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Chapter 15 : Antimicrobial Resistance in of Veterinary Origin

Authors: Geovana B. Michael1, Janine T. Bossé2, Stefan Schwarz3
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Affiliations: 1: Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, D-14163 Germany; 2: Section of Pediatrics, Department of Medicine London, Imperial College London, London W2 1PG, United Kingdom; 3: Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, D-14163 Germany
Content Type: Monograph
Publication Year: 2018

Category: Clinical Microbiology; Environmental Microbiology

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Abstract:

The family (order , class ) comprises a highly heterogeneous group of Gram-negative bacteria. Evaluation by sequence comparison of housekeeping genes, 16s rRNA gene sequence-based phylogenetic analysis, DNA-DNA hybridization, and analysis of the biochemical and physiological capacities has identified a number of distinct genetic and phenotypic groups ( ). As a consequence, the family has undergone numerous reclassifications during the past years and currently (late 2017) contains 25 genera: , , , , , , , , , , , , , , , , , , , , , , , , and (International Committee on Sytematics of Prokaryotes, http://www.the-icsp.org/taxa-covered-family-pasteurellaceae). A new genus, , has recently been proposed. (comb. nov.), which will be reclassified from [] , with NCTC 8141T (also designated CCUG 12398T) as the type strain ( ). The use of square brackets enclosing the genus name indicates that there is a proposal to reclassify the species to another genus or that the species has been shown not to be a member of the genus , as is the case for [] , which is now excluded from based on genetic analysis ( ). Additional information related to reclassification of genera may be found in references , and . The use of quotation marks around “” denotes that this is currently not a validated species name ( ).

Citation: Michael G, Bossé J, Schwarz S. 2018. Antimicrobial Resistance in of Veterinary Origin, p 331-363. In Schwarz S, Cavaco L, Shen J (ed), Antimicrobial Resistance in Bacteria from Livestock and Companion Animals. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.ARBA-0022-2017
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Antimicrobial Resistance in Pasteurellaceae of Veterinary Origin
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Citation: Michael G, Bossé J, Schwarz S. 2018. Antimicrobial Resistance in of Veterinary Origin, p 331-363. In Schwarz S, Cavaco L, Shen J (ed), Antimicrobial Resistance in Bacteria from Livestock and Companion Animals. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.ARBA-0022-2017
/content/10.1128/9781555819804.chap15.fig15-1
Figure 1
Schematic representation of the structure and organization of genes found in (H)-carrying plasmids from , , [.] , and . Comparison of the maps of the partially sequenced plasmids pPMT1 (accession no. Y15510) and pVM111 (accession nos. AJ514834 and U00792), both from , pMHT1 (accession no. Y16103) from , and pPAT1 (accession no. AJ245947) from [.] (accession no. Z21724) and the completely sequenced plasmids p9956 (accession no. AY362554; 5,674 bp) and p12494 (accession no. DQ517426; 14,393 bp), both from . Genes are shown as arrows, with the arrowhead indicating the direction of transcription. The following genes are involved in antimicrobial resistance: -(H) (tetracycline resistance), (sulfonamide resistance), and and (streptomycin resistance); plasmid replication: ; mobilization functions: , , , and ; recombination functions: ; DNA partition: ; virulence: and ; unknown function: the open reading frame indicated by the white arrow. The Δ symbol indicates a truncated functionally inactive gene. The white boxes in the maps of pPMT1 and p12494 indicate the limits of the insertion sequences IS, IS, and IS; the arrows within these boxes indicate the reading frames of the corresponding transposase genes. Gray shaded areas indicate the -(H) gene region common to all these plasmids with ≥95% nucleotide sequence identity. A distance scale in kilobases is shown at the bottom of the figure.
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10.1128/9781555819804/fig15-1.gif
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Figure 1

Schematic representation of the structure and organization of genes found in (H)-carrying plasmids from , , [.] , and . Comparison of the maps of the partially sequenced plasmids pPMT1 (accession no. Y15510) and pVM111 (accession nos. AJ514834 and U00792), both from , pMHT1 (accession no. Y16103) from , and pPAT1 (accession no. AJ245947) from [.] (accession no. Z21724) and the completely sequenced plasmids p9956 (accession no. AY362554; 5,674 bp) and p12494 (accession no. DQ517426; 14,393 bp), both from . Genes are shown as arrows, with the arrowhead indicating the direction of transcription. The following genes are involved in antimicrobial resistance: -(H) (tetracycline resistance), (sulfonamide resistance), and and (streptomycin resistance); plasmid replication: ; mobilization functions: , , , and ; recombination functions: ; DNA partition: ; virulence: and ; unknown function: the open reading frame indicated by the white arrow. The Δ symbol indicates a truncated functionally inactive gene. The white boxes in the maps of pPMT1 and p12494 indicate the limits of the insertion sequences IS, IS, and IS; the arrows within these boxes indicate the reading frames of the corresponding transposase genes. Gray shaded areas indicate the -(H) gene region common to all these plasmids with ≥95% nucleotide sequence identity. A distance scale in kilobases is shown at the bottom of the figure.

