Detection of Enterobacterial Lipopolysaccharides and Experimental Endotoxemia by Means of an Immunolimulus Assay Using Both SerotypeSpecific and Cross-Reactive Antibodies

The immunolimulus (IML) assay system uses solid-phase endotoxin antibodies to capture lipopolysaccharide (LPS), which is then quantified by a modification of the chromogenic limulus amebocyte lysate (CLAL) method. Monoclonal antibodies (MAbs) reactive with selected 0 antigen serotypes of Escherichia coli (O18) and Salmonella typhimurium (O-9,12), when used in the IML, were shown to be highly specific in detecting their respective endotoxins in purified form and in plasma samples from experimentally infected animals. A murine MAb that was broadly cross-reactive with E. coli, Salmonella, and Shigella endotoxins also proved to be highly effective in the IML assay for capturing LPS molecules from both E. coli and S. typhimurium strains. These results indicate that IML assays can detect smooth-type enterobacterial endotoxins in plasma and suggest that such assays have potential for use in the rapid diagnosis of sepsis and endotoxemia caused by different enterobacterial specie

The first human report of mobile colistin resistance gene, mcr-1, in Finland

Colistin resistance mediated by mobile mcr-1 gene has raised concern during the last years. After steep increase in mcr-1 reports, other mcr-gene variants (mcr-2 to mcr-5) have been revealed as well. In 2016, a clinical study was conducted on asymptomatic stool carriage of extended spectrum beta-lactamase (ESBL) producing Escherichia coli and Klebsiella pneumoniae among Finnish adults. All suspected ESBL producing bacterial isolates were first tested by phenotypic ESBL-confirmation methods, and then further analyzed with whole genome sequencing to identify the resistance genes. We found one study subject carrying a colistin resistant E.coli with a transferrable mcr-1 gene. This multi-drug resistant isolate, although initially suspected to be an ESBL producer, did not carry any ESBL genes, but was proven to carry several other resistance genes by using whole genome sequencing. Sequence type was ST93. The mcr-1 gene was connected to IncX4 plasmid which suggests that the colistin resistance gene locates in the respective plasmid. Here, we report the finding of a mcr-1 harboring human E.coli isolate from Finland. Clinical antimicrobial resistance (AMR) rates are low in Finland, and mobile colistin resistance has not been reported previously. This highlights the importance of AMR surveillance also in populations with low levels of resistance

Sequence analysis of pooled bacterial samples enables identification of strain variation in group A streptococcus

Knowledge of the genomic variation among different strains of a pathogenic microbial species can help in selecting optimal candidates for diagnostic assays and vaccine development. Pooled sequencing (Pool-seq) is a cost effective approach for population level genetic studies that require large numbers of samples such as various strains of a microbe. To test the use of Pool-seq in identifying variation, we pooled DNA of 100 Streptococcus pyogenes strains of different emm types in two pools, each containing 50 strains. We used four variant calling tools (Freebayes, UnifiedGenotyper, SNVer, and SAMtools) and one emm1 strain, SF370, as a reference genome. In total 63719 SNPs and 164 INDELs were identified in the two pools concordantly by at least two of the tools. Majority of the variants (93.4%) from six individually sequenced strains used in the pools could be identified from the two pools and 72.3% and 97.4% of the variants in the pools could be mined from the analysis of the 44 complete Str. pyogenes genomes and 3407 sequence runs deposited in the European Nucleotide Archive respectively. We conclude that DNA sequencing of pooled samples of large numbers of bacterial strains is a robust, rapid and cost-efficient way to discover sequence variation

The Psoriasis Risk Allele HLA-C*06:02 Shows Evidence of Association with Chronic or Recurrent Streptococcal Tonsillitis

