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Chapter 14 : Species

Authors: Ben D. Tall1, Gopal Gopinath2, Jayanthi Gangiredla3, Isha R. Patel4, Séamus Fanning5, Angelika Lehner6
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Affiliations: 1: Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland; 2: Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland; 3: Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland; 4: Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland; 5: UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College, Dublin & WHO Collaborating Centre for Cronobacter, Belfield, Dublin, Ireland; 6: Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
Content Type: Reference
Publication Year: 2019

Category: Food Microbiology

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Abstract:

The genus currently consists of seven species, including , , , , , , and This genus is now regarded as an opportunistic group of pathogenic bacteria with remarkable versatility in their abilities to cause disease in humans. It is now realized that infections due to can affect susceptible individuals, including neonates, infants, and elderly individuals, and it continues to attract attention in national and international media. species are recognized as being considerably more ecologically widespread than was once thought, and they have been found to be associated with many low-water-activity foods and environments, including powdered infant formula (PIF) and follow-up formulas, as well as in filth and stable flies, PIF and milk powder production facilities, household environments, and water. Pathogen-specific virulence factors have been discovered that adversely affect a wide range of eukaryotic cell and host processes, including protein synthesis, cell division, and proinflammatory host responses. A variety of mobile genetic elements, such as plasmids, transposons, and pathogenicity islands, have been identified, and this genomic plasticity implies ongoing microevolution with the possible acquisition of new virulence factors that will undoubtedly complicate efforts to classify these organisms into various subgroups or into sharply delineated genomopathotypes. This chapter describes the dynamic nature of , which is a highly diverse, versatile, opportunistic pathogen that will continue to present challenges for the global food safety and public health communities in terms of diagnosis, treatment, and prevention of infections.

Citation: Tall B, Gopinath G, Gangiredla J, Patel I, Fanning S, Lehner A. 2019. Species, p 389-414. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch14
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Cronobacter Species
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Citation: Tall B, Gopinath G, Gangiredla J, Patel I, Fanning S, Lehner A. 2019. Species, p 389-414. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch14
/content/10.1128/9781555819972.ch14.ch14fig1
Figure 14.1
Transmission electron photomicrograph of strain BAA-894 negatively stained with 0.5% sodium phosphotungstate (pH 6.8) showing numerous peritrichous flagella. Bar, 0.5 µm.
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Image of Figure 14.1
Figure 14.1

Transmission electron photomicrograph of strain BAA-894 negatively stained with 0.5% sodium phosphotungstate (pH 6.8) showing numerous peritrichous flagella. Bar, 0.5 µm.

Citation: Tall B, Gopinath G, Gangiredla J, Patel I, Fanning S, Lehner A. 2019. Species, p 389-414. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch14
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Figure 14.2
Revised FDA isolation and detection method, adapted from chapter 29 of the Bacteriological Analytical Manual (https://www.fda.gov/Food/FoodScienceResearch/LaboratoryMethods/ucm289378.htm). BPW, buffered peptone water; PBS, phosphate-buffered saline; R&F, plating medium.
10.1128/9781555819972/9972ch14fig2_thmb.gif
10.1128/9781555819972/9972ch14fig2.gif
Image of Figure 14.2
Figure 14.2

Revised FDA isolation and detection method, adapted from chapter 29 of the Bacteriological Analytical Manual (https://www.fda.gov/Food/FoodScienceResearch/LaboratoryMethods/ucm289378.htm). BPW, buffered peptone water; PBS, phosphate-buffered saline; R&F, plating medium.

Citation: Tall B, Gopinath G, Gangiredla J, Patel I, Fanning S, Lehner A. 2019. Species, p 389-414. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch14
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Figure 14.3
Neighbor net (SplitsTree4) analysis of 126 and phylogenetically related strains which were generated from the microarray-based gene differences described by Tall et al. ( ). The phylogenetic tree illustrates that the microarray could clearly separate the seven species of , with each species forming its own distinct cluster. subclades are designated with roman numerals I through VII. The scale bar represents 0.01 base substitution per site. Reprinted from reference with permission.
10.1128/9781555819972/9972ch14fig3_thmb.gif
10.1128/9781555819972/9972ch14fig3.gif
Image of Figure 14.3
Figure 14.3

Neighbor net (SplitsTree4) analysis of 126 and phylogenetically related strains which were generated from the microarray-based gene differences described by Tall et al. ( ). The phylogenetic tree illustrates that the microarray could clearly separate the seven species of , with each species forming its own distinct cluster. subclades are designated with roman numerals I through VII. The scale bar represents 0.01 base substitution per site. Reprinted from reference with permission.

