Cluster analysis of resistance combinations in Escherichia coli from different human and animal populations in Germany 2014-2017

Integrated surveillance systems for antibiotic resistance in a One Health context: a scoping review

BACKGROUND

Antibiotic resistance (ABR) has emerged as a major threat to health. Properly informed decisions to mitigate this threat require surveillance systems that integrate information on resistant bacteria and antibiotic use in humans, animals, and the environment, in line with the One Health concept. Despite a strong call for the implementation of such integrated surveillance systems, we still lack a comprehensive overview of existing organizational models for integrated surveillance of ABR. To address this gap, we conducted a scoping review to characterize existing integrated surveillance systems for ABR.

METHODS

The literature review was conducted using the PRISMA guidelines. The selected integrated surveillance systems were assessed according to 39 variables related to their organization and functioning, the socio-economic and political characteristics of their implementation context, and the levels of integration reached, together with their related outcomes. We conducted two distinct, complementary analyses on the data extracted: a descriptive analysis to summarize the characteristics of the integrated surveillance systems, and a multiple-correspondence analysis (MCA) followed by a hierarchical cluster analysis (HCA) to identify potential typology for surveillance systems.

RESULTS

The literature search identified a total of 1330 records. After the screening phase, 59 references were kept from which 14 integrated surveillance systems were identified. They all operate in high-income countries and vary in terms of integration, both at informational and structural levels. The different systems combine information from a wide range of populations and commodities -in the human, animal and environmental domains, collection points, drug-bacterium pairs, and rely on various diagnostic and surveillance strategies. A variable level of collaboration was found for the governance and/or operation of the surveillance activities. The outcomes of integration are poorly described and evidenced. The 14 surveillance systems can be grouped into four distinct clusters, characterized by integration level in the two dimensions. The level of resources and regulatory framework in place appeared to play a major role in the establishment and organization of integrated surveillance.

CONCLUSIONS

This study suggests that operationalization of integrated surveillance for ABR is still not well established at a global scale, especially in low and middle-income countries and that the surveillance scope is not broad enough to obtain a comprehensive understanding of the complex dynamics of ABR to appropriately inform mitigation measures. Further studies are needed to better characterize the various integration models for surveillance with regard to their implementation context and evaluate the outcome of these models.

Improvements of weaned pigs barn hygiene to reduce the spread of antimicrobial resistance

The spread of antimicrobial resistance (AMR) in animal husbandry is usually attributed to the use of antibiotics and poor hygiene and biosecurity. We therefore conducted experimental trials to improve hygiene management in weaned pig houses and assessed the impact on the spread. For each of the two groups examined, the experimental group (EG) and the control group (CG), three replicate batches of piglets from the same pig breeder, kept in pre-cleaned flat decks, were analyzed. In the flat decks of the experimental groups, the hygiene conditions (cleaning, disinfection, dust removal and fly control) were improved, while regular hygiene measures were carried out in the control groups. The occurrence and spread of AMR were determined in Escherichia coli (E. coli; resistance indicator) using cultivation-dependent (CFU) and -independent (qPCR) methods as well as whole genome sequencing of isolates in samples of various origins, including feces, flies, feed, dust and swabs. Surprisingly, there were no significant differences (p > 0.05) in the prevalence of resistant E. coli between the flat decks managed with conventional techniques and those managed with improved techniques. Selective cultivation delivered ampicillin- and sulfonamide-resistant E. coli proportions of up to 100% and 1.2%, respectively. While 0.5% E. coli resistant to cefotaxime and no ciprofloxacin resistance were detected. There was a significant difference (p < 0.01) in the abundance of the blaTEM-1 gene in fecal samples between EG and CG groups. The colonization of piglets with resistant pathogens before arrival, the movement of flies in the barn and the treatment of bacterial infections with antibiotics obscured the effects of hygiene improvement. Biocide tolerance tests showed no development of resistance to the farm regular disinfectant. Managing hygiene alone was insufficient for reducing antimicrobial resistances in piglet rearing. We conclude that the complex factors contributing to the presence and distribution of AMR in piglet barns underscore the necessity for a comprehensive management strategy.