Citation: Michael G, Bossé J, Schwarz S. 2018. Antimicrobial Resistance in of Veterinary Origin, p 331-363. In Schwarz S, Cavaco L, Shen J (ed), Antimicrobial Resistance in Bacteria from Livestock and Companion Animals. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.ARBA-0022-2017
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Figure 2
Schematic representation of the structure and organization of -, (L)-, and (B)-carrying plasmids from , , [] , [.] , and . Comparison of the maps of the -carrying streptomycin/spectinomycin resistance plasmid pCCK647 (accession no. AJ884726; 5,198 bp) from , the (L)-carrying tetracycline resistance plasmid pCCK3259 (accession no. AJ966516; 5,317 bp) from , and the (B)-carrying tetracycline resistance plasmids pHS-Tet (accession no. AY862435; 5,147 bp) from [] , pPAT2 (accession no. AJ278685; partially sequenced) from [.] , p11745 (accession no. DQ176855; 5,486 bp) from , pHPS1019 (accession no. HQ622101; 4,597 bp) from [.] , and pB1001 (accession no. EU252517; 5,128 bp) from . Genes are shown as arrows, with the arrowhead indicating the direction of transcription. The following genes are involved in antimicrobial resistance: -(B), (B), and (L) (tetracycline resistance) and (streptomycin/spectinomycin resistance); plasmid replication: ; mobilization functions: , , and ; unknown function: the open reading frames indicated by white arrows. Gray-shaded areas indicate the regions common to plasmids, and the different shades of gray illustrate the percentages of nucleotide sequence identity between the plasmids, as indicated by the scale at the bottom of the figure. A distance scale in kilobases is shown.
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10.1128/9781555819804/fig15-2.gif
Image of Figure 2
Figure 2

Schematic representation of the structure and organization of -, (L)-, and (B)-carrying plasmids from , , [] , [.] , and . Comparison of the maps of the -carrying streptomycin/spectinomycin resistance plasmid pCCK647 (accession no. AJ884726; 5,198 bp) from , the (L)-carrying tetracycline resistance plasmid pCCK3259 (accession no. AJ966516; 5,317 bp) from , and the (B)-carrying tetracycline resistance plasmids pHS-Tet (accession no. AY862435; 5,147 bp) from [] , pPAT2 (accession no. AJ278685; partially sequenced) from [.] , p11745 (accession no. DQ176855; 5,486 bp) from , pHPS1019 (accession no. HQ622101; 4,597 bp) from [.] , and pB1001 (accession no. EU252517; 5,128 bp) from . Genes are shown as arrows, with the arrowhead indicating the direction of transcription. The following genes are involved in antimicrobial resistance: -(B), (B), and (L) (tetracycline resistance) and (streptomycin/spectinomycin resistance); plasmid replication: ; mobilization functions: , , and ; unknown function: the open reading frames indicated by white arrows. Gray-shaded areas indicate the regions common to plasmids, and the different shades of gray illustrate the percentages of nucleotide sequence identity between the plasmids, as indicated by the scale at the bottom of the figure. A distance scale in kilobases is shown.

