WGS-Based Phenotyping and Molecular Characterization of the Resistome, Virulome and Plasmid Replicons in <i>Klebsiella pneumoniae</i> Isolates from Powdered Milk Produced in Germany
The emergence of <i>Klebsiella pneumoniae</i> (<i>K. pneumoniae</i>) in German healthcare is worrying. It is not well-investigated in the veterinary world and food chains. In the current study, antibiotic susceptibility profiles of 24 <i>K. pneumoniae</i> strains...
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MDPI AG
2022-03-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/10/3/564 |
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| author | Gamal Wareth Jörg Linde Philipp Hammer Mathias W. Pletz Heinrich Neubauer Lisa D. Sprague |
| author_facet | Gamal Wareth Jörg Linde Philipp Hammer Mathias W. Pletz Heinrich Neubauer Lisa D. Sprague |
| author_sort | Gamal Wareth |
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| description | The emergence of <i>Klebsiella pneumoniae</i> (<i>K. pneumoniae</i>) in German healthcare is worrying. It is not well-investigated in the veterinary world and food chains. In the current study, antibiotic susceptibility profiles of 24 <i>K. pneumoniae</i> strains isolated from powdered milk samples produced in Germany were investigated by a microdilution test. Next-generation sequencing (NGS) was applied to identify genomic determinants for antimicrobial resistance (AMR), virulence-associated genes and plasmids replicons. All isolates were susceptible to the majority (14/18) of tested antibiotics. Resistance to colistin, fosfomycin, chloramphenicol and piperacillin was found. The ambler class A ß-lactamase, <i>bla</i><sub>SHV</sub> variants were identified in all isolates, of which <i>bla</i><sub>SHV-187</sub> was most prevalent and found in 50% of isolates. Single-nucleotide-variants of <i>oqx</i>A and <i>oqx</i>B conferring resistance to phenicol/quinolone were found in all isolates, and the <i>oqx</i>B17 was the most prevalent found in 46% of isolates. 67% of isolates harbored <i>fos</i>A genes; however, only one was fosfomycin-resistant. Two isolates harbored genes conferring resistance to colistin, despite being susceptible. The majority of identified virulome genes were iron uptake siderophores. Two enterobactins (<i>ent</i>B, <i>fep</i>C), six adherence-related genes belonging to <i>E. coli</i> common pilus (ECP) and one secretion system (<i>omp</i>A gene) were found in all isolates. In contrast, yersiniabactin was found in two isolates. One ST23 strain was susceptible to all tested antibiotics, and harbored determinants discriminatory for hypervirulent strains, e.g., aerobactin, salmochelin, yersiniabactin, enterobactin and regulator of mucoid phenotype A genes that are highly associated with hypervirulent <i>K. pneumoniae</i>. The IncF plasmid family was found in all strains, while almost half of the isolates harbored Col440I-type plasmids and nine isolates harbored various Inc-type plasmids. The presence of <i>K. pneumoniae</i> carrying different resistomes and major virulent specific virulomes in powdered milk samples is alarming. This could threaten public health, particularly of neonates and infants consuming dried milk. |
| first_indexed | 2024-03-09T13:15:51Z |
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| last_indexed | 2024-03-09T13:15:51Z |
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| spelling | doaj.art-c89dcdb065c245b3891f5051f2eda2562023-11-30T21:36:08ZengMDPI AGMicroorganisms2076-26072022-03-0110356410.3390/microorganisms10030564WGS-Based Phenotyping and Molecular Characterization of the Resistome, Virulome and Plasmid Replicons in <i>Klebsiella pneumoniae</i> Isolates from Powdered Milk Produced in GermanyGamal Wareth0Jörg Linde1Philipp Hammer2Mathias W. Pletz3Heinrich Neubauer4Lisa D. Sprague5Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, GermanyFriedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, GermanyDepartment of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, GermanyInstitute for Infectious Diseases and Infection Control, Jena University Hospital, Jena University, 07743 Jena, GermanyFriedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, GermanyFriedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, GermanyThe