[Bacterial zoonoses of public health importance in Germany-incidence, distribution, and modes of transmission]

Bacterial zoonotic pathogens are often the cause of diseases, sometimes with severe outcomes. They are mutually transferable between animals (both wild and domestic) and humans. The transmission paths are very variable and include oral intake via food, respiratory infection via droplets and aerosols, or infections via vectors such as tick bites or rodent contact. Furthermore, the emergence and spread of antibiotic-resistant bacterial pathogens is of paramount public health concern.The likelihood of further spread is influenced by various factors. These include the increase in international trade, the endangerment of animal habitats, and the increasingly closer contact between humans and wild animals. Additionally, changes in livestock and climate change may also contribute. Therefore, research into zoonoses serves to protect human and animal health and is of particular social, political, and economic importance.The aim of this review article is to present the range of infectious diseases caused by bacterial zoonotic pathogens in order to provide a better understanding of the important work in public health services, animal health services, and food safety control. The different transmission routes, epidemic potentials, and epidemiological measures of the exemplary selected diseases show the challenges for the public health system to monitor and control the spread of these bacterial pathogens in order to protect the population from disease.

Clinical epidemiology and case fatality due to antimicrobial resistance in Germany: a systematic review and meta-analysis, 1 January 2010 to 31 December 2021

BackgroundAntimicrobial resistance (AMR) is of public health concern worldwide.AimWe aimed to summarise the German AMR situation for clinicians and microbiologists.MethodsWe conducted a systematic review and meta-analysis of 60 published studies and data from the German Antibiotic-Resistance-Surveillance (ARS). Primary outcomes were AMR proportions in bacterial isolates from infected patients in Germany (2016-2021) and the case fatality rates (2010-2021). Random and fixed (common) effect models were used to calculate pooled proportions and pooled case fatality odds ratios, respectively.ResultsThe pooled proportion of meticillin resistance in Staphylococcus aureus infections (MRSA) was 7.9% with a declining trend between 2014 and 2020 (odds ratio (OR) = 0.89; 95% CI: 0.886-0.891; p < 0.0001), while vancomycin resistance in Enterococcus faecium (VRE) bloodstream infections increased (OR = 1.18; (95% CI: 1.16-1.21); p < 0.0001) with a pooled proportion of 34.9%. Case fatality rates for MRSA and VRE were higher than for their susceptible strains (OR = 2.29; 95% CI: 1.91-2.75 and 1.69; 95% CI: 1.22-2.33, respectively). Carbapenem resistance in Gram-negative pathogens (Klebsiella pneumoniae, Acinetobacter baumannii, Enterobacter spp. and Escherichia coli) was low to moderate (< 9%), but resistance against third-generation cephalosporins and fluoroquinolones was moderate to high (5-25%). Pseudomonas aeruginosa exhibited high resistance against carbapenems (17.0%; 95% CI: 11.9-22.8), third-generation cephalosporins (10.1%; 95% CI: 6.6-14.2) and fluoroquinolones (24.9%; 95% CI: 19.3-30.9). Statistical heterogeneity was high (I2 > 70%) across studies reporting resistance proportions.ConclusionContinuous efforts in AMR surveillance and infection prevention and control as well as antibiotic stewardship are needed to limit the spread of AMR in Germany.

