Amplified-fragment length polymorphism analysis of Propionibacterium isolates implicated in contamination of blood products

Amplified fragment length polymorphism and whole genome sequencing: a comparison of methods in the investigation of a nosocomial outbreak with vancomycin resistant enterococci

Background

Recognition of nosocomial outbreaks with antimicrobial resistant (AMR) pathogens and appropriate infection prevention measures are essential to limit the consequences of AMR pathogens to patients in hospitals. Because unrelated, but genetically similar AMR pathogens may circulate simultaneously, rapid high-resolution molecular typing methods are needed for outbreak management. We compared amplified fragment length polymorphism (AFLP) and whole genome sequencing (WGS) during a nosocomial outbreak of vancomycin-resistant Enterococcus faecium (VRE) that spanned 5 months.

Methods

Hierarchical clustering of AFLP profiles was performed using unweighted pair-grouping and similarity coefficients were calculated with Pearson correlation. For WGS-analysis, core single nucleotide polymorphisms (SNPs) were used to calculate the pairwise distance between isolates, construct a maximum likelihood phylogeny and establish a cut-off for relatedness of epidemiologically linked VRE isolates. SNP-variations in the vanB gene cluster were compared to increase the comparative resolution. Technical replicates of 2 isolates were sequenced to determine the number of core-SNPs derived from random sequencing errors.

Results

Of the 721 patients screened for VRE carriage, AFLP assigned isolates of 22 patients to the outbreak cluster. According to WGS, all 22 isolates belonged to ST117 but only 21 grouped in a tight phylogenetic cluster and carried vanB resistance gene clusters. Sequencing of technical replicates showed that 4-5 core-SNPs were derived by random sequencing errors. The cut-off for relatedness of epidemiologically linked VRE isolates was established at ≤7 core-SNPs. The discrepant isolate was separated from the index isolate by 61 core-SNPs and the vanB gene cluster was absent. In AFLP analysis this discrepant isolate was indistinguishable from the other outbreak isolates, forming a cluster with 92% similarity (cut-off for identical isolates ≥90%). The inclusion of the discrepant isolate in the outbreak resulted in the screening of 250 patients and quarantining of an entire ward.

Conclusion

AFLP was a rapid and affordable screening tool for characterising hospital VRE outbreaks. For in-depth understanding of the outbreak WGS was needed. Compared to AFLP, WGS provided higher resolution typing of VRE isolates with implications for outbreak management.

The infection risk scan (IRIS): standardization and transparency in infection control and antimicrobial use

Background

Infection control needs user-friendly standardized instruments to measure the compliance to guidelines and to implement targeted improvement actions. This abstract describes a tool to measure the quality of infection control and antimicrobial use, the Infection Risk Scan (IRIS). It has been applied in a hospital, several nursing homes and a rehabilitation clinic in the Netherlands.

Method

The IRIS consists of a set of objective reproducible measurements, combining patient- and healthcare related variables, such as: hand hygiene compliance, environmental contamination using ATP measurements, prevalence of resistant microorganisms by active screening, availability of infection control preconditions, personal hygiene of healthcare workers, appropriate use of indwelling medical devices and appropriate use of antimicrobials. Results are visualized in a spider plot using traffic light colors to facilitate the interpretation.

Results

The IRIS provided ward specific results within the hospital that were the basis for targeted improvement programs resulting in measurable improvements. Hand hygiene compliance increased from 43% to 66% (more than 1000 observations per IRIS, p < 0.000) and ATP levels were significantly reduced (p < 0.000). In the nursing homes, large differences were observed with environmental contamination as common denominator. Most remarkable were the difference in Extended Spectrum Beta-Lactamase Enterobacteriaceae (ESBL-E) prevalence (mean 11%, range 0–21%).

Conclusion

The bundle approach and visualization of the IRIS makes it a useful infection prevention tool providing standardization and transparency. Targeted interventions can be started based on the results of the improvement plot and repeated IRIS can show the effect of interventions. In that way, a quality control cycle with continuous improvement can be achieved.

Diarrhea, Urosepsis and Hemolytic Uremic Syndrome Caused by the Same Heteropathogenic Escherichia coli Strain

We describe an 8-month-old girl with diarrhea, urosepsis and hemolytic uremic syndrome caused by Escherichia coli. Typing of cultured E. coli strains from urine and blood revealed the presence of virulence factors from multiple pathotypes of E. coli. This case exemplifies the genome plasticity of E. coli and the resulting heteropathogenic strains.

