Stefanie P. Glaeser (Giessen / DE), Sanjana Balachandran (Giessen / DE), Dipen Pulami (Giessen / DE), Andrew Scott (London / CA), Gabhan Chalmers (Guelph / CA), Nicole Ricker (Guelph / CA), Carmen Chifiriuc (Bucharest / RO), Ed Topp (Dijon Cedex / FR), Heike Schmitt (Bilthoven / NL), Peter Kämpfer (Giessen / DE)
Cultivation of antimicrobial resistant bacteria (ARB) is more and more recognized as a key strategy to understand the spread of antimicrobial resistance (AMR) in the environment. For many years, extraction of environmental DNA and quantification of antimicrobial resistance genes (ARG) was used by many research groups to target environmental AMR spread. But, especially the multi-resistance status of bacteria or plasmid content cannot by covered by these methods and new resistance strategies are overseen. These important data can be obtained by using specific cultivation approaches. However, the cultivation strategies must be carefully selected and critically evaluated to get reliable results.
By selecting specific media and incubation conditions, ESKAPE bacteria can be selectively cultured. By supplementing antibiotics to these media, subgroups of resistant bacteria can be cultured. Nevertheless, there are several challenges which can strongly impact the outcome of these cultivation efforts. Growth of more abundant intrinsically resistant non-target bacteria can disturb the detection of ARGs or low abundant or viable but non culturable (VBNC) potential pathogenic ARBs in environmental samples. This may affect their direct cultivability on agar media. Non-selective or selective pre-enrichment strategies enhancing the cultivability of specific bacteria but can also influence the outcome of these studies, because some strains may have growth benefits during pre-enrichment. Resistance gene exchange during pre-enrichment may also occur.
We will give a critical overview of cultivation efforts for the research on AMR based on our knowledge we obtained in the last 15 years in our AMR research collaborative network projects ( the BMBF funded projects RiskAGuA and the JPI AMR project ARMIS in which the spread of AMR from manure and biogas plant digestates were studied, and the DFG research group PARES in which the spread of AMR in Mexican soils after a shift from irrigation with untreated to treated wastewater is monitored.