865. Methicillin-resistant Staphylococcus aureus (MRSA) prevalence among healthcare workers (HCW) in contact tracings in a Dutch teaching hospital, 2010-2018

Background In The Netherlands, the national guidelines on MRSA prevention and control advocate screening of HCW after unprotected exposure to MRSA carriers. Although this strategy at large is successful, contact tracing of staff is a time consuming and costly component. We evaluated our contact tracing policy for HCW over the years 2010 – 2018. MRSA prevalence among samples in contact tracing Methods A retrospective, observational study was performed in a Dutch teaching hospital. All HCW who had unprotected contact with an MRSA carrier were included in contact tracing. When there had been a long period of unprotected admission prior to an MRSA finding, or when the index case was a HCW, than the entire (nursing) team was tested. All samples of HCWs who were tested for MRSA carriage as part of contact tracing from 2010 until 2018 were included. A pooled nose, throat and perineum swab was collected using the eSwab medium (Copan) and inoculated on chromID MRSA agar plates (bioMérieux) after enrichment in a broth. Results In total, we included 8,849 samples (range: 677 – 1,448 samples per year) from a total of 287 contact tracings (range: 26 – 55 contact tracings per year). Thirty two HCWs were colonized with MRSA (0.36%; 95%CI 0.26 – 0.51). None of them developed a clinical infection. Eight HCWs (0.10%; 95%CI 0.05% – 0.19%) were colonized with the same MLVA type as the index case, and were detected in 6/287 contact tracings (2%). In 4/8 of these cases, a positive HCW was the index for undertaking contact tracing. In 3/8 cases it was clear that the HCW who was identified in the contact tracing was the source of the outbreak and was the cause of invasive MRSA infections in patients. Notably, a different MLVA type as the index case was found in 24 HCWs (0,27%; 95%CI 0,18 – 0,40) of which 7/24 HCW (29,2%) were intermittent carriers. Conclusion This study revealed a sustained low MRSA prevalence among samples in contact tracing of healthcare workers, over nine years. Furthermore, it shows that when MRSA contact tracing is performed according to the national guideline only 1 out 1000 samples results in a secondary case. This is similar to the population carriage rate of MRSA in The Netherlands. More frequently, an unrelated strain is found. These findings raise question marks regarding the efficacy of the current strategy to perform contact tracing after unprotected exposure. Disclosures All Authors: No reported disclosures

ConFindr: rapid detection of intraspecies and cross-species contamination in bacterial whole-genome sequence data

Whole-genome sequencing (WGS) of bacterial pathogens is currently widely used to support public-health investigations. The ability to assess WGS data quality is critical to underpin the reliability of downstream analyses. Sequence contamination is a quality issue that could potentially impact WGS-based findings; however, existing tools do not readily identify contamination from closely-related organisms. To address this gap, we have developed a computational pipeline, ConFindr, for detection of intraspecies contamination. ConFindr determines the presence of contaminating sequences based on the identification of multiple alleles of core, single-copy, ribosomal-protein genes in raw sequencing reads. The performance of this tool was assessed using simulated and lab-generated Illumina short-read WGS data with varying levels of contamination (0–20% of reads) and varying genetic distance between the designated target and contaminant strains. Intraspecies and cross-species contamination was reliably detected in datasets containing 5% or more reads from a second, unrelated strain. ConFindr detected intraspecies contamination with higher sensitivity than existing tools, while also being able to automatically detect cross-species contamination with similar sensitivity. The implementation of ConFindr in quality-control pipelines will help to improve the reliability of WGS databases as well as the accuracy of downstream analyses. ConFindr is written in Python, and is freely available under the MIT License at github.com/OLC-Bioinformatics/ConFindr.

ConFindr: Rapid detection of intraspecies and cross-species contamination in bacterial whole-genome sequence data

Whole-genome sequencing (WGS) of bacterial pathogens is currently widely used to support public-health investigations. The ability to assess WGS data quality is critical to underpin the reliability of downstream analyses. Sequence contamination is a quality issue that could potentially impact WGS-based findings; however, existing tools do not readily identify contamination from closely-related organisms. To address this gap, we have developed a computational pipeline, ConFindr, for detection of intraspecies contamination. ConFindr determines the presence of contaminating sequences based on the identification of multiple alleles of core, single-copy, ribosomal-protein genes in raw sequencing reads. The performance of this tool was assessed using simulated and lab-generated Illumina short-read WGS data with varying levels of contamination (0-20% of reads) and varying genetic distance between the designated target and contaminant strains. Intraspecies and cross-species contamination was reliably detected in datasets containing 5% or more reads from a second, unrelated strain. ConFindr detected intraspecies contamination with higher sensitivity than existing tools, while also being able to automatically detect cross-species contamination with similar sensitivity. The implementation of ConFindr in quality-control pipelines will help to improve the reliability of WGS databases as well as the accuracy of downstream analyses. ConFindr is written in Python, and is freely available under the MIT License at github.com/OLC-Bioinformatics/ConFindr.