Trends in Extended Spectrum Beta-Lactamase (ESBL) Producing Enterobacteriaceae and ESBL Genes in a Dutch Teaching Hospital, Measured in 5 Yearly Point Prevalence Surveys (2010-2014)

This paper describes the trends in prevalence of ESBL producing Enterobacteriaceae (ESBL-E) and ESBL genes, measured in five consecutive yearly Point Prevalence Surveys (PPS). All patients present in the hospital and in a day-care clinic (including patients on dialysis) on the day of the survey, were screened for perianal ESBL-E carriage. Perianal swabs were taken and cultured using an enrichment broth and a selective agar plate. Both phenotypic and genotypic methods were used to detect the production of ESBL, presence of ESBL-genes and clonal relatedness. Out of 2,695 patients, 135 (5.0%) were tested ESBL-E positive. The overall ESBL-E prevalence was stable over the years. Overall 5.2% of all ESBL-E were acquired by nosocomial transmission. A relative decrease of CTX-M-1-1-like ESBL genes (from 44 to 25%, p = 0.026) was observed, possibly related to the strong (>60%) decrease in antibiotic use in livestock in our country during the same period.

Next-generation sequencing for typing and detection of resistance genes: performance of a new commercial method during an outbreak of extended-spectrum-beta-lactamase-producing Escherichia coli

Next-generation sequencing (NGS) has the potential to provide typing results and detect resistance genes in a single assay, thus guiding timely treatment decisions and allowing rapid tracking of transmission of resistant clones. We evaluated the performance of a new NGS assay (Hospital Acquired Infection BioDetection System; Pathogenica) during an outbreak of sequence type 131 (ST131) Escherichia coli infections in a nursing home in The Netherlands. The assay was performed on 56 extended-spectrum-beta-lactamase (ESBL) E. coli isolates collected during 2 prevalence surveys (March and May 2013). Typing results were compared to those of amplified fragment length polymorphism (AFLP), whereby we visually assessed the agreement of the BioDetection phylogenetic tree with clusters defined by AFLP. A microarray was considered the gold standard for detection of resistance genes. AFLP identified a large cluster of 31 indistinguishable isolates on adjacent departments, indicating clonal spread. The BioDetection phylogenetic tree showed that all isolates of this outbreak cluster were strongly related, while the further arrangement of the tree also largely agreed with other clusters defined by AFLP. The BioDetection assay detected ESBL genes in all but 1 isolate (sensitivity, 98%) but was unable to discriminate between ESBL and non-ESBL TEM and SHV beta-lactamases or to specify CTX-M genes by group. The performance of the hospital-acquired infection (HAI) BioDetection System for typing of E. coli isolates compared well with the results of AFLP. Its performance with larger collections from different locations, and for typing of other species, was not evaluated and needs further study.

Antimicrobial resistance, toxinotype, and genotypic profiling of Clostridium difficile isolates of swine origin

The occurrence of Clostridium difficile infections in patients that do not fulfill the classical risk factors prompted us to investigate new risk factors of disease. The goal of this study was to characterize strains and associated antimicrobial resistance determinants of C. difficile isolated from swine raised in Ohio and North Carolina. Genotypic approaches used include PCR detection, toxinotyping, DNA sequencing, and pulsed-field gel electrophoresis (PFGE) DNA fingerprinting. Thirty-one percent (37/119) of isolates carried both tetM and tetW genes. The ermB gene was found in 91% of isolates that were resistant to erythromycin (68/75). Eighty-five percent (521/609) of isolates were toxin gene tcdB and tcdA positive. A total of 81% (494/609) of isolates were positive for cdtB and carry a tcdC gene (a toxin gene negative regulator) with a 39-bp deletion. Overall, 88% (196/223) of pigs carry a single C. difficile strain, while 12% (27/223) of pigs carried multiple strains. To the best of our knowledge, this is the first report of individual pigs found to carry more than one strain type of C. difficile. A significant difference in toxinotype profiles in the two geographic locations was noted, with a significantly (P < 0.001) higher prevalence of toxinotype V found in North Carolina (84%; 189/224) than in Ohio (55%; 99/181). Overall, the study findings indicate that significant proportions of C. difficile in swine are toxigenic and often are associated with antimicrobial resistance genes, although they are not resistant to drugs that are used to treat C. difficile infections.

Molecular relatedness of Propionibacterium species isolated from blood products and on the skin of blood donors

BACKGROUND

In this study it was investigated whether Propionibacterium acnes present in platelet concentrates (PCs) and related red blood cells (RBCs), originate from the skin of the donor.

STUDY DESIGN AND METHODS

P. acnes that were cultured throughout 2007 and 2008 from PCs and their accompanying RBCs and in 2010 from the phlebotomy site of a selection of the respective donors (n = 22) were typed by amplified fragment length polymorphism. A part of the strains was also determined to species level by sequencing of the 16S rRNA and recA genes.

RESULTS

Three different phylogenetic groups of P. acnes were found. The distribution of the P. acnes in three groups was confirmed by sequencing of the recA gene. All strains that were found in PCs and their accompanying RBCs were identical, which indicates that the strain is already present in the whole blood donation. P. acnes could be found on the skin of almost all screened donors. In eight of 22 cases (36.4%), one of the strains from the donor skin was identical to the strains found in PCs and their accompanying RBCs. In two other cases the strains belonged to the same phylogenetic group.

CONCLUSION

This study supports the theory that the source of P. acnes contamination is in many cases the skin of the donor. However, further study is necessary to rule out other sources of contamination. Because it is difficult to prevent bacterial contamination by P. acnes completely, it is necessary to further investigate the clinical significance of blood products contaminated with P. acnes.