Genomic analysis of Escherichia coli circulating in the Brazilian poultry sector

Escherichia coli are gut commensal bacteria and opportunistic pathogens, and the emergence of antimicrobial resistance threatens the safety of the food chain. To know the E. coli strains circulating in the Brazilian poultry sector is important since the country corresponds to a significant chicken meat production. Thus, we analyzed 90 publicly genomes available in a database using web-based tools. Genomic analysis revealed that sul alleles were the most detected resistance genes, followed by aadA, bla_CTX-M, and dfrA. Plasmids of the IncF family were important, followed by IncI1-Iα, Col-like, and p0111. Genes of specific metabolic pathways that contribute to virulence (terC and gad) were predominant, followed by sitA, traT, and iss. Additionally, pap, usp, vat, sfa/foc, ibeA, cnf1, eae, and sat were also predicted. In this regard, 11 E. coli were characterized as avian pathogenic E. coli and one as atypical enteropathogenic E. coli. Phylogenetic analysis confirmed the predominant occurrence of B1 but also A, D, B2, F, E, G, C, and Clade I phylogroups, whereas international clones ST38, ST73, ST117, ST155, and ST224 were predicted among 53 different sequence types identified. Serotypes O6:H1 and:H25 were prevalent, and fimH31 and fimH32 were the most representatives among the 36 FimH types detected. Finally, single nucleotide polymorphisms-based phylogenetic analysis confirmed high genomic diversity among E. coli strains. While international E. coli clones have adapted to the Brazilian poultry sector, the virulome background of these strains support a pathogenic potential to humans and animals, with lineages carrying resistance genes that can lead to hard-to-treat infections.

Antibiotic Resistance of Bacterial Isolates from Smallholder Poultry Droppings in the Guinea Savanna Zone of Nigeria

There is a growing risk of antibiotic resistance (AR) in smallholder poultry (SP). This study, therefore, aimed to investigate AR pattern of bacterial isolates from SP in the Guinea Savanna agro-ecological zone of Nigeria. A total of 120 fresh poultry droppings were aseptically collected, randomly, from two tropically adapted (FUNAAB Alpha and Noiler) and local chickens. The chickens were raised either using ethnoveterinary medicines (n = 60) or antibiotics (n = 60). Bacterial isolates were characterized and analyzed using standard protocols, and appropriate statistical tools. Compared to Pseudomonas spp. (2.5%) and Klebsiella spp. (5.8%), Salmonella spp. (57.5%) and Escherichia coli (34.2%) were the most prevalent (χ2 = 96.67; p < 0.001). Prevalence of bacterial species was significantly (p = 0.024; Odds Ratio = 2.552) influenced by antibiotics usage. All four species were multi-drug resistant. In total, 30% of the isolates had a multiple AR index ≥ 0.2. Bacterial isolates from FUNAAB Alpha (58.0%) and Noiler (44.0%) were highly resistant to quinolones, while isolates from the local chickens (22.6%) were most resistant to aminoglycosides. Bacterial species isolated from FUNAAB Alpha and local chickens exhibited the lowest and highest percentage of AR, respectively. Clustering of isolates with similar antibiogram revealed inter-species dependence with possibility for inter-species gene transfer. These findings provide a background to investigate the metagenomics of local and improved chickens for AR.

A Joint Regional Analysis of Resistance Combinations in Escherichia coli in Humans and Different Food-Producing Animal Populations in Germany Between 2014 and 2017

A joint comparative regional analysis of different resistance combinations across human and veterinary medicine has not been previously conducted in Germany. This study analyses 16 resistance combinations from four antibiotics in E. coli from different human and food-producing animal populations in three German regions: East, North West and South West. The E. coli data were collected from the three national surveillance and monitoring systems for antimicrobial resistance (AMR) bacteria in humans (ARS), food-safety (Zoonosis Monitoring) and animal pathogens (GERM-Vet) from January 2014 to December 2017. Analyses were performed using cluster analysis (hierarchical clustering, average linkage) in R. We included data from 537,215 E. coli isolates from human clinical isolates, from clinical as well as non-clinical isolates from food-producing animals and from food. The majority of the data originated from the North West region. There were two main clusters built on 54 different human and animal populations. We observed close similarities of resistance combinations in human isolates from the different regions within the same human populations from outpatient cares, general wards and ICUs. These resistance combinations clustered separately from non-clinical isolates from broilers, turkeys, cattle and pigs; except for some of clinical isolates from these populations which clustered closely to isolates from human populations. Frequently, the resistance combinations in E. coli isolates from farms clustered closely to the resistance combinations in isolates from slaughterhouses from broilers and turkeys over all regions. However, the resistance combinations in E. coli isolates from retail meat populations tended to cluster separately within their respective populations in between all regions.

Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome

A global rise in antimicrobial resistance among pathogenic bacteria has proved to be a major public health threat, with the rate of multidrug-resistant bacterial infections increasing over time. The gut microbiome has been studied as a reservoir of antibiotic resistance genes (ARGs) that can be transferred to bacterial pathogens via horizontal gene transfer (HGT) of conjugative plasmids and mobile genetic elements (the gut resistome). Advances in metagenomic sequencing have facilitated the identification of resistome modulators, including live microbial therapeutics such as probiotics and fecal microbiome transplantation that can either expand or reduce the abundances of ARG-carrying bacteria in the gut. While many different gut microbes encode for ARGs, they are not uniformly distributed across, or transmitted by, various members of the microbiome, and not all are of equal clinical relevance. Both experimental and theoretical approaches in microbial ecology have been applied to understand differing frequencies of ARG horizontal transfer between commensal microbes as well as between commensals and pathogens. In this commentary, we assess the evidence for the role of commensal gut microbes in encoding antimicrobial resistance genes, the degree to which they are shared both with other commensals and with pathogens, and the host and environmental factors that can impact resistome dynamics. We further discuss novel sequencing-based approaches for identifying ARGs and predicting future transfer events of clinically relevant ARGs from commensals to pathogens.

Animal source food eating habits of outpatients with antimicrobial resistance in Bukavu, D.R. Congo

BACKGROUND

Antibiotic resistance is a public health concern in Democratic Republic Congo and worldwide. It is usually caused by antibiotic over prescription or dispensing practices. The consumption of animal source food (ASF) could be another source of antibiotic resistance but is rarely studied. The objective of the study was to evaluate the eating habits of ASF by outpatients with antimicrobial resistance through an analysis of (i) the association of their antimicrobial resistance with ASF consumption; (ii) the influence of the types of ASF on their antimicrobial resistance.

METHODS

This is a retrospective analytical study conducted at three major Hospitals in Bukavu City (D. R. Congo). A total number of 210 patients, whose samples (mainly faeces and urine) had been subjected to bacterial examination, was included in this study. Morphological, biochemical and antibiotic susceptibility (using disc diffusion method) tests were performed on the samples. This served to isolate and identify resistant bacteria. Afterwards, patients responded to questions about the types and quantity of ASF eaten in the last week. We analysed data using descriptive statistics, logistic regression and non-parametric ranking tests.

RESULTS

Escherichia coli (37.1%), Klebsiella pneumonae (14.7%), and Staphylococcus aureus (13.8%) were the most prevalent bacteria. E. coli (68.4%) and K. pneumonae (87.5%) were multidrug resistant (MDR), while S. aureus (7.7%) was minor. Low beef (O.R. 0.737, C.I. 0.542-1.002) and pork (O.R. 0.743, C.I. 0.560 - 0.985) consumption led to significantly (p < 0.05) lower risks of resistance to ciprofloxacin. Patients eating three different ASF per week had the highest resistance score (20.67) and high consumption rates of goat meat, pork and milk (41.5%).

CONCLUSION

The findings of this study suggest a contribution of human nutrition to antimicrobial resistance frequency. Our results show the existence of a high prevalence of multi-drug resistant bacteria in patients for which eating beef, pork and drinking milk are major risk factors. Therefore, a stricter control of antibiotic usage in livestock production and of their presence in ASF is recommended.