Serena Caucci

Seasonality of antibiotic prescriptions for outpatients and resistance genes in sewers and wastewater treatment plant outflow

To test the hypothesis of a seasonal relationship of antibiotic prescriptions for outpatients and the abundance of antibiotic resistance genes (ARGs) in the wastewater, we investigated the distribution of prescriptions and different ARGs in the Dresden sewer system and wastewater treatment plant during a two-year sampling campaign. Based on quantitative PCR (qPCR), our results show a clear seasonal pattern for relative ARGs abundances. The higher ARGs levels in autumn and winter coincide with the higher rates of overall antibiotic prescriptions. While no significant differences of relative abundances were observed before and after the wastewater treatment for most of the relative ARGs, the treatment clearly influenced the microbial community composition and abundance. This indicates that the ARGs are probably not part of the dominant bacterial taxa, which are mainly influenced by the wastewater treatment processes, or that plasmid carrying bacteria remain constant, while plasmid free bacteria decrease. An exception was vancomycin (vanA), showing higher relative abundance in treated wastewater. It is likely that a positive selection or community changes during wastewater treatment lead to an enrichment of vanA. Our results demonstrate that in a medium-term study the combination of qPCR and next generation sequencing corroborated by drug-related health data is a suitable approach to characterize seasonal changes of ARGs in wastewater and treated wastewater.

Environmental and public health implications of antibiotic-resistance genes in municipal wastewaters

Aim and subjectAntibiotic resistance is a serious threat to public health in Europe leading to increasing health-care costs and deaths. Combating antibiotic resistance requires an understanding of the ecology of antibiotic-resistance genes (ARGs), their selection, and their spread in the environment. Although antibiotic resistance has involved research in clinically relevant human pathogens, environmental reservoirs and the contribution of ARGs in clinical settings have only been considered recently.ResultsIn this article we discuss the links between human activities and the natural ecosystem that might influence the evolution and spread of ARGs with a special focus on wastewater treatment plants (WWTPs). Moreover, traditional and novel techniques aiming toward a better understanding of this problem are elucidated.ConclusionRoutine monitoring programs are recommended to provide background data for mitigation activities in WWTPs based on the presence of ARGs, the abundance of antibiotics, as well as the presence of resistant bacteria in the environment.ZusammenfassungHintergrund und FragestellungAntibiotikaresistenzen sind eine ernstzunehmende Bedrohung für das Gesundheitswesen in Europa und mit steigenden Gesundheitskosten und erhöhten Mortalitätsraten verbunden. Der Kampf gegen Antibiotikaresistenzen erfordert ein Verständnis bezüglich der Ökologie von Antibiotikaresistenzgenen (ARG), deren Selektion und Verbreitung in der Umwelt. Obwohl Antibiotikaresistenzen im Zusammenhang mit klinisch relevanten Krankheitserregern mittlerweile einen Forschungsschwerpunkt darstellen, werden deren Vorkommen in der Umwelt und der Einfluss von Antibiotikaresistenzgenen erst seit Kurzem betrachtet.ErgebnisseMit besonderem Fokus auf Kläranlagen wird in diesem Beitrag die Verbindung des Menschen mit dem natürlichen Ökosystem hergestellt und dabei der potenzielle Einfluss auf die Entwicklung und Verbreitung von Antibiotikaresistenzgenen diskutiert. Darüber hinaus werden traditionelle und innovative Techniken, die zu einem verbesserten Verständnis der Problematik beitragen, erläutert.SchlussfolgerungRoutinemäßige Monitoringprogramme tragen dazu bei, Daten zu generieren, welche anhand des Vorkommens von Resistenzgenen, der Häufigkeit von Antibiotika und der resistenten Bakterien in der Umwelt eine Risikominderung in Kläranlagen anzeigen können.

Extended Spectrum Beta-Lactamase (ESBL)-Producing Bacteria Isolated from Hospital Wastewaters, Rivers and Aquaculture Sources in Nigeria

Untreated wastewater is a risk factor for the spread of antibiotic resistance in the environment. However, little is known about the contribution of untreated wastewater to the burden of antibiotic resistance in the Nigerian environment. In this study, a total of 143 ceftazidime-/cefpodoxime-resistant bacteria isolated from untreated wastewater and untreated wastewater-contaminated surface and groundwater in Nigeria were screened for extended-spectrum β-lactamase (ESBL) genes, integrons and integron gene cassettes by PCR. The genetic environment of blaCTX-M-15 was mapped by PCR and potentially conjugative plasmids were detected among the isolates by degenerate primer MOB typing (DPMT). ESBL production was confirmed in 114 (79.7%) isolates and ESBL genes (blaSHV, blaCTX-M-15 and blaTEM) were detected in 85 (74.6%) ESBL-producing isolates. blaCTX-M-15 was associated with ISEcp1 and with orf477 in 12 isolates and with ISEcp1, IS26 and orf477 in six others. To the best of our knowledge, this is the first report of blaCTX-M-15 in hand-dug wells and borehole serving as sources of drinking water and a first report of the genetic environment of blaCTX-M-15 in environmental bacteria from Nigeria. The results of this study confirm untreated wastewater as an important medium for the spread of ESBL-producing bacteria within the Nigerian environment. Hence, the widespread practice of discharging untreated wastewater into the aquatic ecosystem in Nigeria is a serious risk to public health.