Citation: Michael G, Bossé J, Schwarz S. 2018. Antimicrobial Resistance in of Veterinary Origin, p 331-363. In Schwarz S, Cavaco L, Shen J (ed), Antimicrobial Resistance in Bacteria from Livestock and Companion Animals. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.ARBA-0022-2017
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Figure 3
Schematic representation of the structure and organization of the -carrying resistance plasmids from , [] , , , and “.” Comparison of the maps of -carrying resistance plasmids pAB2 (accession no. Z21724; 4,316 bp) from , pB1000 (accession no. DQ840517; 4,613 bp) from [] , pB1002 (accession no. EU283341; 5,685 bp) from , APP7_A (accession no. CP001094; 5,685 bp) from , pIMD50 (accession no. AJ830711; 8,751 bp) from “,” and pHB0503 (accession no. EU715370; 15,079 bp) from . It should be noted that another three pIMD50-related -carrying resistance plasmids from “” have been sequenced completely: pKMA5 (accession no. AM748705), pKMA202 (accession no. AM748706), and pKMA1467 (accession no. AJ830712). Genes are shown as arrows, with the arrowhead indicating the direction of transcription. The following genes are involved in antimicrobial resistance: (sulfonamide resistance), and (streptomycin resistance), (β-lactam resistance), (gentamicin resistance), (chloramphenicol resistance), and (kanamycin/neomycin resistance); plasmid replication: ; mobilization functions: , , and ; resolvase function: ; DNA partition: ; unknown function: open reading frames indicated by white arrows. The prefix Δ indicates a truncated functionally inactive gene. Gray-shaded areas indicate the regions common to plasmids, and the different shades of gray illustrate the percentages of nucleotide sequence identity between the plasmids, as indicated by the scale at the bottom of the figure. A distance scale in kilobases is shown.
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Figure 3

Schematic representation of the structure and organization of the -carrying resistance plasmids from , [] , , , and “.” Comparison of the maps of -carrying resistance plasmids pAB2 (accession no. Z21724; 4,316 bp) from , pB1000 (accession no. DQ840517; 4,613 bp) from [] , pB1002 (accession no. EU283341; 5,685 bp) from , APP7_A (accession no. CP001094; 5,685 bp) from , pIMD50 (accession no. AJ830711; 8,751 bp) from “,” and pHB0503 (accession no. EU715370; 15,079 bp) from . It should be noted that another three pIMD50-related -carrying resistance plasmids from “” have been sequenced completely: pKMA5 (accession no. AM748705), pKMA202 (accession no. AM748706), and pKMA1467 (accession no. AJ830712). Genes are shown as arrows, with the arrowhead indicating the direction of transcription. The following genes are involved in antimicrobial resistance: (sulfonamide resistance), and (streptomycin resistance), (β-lactam resistance), (gentamicin resistance), (chloramphenicol resistance), and (kanamycin/neomycin resistance); plasmid replication: ; mobilization functions: , , and ; resolvase function: ; DNA partition: ; unknown function: open reading frames indicated by white arrows. The prefix Δ indicates a truncated functionally inactive gene. Gray-shaded areas indicate the regions common to plasmids, and the different shades of gray illustrate the percentages of nucleotide sequence identity between the plasmids, as indicated by the scale at the bottom of the figure. A distance scale in kilobases is shown.

Citation: Michael G, Bossé J, Schwarz S. 2018. Antimicrobial Resistance in of Veterinary Origin, p 331-363. In Schwarz S, Cavaco L, Shen J (ed), Antimicrobial Resistance in Bacteria from Livestock and Companion Animals. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.ARBA-0022-2017
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Figure 4
Schematic representation of the structure and organization of selected -based (multi-)resistance plasmids from , “,” , , [.] , , unnamed taxon 10, , and . Comparison of the maps of the plasmids pKMA2425 (accession no. AJ830714; 3,156 bp) from , pARD3079 (accession no. AM748707; 4,065 bp) from , pKMA757 (accession no. AJ830713; 4,556 bp) from “,” ABB7_B (accession no. NC_010941; 4,236 bp) from , pIG1 (accession no. U57647) from , pYFC1 (accession no. M83717) from , pFZG1012 (accession no. HQ015158; partially sequenced) from [.] , pLS88 (accession no. L23118; 4,772 bp) from , pYMH5 (accession no. EF015636; 4,772 bp) from , pM3224T (accession no. KP197004; 6,050 bp) from , pMS260 (accession no. AB109805; 8,124 bp) from , pMVSCS1 (accession no. AJ319822; 5,621 bp) from , pMHSCS1 (accession no. AJ249249; 4,992 bp) from unnamed taxon 10, pFZ51 (accession no. JN202624; 15,672 bp) from [.] , and pKMA757 (accession no. AJ830713; 4,556 bp) from “.” The map of another -based multiresistance plasmid, pIMD50 (accession no. AJ830711) from “,” is displayed in Fig. 3 . Genes are shown as arrows, with the arrowhead indicating the direction of transcription. The following genes are involved in antimicrobial resistance: (sulfonamide resistance), and (streptomycin resistance), (chloramphenicol resistance), (kanamycin/neomycin resistance), and (β-lactam resistance); plasmid replication: , , , and ; mobilization functions: , , , , , and ; unknown function: open reading frames indicated by white arrows. The prefix Δ indicates a truncated functionally inactive gene. Gray-shaded areas indicate the regions common to plasmids and the different shades of gray illustrate the percentages of nucleotide sequence identity between the plasmids, as indicated by the scale at the bottom of the figure. A distance scale in kilobases is shown.
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10.1128/9781555819804/fig15-4.gif
Image of Figure 4
Figure 4

