WGS-Based Phenotyping and Molecular Characterization of the Resistome, Virulome and Plasmid Replicons in Klebsiella pneumoniae Isolates from Powdered Milk Produced in Germany

Abstract

The emergence of Klebsiella pneumoniae (K. pneumoniae) 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 K. pneumoniae 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, blaSHV variants were identified in all isolates, of which blaSHV-187 was most prevalent and found in 50% of isolates. Single-nucleotide-variants of oqxA and oqxB conferring resistance to phenicol/quinolone were found in all isolates, and the oqxB17 was the most prevalent found in 46% of isolates. 67% of isolates harbored fosA 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 (entB, fepC), six adherence-related genes belonging to E. coli common pilus (ECP) and one secretion system (ompA 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 K. pneumoniae. 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 K. pneumoniae 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.

Epidemiological Features of Klebsiella pneumoniae Infection in the Hepatobiliary System of Patients in Yantai, China, Based on Clinical and Genetic Analyses

“… 21 The regulator of mucoid phenotype rmpA/rmpA2, allS (involved in allantoin metabolism) and mceG (an energy-related gene) are also used to distinguish between hvKP and cKP strains. 22 , 23 A combination of these biomarkers (eg, peg-344, iroB, iucA and rmpA/rmpA2 ) showed higher accuracy in the diagnosis of hvKP than a single phenotype or single virulence-associated gene alone.…”

Antimicrobial susceptibility profile of Klebsiella pneumoniae isolated from some dairy products in Libya as a foodborne pathogen

“…As reported by Liu et al [20], K. pneumoniae has been recovered from modular industrialized enteral diets and milk-based and food supplements used in public hospitals. As documented by Wareth et al [14], K. pneumoniae is among the most frequently isolated bacterial species in milk substitution formulas for infants collected from 35 countries. Pasteurized milk and whole milk powder samples collected from retail shops in Mexico, there has been a high incidence of MDR strains, which represents a public health hazard.…”

“…pneumoniae was isolated from 2 samples (20%) of full cream milk powder (Table-1). For instance, Wareth et al [14] obtained 24 isolates of K. pneumoniae from milk powder producer companies in Libya. To the best of our knowledge, this is the first report to describe the presence of K. pneumoniae in milk powder in Libya, which may be a result of post-processing contamination.…”

Genomic characterisation of an extended-spectrum β-Lactamase- producing Klebsiella pneumoniae isolate assigned to a novel sequence type (6914)

“…The only plasmids found in the present genome were IncFIB(K)-1-Kpn3 and Col440I_1. These plasmids were respectively detected in 16 (67%) and 11 (46%) of 24 K. pneumoniae isolates from powdered milk from Germany [17]. Additionally, ve bacteriophages were detected, of which three (Klebsi phiKO2, Escher 500465, Entero cdtI) were intact, one (Salmon 118970 sal3) was incomplete, and one (Escher RCS47) yielded inconclusive results.…”