High genomic diversity of multi-drug resistant wastewater Escherichia coli

Wastewater treatment plants play an important role in the emergence of antibiotic resistance. They provide a hot spot for exchange of resistance within and between species. Here, we analyse and quantify the genomic diversity of the indicator Escherichia coli in a German wastewater treatment plant and we relate it to isolates’ antibiotic resistance. Our results show a surprisingly large pan-genome, which mirrors how rich an environment a treatment plant is. We link the genomic analysis to a phenotypic resistance screen and pinpoint genomic hot spots, which correlate with a resistance phenotype. Besides well-known resistance genes, this forward genomics approach generates many novel genes, which correlated with resistance and which are partly completely unknown. A surprising overall finding of our analyses is that we do not see any difference in resistance and pan genome size between isolates taken from the inflow of the treatment plant and from the outflow. This means that while treatment plants reduce the amount of bacteria released into the environment, they do not reduce the potential for antibiotic resistance of these bacteria.

Safe Use of Wastewater in Agriculture: The Golden Example of Nexus Approach

Water, soil, and waste are three key resources associated with agriculture and thus food production as they are closely related to each other. An integrated management of these three resources can bring more benefits to society through increased resource usage efficiency. This approach is commonly known as the Nexus Approach. Safe use of wastewater in agriculture (SUWA) is a simple but powerful example of the Nexus Approach in action. It demonstrates how the sustainable management of one resource in a nexus can benefit the other resources in the same nexus. Wastewater irrigation not only addresses the water demand issues in water stressed areas, but also helps us “recycle” the nutrients in it. The process begins in the waste sector, but the implementation of such a management model can ultimately make a positive impact on the water sector as well as in soil and land management. On a global scale, over 20 million hectares of agricultural land are irrigated using wastewater. Developing countries and countries in transition need clear institutional arrangements and skilled human resources to address the technical, institutional, and policy challenges related to SUWA. From the UN perspective, SUWA also supports achieving some of the key Sustainable Development Goals (SDGs). Taking the wastewater irrigation in the Mezquital Valley in Mexico as an entry point, this chapter builds upon all above facts to provide an introduction to the book and also to illustrate SUWA as a Nexus Approach example.

Whole genome analysis reveals pathogenic potential of multi-drug resistant wastewater Escherichia coli

Wastewater treatment plants play an important role in the release of antibiotic resistance into the environment. It has been shown that wastewater contains multi-drug resistant Escherichia coli, but information on strain diversity is surprisingly scarce. Here we present an exceptionally large dataset on multidrug resistant Escherichia coli, originating from wastewater, over a thousand isolates were phenotypically characterized for twenty antibiotics and for 103 isolates whole genomes were sequenced. To our knowledge this is the first study documenting such a comprehensive diversity of multi-drug resistant Escherichia coli in wastewater. The genomic diversity of the isolates was unexpectedly high and contained a high number of resistance and virulence genes. To illustrate the genomic diversity of the isolates we calculated the pan genome of the wastewater Escherichia coli and found it to contain over sixteen thousand genes. To analyse this diverse dataset, we devised a computational approach correlating genotypic variation and resistance phenotype, this way we were able to identify not only known, but also candidate resistance genes. Finally, we could verify that the effluent of a wastewater treatment plant will contain multi-drug resistant Escherichia coli belonging to clinically important clonal groups.Wastewater treatment plants play an important role in antibiotic resistance development. While it has been shown that wastewater effluents contain resistant bacteria, resistance genes, and antibiotics, there is little knowledge on the link between resistance genotype and phenotype. Here we present the first study, which combines a culture-based phenotypic screen with the analysis of whole genome sequences for the indicator species Escherichia coli of the inflow and outflow of a sewage treatment plant. Our analysis reveals that nearly all isolates are multi-drug resistant and many are potentially pathogenic. This holds in particular for the outflow of the treatment plant. We devise a computational approach correlating genotypic variation and resistance phenotype, which identifies known and candidate resistance genes. The identified genes stem from the pan genome, which is large and thus reflects the genomic heterogeneity of a treatment plant. Overall, the screen and analysis show that sewage treatment plants provide a favourable environment for antibiotic resistance development and that resistant bacteria do not appear to suffer from a competitive disadvantage in wastewater. These findings should find consideration in future improvements of wastewater treatment.