Schematic representation of the structure and organization of selected -based (multi-)resistance plasmids from , “,” , , [.] , , unnamed taxon 10, , and . Comparison of the maps of the plasmids pKMA2425 (accession no. AJ830714; 3,156 bp) from , pARD3079 (accession no. AM748707; 4,065 bp) from , pKMA757 (accession no. AJ830713; 4,556 bp) from “,” ABB7_B (accession no. NC_010941; 4,236 bp) from , pIG1 (accession no. U57647) from , pYFC1 (accession no. M83717) from , pFZG1012 (accession no. HQ015158; partially sequenced) from [.] , pLS88 (accession no. L23118; 4,772 bp) from , pYMH5 (accession no. EF015636; 4,772 bp) from , pM3224T (accession no. KP197004; 6,050 bp) from , pMS260 (accession no. AB109805; 8,124 bp) from , pMVSCS1 (accession no. AJ319822; 5,621 bp) from , pMHSCS1 (accession no. AJ249249; 4,992 bp) from unnamed taxon 10, pFZ51 (accession no. JN202624; 15,672 bp) from [.] , and pKMA757 (accession no. AJ830713; 4,556 bp) from “.” The map of another -based multiresistance plasmid, pIMD50 (accession no. AJ830711) from “,” is displayed in Fig. 3 . Genes are shown as arrows, with the arrowhead indicating the direction of transcription. The following genes are involved in antimicrobial resistance: (sulfonamide resistance), and (streptomycin resistance), (chloramphenicol resistance), (kanamycin/neomycin resistance), and (β-lactam resistance); plasmid replication: , , , and ; mobilization functions: , , , , , and ; unknown function: open reading frames indicated by white arrows. The prefix Δ indicates a truncated functionally inactive gene. Gray-shaded areas indicate the regions common to plasmids and the different shades of gray illustrate the percentages of nucleotide sequence identity between the plasmids, as indicated by the scale at the bottom of the figure. A distance scale in kilobases is shown.

Citation: Michael G, Bossé J, Schwarz S. 2018. Antimicrobial Resistance in of Veterinary Origin, p 331-363. In Schwarz S, Cavaco L, Shen J (ed), Antimicrobial Resistance in Bacteria from Livestock and Companion Animals. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.ARBA-0022-2017
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Figure 5
Schematic representation of the structure and organization of selected -based (multi-)resistance plasmids from compared to an in-part-related plasmid from [] , and , [.] , , and -based (multi-)resistance plasmids from and [.] . Comparison of the maps of plasmids pCCK13698 (accession no. AM183225) from and its in-part-related plasmid pHS-Rec (accession no. AY862436; 9,462 bp) from [.] , pCCK381 (accession no. AJ871969; 10,874 bp) from , pCCK1900 (accession no. FM179941; 10,226 bp) from , pHPSF1 (accession no. KR262062; 6,328 bp) from [.] , pM3446F (accession no. KP696484; 7,709 bp) from , pMh1405 (accession no. NC_019260; 7,674 bp) from , p518 (accession no. KT355773; 3,937 bp) from , pFZG1012 (accession no. HQ015158; partially sequenced) from [.] , and pLS88 (accession no. L23118; 4,772 bp) from . Genes are shown as arrows, with the arrowhead indicating the direction of transcription. The following genes are involved in antimicrobial resistance: (sulfonamide resistance), and (streptomycin resistance), (chloramphenicol resistance), (chloramphenicol/florfenicol resistance), and (kanamycin/neomycin resistance); plasmid replication: , , , and ; mobilization functions: , , , and ; transposition functions: ; recombinase or integrase functions: and ; DNA partition: ; unknown function: open reading frames indicated by white arrows. The prefix Δ indicates a truncated functionally inactive gene. The boxes in the map of pCCK13698 indicate the limits of the insertion sequences IS and IS; the arrows within these boxes indicate the reading frames of the corresponding transposase genes. Gray-shaded areas indicate the regions common to plasmids, and the different shades of gray illustrate the percentages of nucleotide sequence identity between the plasmids, as indicated by the scale at the bottom of the figure. A distance scale in kilobases is shown.
10.1128/9781555819804/fig15-5_thmb.gif
10.1128/9781555819804/fig15-5.gif
Image of Figure 5
Figure 5