Pharyngeal tonsillitis is one of the most common upper respiratory tract infections, and group A streptococcus is the most important bacterial pathogen causing it. While most patients experience tonsillitis only rarely, a subset of patients suffers from recurrent or chronic tonsillitis or pharyngitis. The predisposing factors for recurring or chronic forms of this disease are not yet fully understood, but genetic predisposition has been suggested. A genetic association study using Illumina's Immunochip single-nucleotide polymorphism (SNP) array was performed to search for new genetic biomarkers in pharyngeal tonsillitis. More than 100,000 SNPs relevant to immune-mediated diseases were analyzed in a cohort of 95 patients subjected to tonsillectomy due to recurrent/chronic tonsillitis and 504 controls. Genetic association between the cases and controls showed strongest association with two peaks in the HLA locus (odds ratio [OR], 3.7 to 4.7; P = 4.9 x 10(-6) to 5.7 x 10(-6)). Further analysis with imputed classical HLA alleles suggested the known psoriasis risk allele HLA-C*06:02 as a risk factor for tonsillitis (P = 4.8 x 10(-4); OR, 2.3). In addition, the imputed HLA haplotype HLA-C*06:02/HLA-B*57:01, a reported risk haplotype in psoriasis, had the strongest risk for tonsillitis (P = 3.2 x 10(-4); OR, 6.5). These findings further support the previously reported link between streptococcal throat infections and psoriasis

Antimicrobial resistance among bacteria isolated from urinary tract infections in females in Namibia, 2016-2017

Background: The emergence of antimicrobial resistance (AMR) among bacterial pathogens demands a local understanding of the epidemiological situation. This information is needed both for clinical treatment decision-making purposes as well as for the revision of current care guidelines. Clinical AMR data from Namibia is sparse, whilst urinary tract infections remain not only widespread but they disproportionally affect females. This paper aims to describe the national antimicrobial resistance situation of major bacterial uropathogens in females within the 14 Namibian regions.Method: Retrospective countrywide information on clinical urine cultures performed in females in Namibia in 2016-2017 was obtained from the national public health laboratory, Namibia Institute of Pathology (NIP). The data set included both microbiological findings as well as antimicrobial susceptibility test (AST) results. The AST was done as per the Clinical and Laboratory Standards Institute (CLSI) guidelines. Resistance to 3rd generation cephalosporins was indicative of Extended Spectrum-ß-lactamase (ESBL) production. Data analysis was done with WHONET using expert interpretation rules.Results: In total, 22,259 urinary cultures were performed, of which 13,673 (61.4%) were culture positive. Gram-negative bacterial species accounted for 72.6% of the findings. The most common pathogens identified were Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis. Most of these were from young females, with a median age ranging from 28 to 32 years for the various pathogens. Resistance to ampicillin was 77.7% in E. coli and 84.9% in K. pneumoniae. In E. coli, resistance to 1st line empiric therapy antibiotic, nitrofurantoin, was below 13%, except for one region that showed 59.2% resistance. Resistance to third generation cephalosporin (3GC) was used as a proxy for ESBL production. By year 2017, 3GC resistance was 22%, 31.4% and 8.3% for E. coli, K. pneumoniae and P. mirabilis, respectively.Conclusion: We report high resistance to ampicillin, quinolones and sulfamethoxazole-trimethoprim amongst E. coli. Resistance rates to third-generation cephalosporins was also concerningly high at 22%. Resistance to carbapenems was low. However, superiority of nitrofurantoin was found, which provides rational support for the usefulness of nitrofurantoin as an empiric therapy regimen for the treatment of urinary tract infections in this setting.</p

Assessment of resolution and intercenter reproducibility of results of genotyping Staphylococcus aureus by pulsed-field gel electrophoresis of SmaI macrorestriction fragments: a multicenter study

Twenty well-characterized isolates of methicillin-resistant Staphylococcus aureus were used to study the optimal resolution and interlaboratory reproducibility of pulsed-field gel electrophoresis (PFGE) of DNA macrorestriction fragments. Five identical isolates (one PFGE type), 5 isolates that produced related PFGE subtypes, and 10 isolates with unique PFGE patterns were analyzed blindly in 12 different laboratories by in-house protocols. In several laboratories a standardized PFGE protocol with a commercial kit was applied successfully as well. Eight of the centers correctly identified the genetic homogeneity of the identical isolates by both the in-house and standard protocols. Four of 12 laboratories failed to produce interpretable data by the standardized protocol, due to technical problems (primarily plug preparation). With the five rel