Citation: Tall B, Gopinath G, Gangiredla J, Patel I, Fanning S, Lehner A. 2019. Species, p 389-414. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch14
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Figure 14.4
Phylogenetic analysis using the neighbor-joining algorithm of 34 , 10 , and eight -related genomes based on the alignment of SNPs from 300 orthologous genes as described by Stephan et al. ( ). Clades are represented by roman numerals 1 through V. Clade I represents genomes from species. Clade II represents genomes from and strains. Clade III represents genomes from two strains and genomes from , , , and strains. Clade IV represents genomes from strains. Lastly, genomes from two strains are represented in clade V. The scale bar represents 0.05 base substitution per site. Reprinted from reference with permission.
10.1128/9781555819972/9972ch14fig4_thmb.gif
10.1128/9781555819972/9972ch14fig4.gif
Image of Figure 14.4
Figure 14.4

Phylogenetic analysis using the neighbor-joining algorithm of 34 , 10 , and eight -related genomes based on the alignment of SNPs from 300 orthologous genes as described by Stephan et al. ( ). Clades are represented by roman numerals 1 through V. Clade I represents genomes from species. Clade II represents genomes from and strains. Clade III represents genomes from two strains and genomes from , , , and strains. Clade IV represents genomes from strains. Lastly, genomes from two strains are represented in clade V. The scale bar represents 0.05 base substitution per site. Reprinted from reference with permission.

Citation: Tall B, Gopinath G, Gangiredla J, Patel I, Fanning S, Lehner A. 2019. Species, p 389-414. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch14
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Figure 14.5
Sequence alignment of plasmids pESA3 and pCTU1 produced with the Artemis comparison tool as described by Franco et al. ( ) and showing regions of homology. In the middle section, the red color indicates significant nucleotide homology, as determined by BLASTn analysis, between pESA3 and pCTU1, and the location on each plasmid, for example, , , , and . White areas indicate regions or loci present on one plasmid and absent on the other, e.g., , T6SS genes, and FHA genes. The sequence of pESA3 was modified by rejoining the gene at the 3′ end, which is split in the GenBank sequence (NCBI RefSeq accession no. NC_009780.1). pESA3 and pCTU1 (NCBI RefSeq accession no. NC_009780.1) possess molecular sizes of 131,196 and 138,339 kb and mean G+C contents of 56.85% and 56.05%, respectively. Selected genes or loci are shown in color as follows: , red; , orange; and , purple; integrase genes, black, and associated genes, white; , teal; T6SS genes, blue; and FHA genes, brown. Reproduced from reference with permission.
10.1128/9781555819972/9972ch14fig5_thmb.gif
10.1128/9781555819972/9972ch14fig5.gif
Image of Figure 14.5
Figure 14.5

Sequence alignment of plasmids pESA3 and pCTU1 produced with the Artemis comparison tool as described by Franco et al. ( ) and showing regions of homology. In the middle section, the red color indicates significant nucleotide homology, as determined by BLASTn analysis, between pESA3 and pCTU1, and the location on each plasmid, for example, , , , and . White areas indicate regions or loci present on one plasmid and absent on the other, e.g., , T6SS genes, and FHA genes. The sequence of pESA3 was modified by rejoining the gene at the 3′ end, which is split in the GenBank sequence (NCBI RefSeq accession no. NC_009780.1). pESA3 and pCTU1 (NCBI RefSeq accession no. NC_009780.1) possess molecular sizes of 131,196 and 138,339 kb and mean G+C contents of 56.85% and 56.05%, respectively. Selected genes or loci are shown in color as follows: , red; , orange; and , purple; integrase genes, black, and associated genes, white; , teal; T6SS genes, blue; and FHA genes, brown. Reproduced from reference with permission.

Citation: Tall B, Gopinath G, Gangiredla J, Patel I, Fanning S, Lehner A. 2019. Species, p 389-414. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch14
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Tables

Cronobacter Species
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Citation: Tall B, Gopinath G, Gangiredla J, Patel I, Fanning S, Lehner A. 2019. Species, p 389-414. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch14
/content/10.1128/9781555819972.ch14.ch14tab1
Table 14.1
Generic image for table
Table 14.1

Citation: Tall B, Gopinath G, Gangiredla J, Patel I, Fanning S, Lehner A. 2019. Species, p 389-414. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch14
/content/10.1128/9781555819972.ch14.ch14tab2
Table 14.2
Generic image for table
Table 14.2

Citation: Tall B, Gopinath G, Gangiredla J, Patel I, Fanning S, Lehner A. 2019. Species, p 389-414. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch14
/content/10.1128/9781555819972.ch14.ch14tab3
Table 14.3
Generic image for table
Table 14.3

Citation: Tall B, Gopinath G, Gangiredla J, Patel I, Fanning S, Lehner A. 2019. Species, p 389-414. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch14

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