Schematic representation of the structure and organization of selected -based (multi-)resistance plasmids from compared to an in-part-related plasmid from [] , and , [.] , , and -based (multi-)resistance plasmids from and [.] . Comparison of the maps of plasmids pCCK13698 (accession no. AM183225) from and its in-part-related plasmid pHS-Rec (accession no. AY862436; 9,462 bp) from [.] , pCCK381 (accession no. AJ871969; 10,874 bp) from , pCCK1900 (accession no. FM179941; 10,226 bp) from , pHPSF1 (accession no. KR262062; 6,328 bp) from [.] , pM3446F (accession no. KP696484; 7,709 bp) from , pMh1405 (accession no. NC_019260; 7,674 bp) from , p518 (accession no. KT355773; 3,937 bp) from , pFZG1012 (accession no. HQ015158; partially sequenced) from [.] , and pLS88 (accession no. L23118; 4,772 bp) from . Genes are shown as arrows, with the arrowhead indicating the direction of transcription. The following genes are involved in antimicrobial resistance: (sulfonamide resistance), and (streptomycin resistance), (chloramphenicol resistance), (chloramphenicol/florfenicol resistance), and (kanamycin/neomycin resistance); plasmid replication: , , , and ; mobilization functions: , , , and ; transposition functions: ; recombinase or integrase functions: and ; DNA partition: ; unknown function: open reading frames indicated by white arrows. The prefix Δ indicates a truncated functionally inactive gene. The boxes in the map of pCCK13698 indicate the limits of the insertion sequences IS and IS; the arrows within these boxes indicate the reading frames of the corresponding transposase genes. Gray-shaded areas indicate the regions common to plasmids, and the different shades of gray illustrate the percentages of nucleotide sequence identity between the plasmids, as indicated by the scale at the bottom of the figure. A distance scale in kilobases is shown.

Citation: Michael G, Bossé J, Schwarz S. 2018. Antimicrobial Resistance in of Veterinary Origin, p 331-363. In Schwarz S, Cavaco L, Shen J (ed), Antimicrobial Resistance in Bacteria from Livestock and Companion Animals. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.ARBA-0022-2017
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Tables

Antimicrobial Resistance in Pasteurellaceae of Veterinary Origin
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Citation: Michael G, Bossé J, Schwarz S. 2018. Antimicrobial Resistance in of Veterinary Origin, p 331-363. In Schwarz S, Cavaco L, Shen J (ed), Antimicrobial Resistance in Bacteria from Livestock and Companion Animals. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.ARBA-0022-2017
/content/10.1128/9781555819804.chap15.tab15-1
Table 1
Percentages of resistance of , , , and isolates from different animal sources against selected antimicrobial agents
Generic image for table
Table 1

Percentages of resistance of , , , and isolates from different animal sources against selected antimicrobial agents

Citation: Michael G, Bossé J, Schwarz S. 2018. Antimicrobial Resistance in of Veterinary Origin, p 331-363. In Schwarz S, Cavaco L, Shen J (ed), Antimicrobial Resistance in Bacteria from Livestock and Companion Animals. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.ARBA-0022-2017
/content/10.1128/9781555819804.chap15.tab15-2
Table 2
Antimicrobial resistance genes and mutations identified in , , , , and isolates of veterinary importance
Generic image for table
Table 2

Antimicrobial resistance genes and mutations identified in , , , , and isolates of veterinary importance

Citation: Michael G, Bossé J, Schwarz S. 2018. Antimicrobial Resistance in of Veterinary Origin, p 331-363. In Schwarz S, Cavaco L, Shen J (ed), Antimicrobial Resistance in Bacteria from Livestock and Companion Animals. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.ARBA-0022-2017
/content/10.1128/9781555819804.chap15.tab15-3
Table 3
Subset of resistance plasmids identified in , , and of veterinary importance
Generic image for table
Table 3

Subset of resistance plasmids identified in , , and of veterinary importance

Citation: Michael G, Bossé J, Schwarz S. 2018. Antimicrobial Resistance in of Veterinary Origin, p 331-363. In Schwarz S, Cavaco L, Shen J (ed), Antimicrobial Resistance in Bacteria from Livestock and Companion Animals. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.ARBA-0022-2017

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