The aims of this study were (i) to detect extended-spectrum β-lactamase (ESBL) genes among 1378 Escherichia coli isolates from defined disease conditions of companion and farm animals and (ii) to determine the localization and organization of ESBL genes. E. coli isolates from the German resistance monitoring programme GERM-Vet were included in the study. Plasmids were transferred by conjugation or transformation and typed by PCR-based replicon typing. ESBL genes were detected by PCR; the complete ESBL genes and their flanking regions were sequenced by primer walking. Phylogenetic grouping and multilocus sequence typing (MLST) were performed for all ESBL-producing E. coli isolates. Of the 27 ESBL-producing E. coli isolates detected, 22 carried bla_CTX-M-1 genes on IncN (n = 16), IncF (n = 3), IncI1 (n = 2) or multireplicon (n = 1) plasmids. A bla_CTX-M-3 gene was located on an IncN plasmid and a bla_CTX-M-15 gene was located on an IncF plasmid. A multireplicon plasmid and an IncHI1 plasmid harboured bla_CTX-M-2. A bla_TEM-52c gene was identified within Tn2 on an IncI1 plasmid. The bla_CTX-M genes located within the same or related genetic contexts showed differences due to the integration of insertion sequences. Various MLST types were detected, with ST10 (n = 7), ST167 (n = 4) and ST100 (n = 3) being the most common. This study showed that the bla_CTX-M-1 gene is the predominant ESBL gene among E. coli isolates from diseased animals in Germany and a considerable structural heterogeneity was found in the regions flanking the bla_CTX-M-1 gene. Insertion sequences, transposons and recombination events are likely to be involved in alterations of the ESBL gene regions.

Bordetella bronchiseptica is involved in respiratory tract infections mainly in dogs and pigs but may also cause infections in humans. Valid and representative data on antimicrobial susceptibility of B. bronchiseptica is rare. Approved antimicrobial susceptibility testing methods have been published, but very few clinical breakpoints are available. The MIC values are low for most agents but high for β-lactam antibiotics and macrolides. Information on the genetic basis of resistance is scarce. For a small number of isolates that are resistant or show elevated MICs, the molecular basis of resistance was identified. Three tetracycline resistance genes, tet (A), tet (C), and tet (31), coding for major facilitator superfamily efflux pumps, were identified. Two other major facilitator superfamily exporter genes confer resistance to chloramphenicol ( cmlB1 ) or to chloramphenicol and florfenicol ( floR ). Two class B chloramphenicol acetyltransferase genes ( catB1 and catB3 ), which confer resistance to nonfluorinated phenicols by enzymatic inactivation, have been identified in B. bronchiseptica . Like the trimethoprim resistance genes dfrA1 and dfrB1 , which code for trimethoprim-insensitive dihydrofolate reductases, the genes catB1 and catB3 were located on gene cassettes and found in class 1 integrons also harboring the sulfonamide resistance gene sul1 . In addition, the gene sul2 has also been detected. Both sul1 and sul2 code for sulfonamide-insensitive dihydropteroate synthases. A gene cassette harboring the β-lactamase gene bla _OXA-2 was also identified, whereas β-lactam resistance in B. bronchiseptica seems to be more likely due to reduced influx in combination with the species-specific β-lactamase encoded by bla _BOR-1 . The resistance genes were mostly located on conjugative plasmids.

In this study, 417 Escherichia coli isolates from defined disease conditions of companion and farm animals collected in the BfT-GermVet study were investigated for the presence of extended-spectrum β-lactamase (ESBL) genes. Three ESBL-producing E. coli isolates were identified among the 100 ampicillin-resistant isolates. The E. coli isolates 168 and 246, of canine and porcine origins, respectively, harbored bla _CTX-M-1 , and the canine isolate 913 harbored bla _CTX-M-15 , as confirmed by PCR and sequence analysis. The isolates 168 and 246 belonged to the novel multilocus sequence typing (MLST) types ST1576 and ST1153, respectively, while isolate 913 had the MLST type ST410. The ESBL genes were located on structurally related IncN plasmids in isolates 168 and 246 and on an IncF plasmid in isolate 913. The bla _CTX-M-1 upstream regions of plasmids pCTX168 and pCTX246 were similar, whereas the downstream regions showed structural differences. The genetic environment of the bla _CTX-M-15 gene on plasmid pCTX913 differed distinctly from that of both bla _CTX-M-1 genes. Detailed sequence analysis showed that the integration of insertion sequences, as well as interplasmid recombination events, accounted for the structural variability in the bla _CTX-M gene regions.

Sulfonamide-trimethoprim-resistant Aeromonas salmonicida and motile Aeromonas spp. from diseased fish of the GE RM -Vet study carried the sul1 gene together with mostly cassette-borne trimethoprim resistance genes, including the novel gene dfrA28 . The seven dfrA and dfrB genes identified were located mostly in class 1 integrons which commonly harbored other gene cassettes.