to post‐chilling, with meta‐regression applied to explore modifier variables. Data from 161 studies published between 1998 and 2022 was extracted from thirty‐five articles identified in the systematic review process with meta‐analysis and meta‐regression performed using the metafor package (version 2.0‐0) in R statistical environment (version 3.6.0). The analysis revealed carcass wash (1.31 log$_{10}$ CFU/carcass reduction in odds; P < 0.01) and chilling (121.50% reduction in relative risk; P < 0.01) had significant reduction on Salmonella concentration and prevalence, respectively. Chemical additives reduced the concentration (0.98 log$_{10}$ CFU/carcass; P < 0.01) and prevalence (64.74% relative risk; P < 0.01) but the efficacy of physical methods was not conclusive. Application of decontaminants through immersion was superior (0.90 log$_{10}$ CFU/carcass; P < 0.01) to spraying (0.72 log$_{10}$ CFU/carcass; P < 0.01). Adjusting the pH sequentially of electrolysed water, acetic acid and trisodium phosphate reduced the odds of Salmonella concentration by more than 2 log cycles and the relative risk by more than 100%. The results provide trends in the concentration and prevalence of Salmonella during the broilers slaughter process with application of decontamination interventions and provide a basis for control decision‐making and quantitative microbial risk assessment

Systematic-review and meta-analysis on effect of decontamination interventions on prevalence and concentration of Campylobacter spp. during primary processing of broiler chickens

Please read abstract in the article.Partly supported by the Australia Awards Africa Post-Doctoral Fellowship.https://www.elsevier.com/locate/fmhj2023Consumer ScienceFood Scienc

Development of disease-specific, context-specific surveillance models : avian influenza (H5N1)-related risks and behaviours in African countries

Avian influenza virus (H5N1) is a rapidly disseminating infection that affects poultry and, potentially, humans. Because the avian virus has already adapted to several mammalian species, decreasing the rate of avian-mammalian contacts is critical to diminish the chances of a total adaptation of H5N1 to humans. To prevent the pandemic such adaptation could facilitate, a biology-specific disease surveillance model is needed, which should also consider geographical and socio-cultural factors. Here we conceptualized a surveillance model meant to capture H5N1-related biological and cultural aspects, which included food processing, trade, and cooking-related practices, as well as incentives (or disincentives) for desirable behaviours. This proof-of-concept was tested with data collected from 378 Egyptian and Nigerian sites (local [backyard] producers/ live bird markets /village abattoirs/ commercial abattoirs and veterinary agencies). Findings revealed numerous opportunities for pathogens to disseminate, as well as lack of incentives to adopt preventive measures, and factors that promoted epidemic dissemination. Supporting such observations, the estimated risk for H5N1-related human mortality was higher than previously reported. The need for multi-dimensional disease surveillance models, which may detect risks at higher levels than models that only measure one factor or outcome, was supported. To develop efficient surveillance systems, interactions should be captured, which include but exceed biological factors. This low-cost and easily implementable model, if conducted over time, may identify focal instances where tailored policies may diminish both endemicity and the total adaptation of H5N1 to the human species.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1863-23782017-02-28hb2016Food ScienceProduction Animal Studie