Whole genome analyses of CMY-2-producing Escherichia coli isolates from humans, animals and food in Germany

Abstract

BackgroundResistance to 3rd-generation cephalosporins in Escherichia coli is mostly mediated by extended-spectrum beta-lactamases (ESBLs) or AmpC beta-lactamases. Besides overexpression of the species-specific chromosomal ampC gene, acquisition of plasmid-encoded ampC genes, e.g. blaCMY-2, has been described worldwide in E. coli from humans and animals. To investigate a possible transmission of blaCMY-2 along the food production chain, we conducted a next-generation sequencing (NGS)-based analysis of 164 CMY-2-producing E. coli isolates from humans, livestock animals and foodstuff from Germany.ResultsThe data of the 164 sequenced isolates revealed 59 different sequence types (STs); the most prevalent ones were ST38 (n = 19), ST131 (n = 16) and ST117 (n = 13). Two STs were present in all reservoirs: ST131 (human n = 8; food n = 2; animal n = 6) and ST38 (human n = 3; animal n = 9; food n = 7). All but one CMY-2-producing ST131 isolates belonged to the clade B (fimH22) that differed substantially from the worldwide dominant CTX-M-15-producing clonal lineage ST131-O25b clade C (fimH30). Plasmid replicon types IncI1 (n = 61) and IncK (n = 72) were identified for the majority of blaCMY-2-carrying plasmids. Plasmid sequence comparisons showed a remarkable sequence identity, especially for IncK plasmids. Associations of replicon types and distinct STs were shown for IncK and ST57, ST429 and ST38 as well as for IncI1 and ST58. Additional β-lactamase genes (blaTEM, blaCTX-M, blaOXA, blaSHV) were detected in 50% of the isolates, and twelve E. coli from chicken and retail chicken meat carried the colistin resistance gene mcr-1.ConclusionWe found isolates of distinct E. coli clonal lineages (ST131 and ST38) in all three reservoirs. However, a direct clonal relationship of isolates from food animals and humans was only noticeable for a few cases. The CMY-2-producing E. coli-ST131 represents a clonal lineage different from the CTX-M-15-producing ST131-O25b cluster. Apart from the STdriven spread, plasmid-mediated spread, especially via IncI1 and IncK plasmids, likely plays an important role for emergence and transmission of blaCMY-2 between animals and humans.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4976-3) contains supplementary material, which is available to authorized users.

Reduced antibacterial drug resistance and blaCTX-M β-lactamase gene carriage in cattle-associated Escherichia coli at low temperatures, at sites dominated by older animals and on pastureland: implications for surveillance

“…Whilst unpublished, the other plasmid (pTC_N40607) has been identified in E. coli in the USA so is likely to be similarly widespread. Accordingly, whilst there is some evidence of shared circulating plasmids, as reported in a number of recent studies (35–37), the overall level of overlap between farm and human bla CTX-M E. coli identified in this study was very small and not suggestive of any novel or recent transmission events.…”

Molecular Characterization of Fecal Extended-Spectrum β-Lactamase- and AmpC β-Lactamase-Producing Escherichia coli From Healthy Companion Animals and Cohabiting Humans in South Korea

“…CTX-M-type ESBL, especially CTX-M-15, is commonly more dominant than CMY-type AmpC β-lactamases in humans (Lee et al, 2018), but CMY-2-producing E. coli isolates have been frequently detected as much as CTX-M-type in veterinary medicine worldwide (Pietsch et al, 2018;Donà et al, 2019;Hong et al, 2019). Interestingly, cefoxitin is often used in the veterinary field for treating gram-positive and anaerobic bacterial infections (Brook et al, 2013;Lappin et al, 2017).…”

Genomic analysis of avian-pathogenic Escherichia coli (APEC) isolated from diseased chicken

“…Both ST429 and ST23 are considered as predominant APEC lineages that are frequently isolated from poultry with clinically manifested disease (35,37), but also poultry products (26). Although representing quite unrelated APEC clades, they both appear to be poultry-specific, with little pathogenic potential for humans (7,17).…”

“…(20). Whereas some of them are associated exclusively with human infections, others are frequently isolated from diseased poultry or poultry products (21)(22)(23)(24)(25)(26). It is however difficult to assess the real importance of poultry as a source of human infections.…”