emergence of <i>Klebsiella pneumoniae</i> (<i>K. pneumoniae</i>) in German healthcare is worrying. It is not well-investigated in the veterinary world and food chains. In the current study, antibiotic susceptibility profiles of 24 <i>K. pneumoniae</i> strains isolated from powdered milk samples produced in Germany were investigated by a microdilution test. Next-generation sequencing (NGS) was applied to identify genomic determinants for antimicrobial resistance (AMR), virulence-associated genes and plasmids replicons. All isolates were susceptible to the majority (14/18) of tested antibiotics. Resistance to colistin, fosfomycin, chloramphenicol and piperacillin was found. The ambler class A ß-lactamase, <i>bla</i><sub>SHV</sub> variants were identified in all isolates, of which <i>bla</i><sub>SHV-187</sub> was most prevalent and found in 50% of isolates. Single-nucleotide-variants of <i>oqx</i>A and <i>oqx</i>B conferring resistance to phenicol/quinolone were found in all isolates, and the <i>oqx</i>B17 was the most prevalent found in 46% of isolates. 67% of isolates harbored <i>fos</i>A genes; however, only one was fosfomycin-resistant. Two isolates harbored genes conferring resistance to colistin, despite being susceptible. The majority of identified virulome genes were iron uptake siderophores. Two enterobactins (<i>ent</i>B, <i>fep</i>C), six adherence-related genes belonging to <i>E. coli</i> common pilus (ECP) and one secretion system (<i>omp</i>A gene) were found in all isolates. In contrast, yersiniabactin was found in two isolates. One ST23 strain was susceptible to all tested antibiotics, and harbored determinants discriminatory for hypervirulent strains, e.g., aerobactin, salmochelin, yersiniabactin, enterobactin and regulator of mucoid phenotype A genes that are highly associated with hypervirulent <i>K. pneumoniae</i>. The IncF plasmid family was found in all strains, while almost half of the isolates harbored Col440I-type plasmids and nine isolates harbored various Inc-type plasmids. The presence of <i>K. pneumoniae</i> carrying different resistomes and major virulent specific virulomes in powdered milk samples is alarming. This could threaten public health, particularly of neonates and infants consuming dried milk.https://www.mdpi.com/2076-2607/10/3/564<i>Klebsiella pneumoniae</i>WGSresistomeplasmidomevirulomepowdered milk |
| spellingShingle | Gamal Wareth Jörg Linde Philipp Hammer Mathias W. Pletz Heinrich Neubauer Lisa D. Sprague WGS-Based Phenotyping and Molecular Characterization of the Resistome, Virulome and Plasmid Replicons in <i>Klebsiella pneumoniae</i> Isolates from Powdered Milk Produced in Germany Microorganisms <i>Klebsiella pneumoniae</i> WGS resistome plasmidome virulome powdered milk |
| title | WGS-Based Phenotyping and Molecular Characterization of the Resistome, Virulome and Plasmid Replicons in <i>Klebsiella pneumoniae</i> Isolates from Powdered Milk Produced in Germany |
| title_full | WGS-Based Phenotyping and Molecular Characterization of the Resistome, Virulome and Plasmid Replicons in <i>Klebsiella pneumoniae</i> Isolates from Powdered Milk Produced in Germany |
| title_fullStr | WGS-Based Phenotyping and Molecular Characterization of the Resistome, Virulome and Plasmid Replicons in <i>Klebsiella pneumoniae</i> Isolates from Powdered Milk Produced in Germany |
| title_full_unstemmed | WGS-Based Phenotyping and Molecular Characterization of the Resistome, Virulome and Plasmid Replicons in <i>Klebsiella pneumoniae</i> Isolates from Powdered Milk Produced in Germany |
| title_short | WGS-Based Phenotyping and Molecular Characterization of the Resistome, Virulome and Plasmid Replicons in <i>Klebsiella pneumoniae</i> Isolates from Powdered Milk Produced in Germany |
| title_sort | wgs based phenotyping and molecular characterization of the resistome virulome and plasmid replicons in i klebsiella pneumoniae i isolates from powdered milk produced in germany |
| topic | <i>Klebsiella pneumoniae</i> WGS resistome plasmidome virulome powdered milk |
| url | https://www.mdpi.com/2076-2607/10/3/564 |
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