Methicillin-resistant Staphylococcus aureus in meat products, the Netherlands

A new methicillin-resistant Staphylococcus aureus (MRSA) clone related to pig and cattle farming was detected in the Netherlands. We investigated the extent of S. aureus presence in meat and found 36 S. aureus strains in 79 samples. Two strains were MRSA; 1 was multilocus sequence type 398, the clone related to farming.

Comparison of seven techniques for typing international epidemic strains of Clostridium difficile: restriction endonuclease analysis, pulsed-field gel electrophoresis, PCR-ribotyping, multilocus sequence typing, multilocus variable-number tandem-repeat analysis, amplified fragment length polymorphism, and surface layer protein A gene sequence typing

Using 42 isolates contributed by laboratories in Canada, The Netherlands, the United Kingdom, and the United States, we compared the results of analyses done with seven Clostridium difficile typing techniques: multilocus variable-number tandem-repeat analysis (MLVA), amplified fragment length polymorphism (AFLP), surface layer protein A gene sequence typing (slpAST), PCR-ribotyping, restriction endonuclease analysis (REA), multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE). We assessed the discriminating ability and typeability of each technique as well as the agreement among techniques in grouping isolates by allele profile A (AP-A) through AP-F, which are defined by toxinotype, the presence of the binary toxin gene, and deletion in the tcdC gene. We found that all isolates were typeable by all techniques and that discrimination index scores for the techniques tested ranged from 0.964 to 0.631 in the following order: MLVA, REA, PFGE, slpAST, PCR-ribotyping, MLST, and AFLP. All the techniques were able to distinguish the current epidemic strain of C. difficile (BI/027/NAP1) from other strains. All of the techniques showed multiple types for AP-A (toxinotype 0, binary toxin negative, and no tcdC gene deletion). REA, slpAST, MLST, and PCR-ribotyping all included AP-B (toxinotype III, binary toxin positive, and an 18-bp deletion in tcdC) in a single group that excluded other APs. PFGE, AFLP, and MLVA grouped two, one, and two different non-AP-B isolates, respectively, with their AP-B isolates. All techniques appear to be capable of detecting outbreak strains, but only REA and MLVA showed sufficient discrimination to distinguish strains from different outbreaks.

High density whole genome fingerprinting of methicillin-resistant and -susceptible strains of Staphylococcus aureus in search of phenotype-specific molecular determinants

AFLP is a selective restriction fragment amplification method generating DNA fingerprints for microbial isolates. We present high-throughput AFLP (htAFLP) to characterize molecular markers associated with bacterial phenotypes. Methicillin-resistant and -susceptible isolates of Staphylococcus aureus have been used for this model study in conjunction with the available S. aureus genome sequences. This facilitates the calculation of theoretical AFLP fingerprints, comparison of these fingerprints with genuine experimental fingerprints, and the subsequent identification of polymorphic AFLP markers without sequence analysis. Analysis of 46 MRSA and 46 MSSA strains by 39 different AFLP reactions generated more than 2500 fragments per strain and an overall number of 6180 scorable markers within all strains. We successfully identify MRSA specific markers and elaborate on the general applicability of the htAFLP approach. This method can be applied to any microbial species for which at least one full-genome sequence is available.

Bacterial contamination of platelet concentrates: results of a prospective multicenter study comparing pooled whole blood-derived platelets and apheresis platelets

BACKGROUND

The GERMS Group initiated a prospective multicenter study to assess prevalence and nature of bacterial contamination of pooled buffy-coat platelet concentrates (PPCs) and apheresis platelet concentrates (APCs) by routine screening with a bacterial culture system.

STUDY DESIGN AND METHODS

In nine centers overall, 52,243 platelet (PLT) concentrates (15,198 APCs, 37,045 PPCs) were analyzed by aerobic and anaerobic cultures (BacT/ALERT, bioMérieux).

RESULTS

In 135 PLT concentrates (PCs; 0.26%), bacteria could be identified in the first culture (0.4% for APCs vs. 0.2% for PPCs; p < 0.001). In 37 (0.07%) of these PC units, the same bacteria strain could be identified in a second culture from the sample bag and/or the PC unit. The rate of confirmed-positive units did not differ significantly between APC (0.09%; 1/1169) and PPC units (0.06%; 1/1544). Bacteria from skin flora (Propionibacterium acnes, Staphylococcus epidermidis) were the most prevalent contaminants. Median times to first positive culture from start of incubation were 0.7 and 3.7 days in aerobic and anaerobic cultures for confirmed-positive units. With a "negative-to-date" issue strategy, most PC units (55%) had already been issued by time of the first positive culture.

CONCLUSION

The rate of confirmed bacterial contamination of PC units was low. Nevertheless, clinicians must be aware of this risk. The risk of bacterial contamination does not warrant universal preference of APCs. It must be questioned whether routine bacterial screening by a culture method can sufficiently prevent contaminated products from being transfused due to the delay until a positive signal in the culture system and due to false-negative results.