ConFindr: Rapid detection of intraspecies and cross-species contamination in bacterial whole-genome sequence data

Whole-genome sequencing (WGS) of bacterial pathogens is currently widely used to support public-health investigations. The ability to assess WGS data quality is critical to underpin the reliability of downstream analyses. Sequence contamination is a quality issue that could potentially impact WGS-based findings; however, existing tools do not readily identify contamination from closely-related organisms. To address this gap, we have developed a computational pipeline, ConFindr, for detection of intraspecies contamination. ConFindr determines the presence of contaminating sequences based on the identification of multiple alleles of core, single-copy, ribosomal-protein genes in raw sequencing reads. The performance of this tool was assessed using simulated and lab-generated Illumina short-read WGS data with varying levels of contamination (0-20% of reads) and varying genetic distance between the designated target and contaminant strains. Intraspecies and cross-species contamination was reliably detected in datasets containing 5% or more reads from a second, unrelated strain. ConFindr detected intraspecies contamination with higher sensitivity than existing tools, while also being able to automatically detect cross-species contamination with similar sensitivity. The implementation of ConFindr in quality-control pipelines will help to improve the reliability of WGS databases as well as the accuracy of downstream analyses. ConFindr is written in Python, and is freely available under the MIT License at github.com/OLC-Bioinformatics/ConFindr.

Pseudomonas aeruginosa blood stream infection isolates from patients with recurrent blood stream infection: Is it the same genotype?

SUMMARYThe type identity of strains of Pseudomonas aeruginosa from primary and recurrent blood stream infection (BSI) has not been widely studied. Twenty-eight patients were identified retrospectively from 2008 to 2013 from five different laboratories; available epidemiological, clinical and microbiological data were obtained for each patient. Isolates were genotyped by iPLEX MassARRAY MALDI-TOF MS and rep-PCR. This showed that recurrent P. aeruginosa BSI was more commonly due to the same genotypically related strain as that from the primary episode. Relapse due to a genotypically related strain occurred earlier in time than a relapsing infection from an unrelated strain (median time: 26 vs. 91 days, respectively). Line related infections were the most common source of suspected BSI and almost half of all BSI episodes were associated with neutropenia, possibly indicating translocation of the organism from the patient's gut in this setting. Development of meropenem resistance occurred in two relapse isolates, which may suggest that prior antibiotic therapy for the primary BSI was a driver for the subsequent development of resistance in the recurrent isolate.

Investigation of clonal relationships of K. pneumoniae isolates from neonatal intensive care units by PFGE and rep-PCR

Introduction: Clonal relationships of Klebsiella pneumoniae strains obtained during an epidemic and after a one-year post-epidemic (non-epidemic) period in the same neonatal intensive care unit (NICU) using pulsed-field gel electrophoresis (PFGE) and repetitive polymerase chain reaction (rep-PCR) by the DiversiLab (DL) system were investigated, and the results of both molecular techniques were evaluated. Methodology: Fifteen K. pneumoniae strains were included in this study. All identified bacterial strains were confirmed by 16S rDNA sequencing and analyzed by PFGE and the DL system. Results: According to the PFGE results, 15 isolates showed 10 different band profiles. Nine of these 15 isolates were included in one of the formed clusters, and the remaining six isolates were not included in any of them. According to the DL system results, 15 isolates showed two different clusters, with three strains in one cluster and four strains in the other. The remaining strains could not be placed any one of the clusters. PFGE was used as the gold standard based on its strong genetic discriminatory power. The DL system results showed that PFGE missed the relationship of the two epidemic-related strains and demonstrated one epidemic-unrelated strain to be epidemic related. Conclusions: Both systems may easily be used for clonal relationships of K. pneumoniae strains. The DL system was clearly more rapid and convenient than PFGE, but its discriminatory power seemed to be inferior to that of PFGE based on 15 K. pneumoniae strains.

Protective Efficacy of the Calicivirus Valency of the Leucofeligen Vaccine against a Virulent Heterologous Challenge in Kittens

Feline calicivirus (FCV) is a common feline pathogen with a potential for antigenic diversity. This study aimed to evaluate and characterize the protective efficacy of the FCV-F9 valency of a tetravalent vaccine, Leucofeligen, against challenge with an unrelated strain. Ten 9-week-old kittens were vaccinated while 10 remained as unvaccinated controls. The vaccinated cats received Leucofeligen twice subcutaneously with a 3-week interval. Four weeks after the second vaccination, all cats were challenged with virulent heterologous FCV and followed up for 21 days, monitoring their general condition, clinical signs, and immunological responses. During the vaccination phase, rectal temperatures and body weights were indistinguishable between the two groups. Only vaccinated cats showed FCV-specific seroconversion (both total and neutralizing antibodies). In the first week after challenge, the vaccinated cats had an 82.6% reduction in median clinical score compared to controls. Leucofeligen was thus shown to provide a significant clinical protection to kittens challenged with heterologous virulent FCV. This protection was similar whether the cats had neutralizing antibody or not, indicating a key role for cellular immunity in the overall protection. This also suggests that previously reported seroneutralisation studies may underestimate the level of cross-protection against field strains obtained with this modified live FCV-F9 vaccine.

Impact of Helicobacter pylori resistance in unsuccessfully pluritreated patients in a Department of Infectious Diseases in Rome

Twenty-five pluritreated patients were examined. Fifty-six percent yielded Helicobacter pylori (H. Pilory); of these, 9 patients showed a concomitant colonization of the three gastric regions. The highest resistance rate was found for metronidazole (71.8%) followed by chlaritromycin (53.1%). Amoxycillin showed the best susceptibility (only 6% of resistance), tetracycline showed 12% of resistant strains and levofloxacin appeared to be a promising antibacterial agent (18% of resistance). The E-test method was shown to be more suitable than disk diffusion technique for resistance testing. Combined resistance to both chlaritromycin and metronidazole appeared in 50% of the strains. The isolates showing this dual resistance are known to be difficult to eradicate. Resistotypes were shown to be genotypically different even if the strains with the resistance to both chlaritromycin and metronidazole are more likely to belong to genotype cagA+ and vacA s1m1. Heteroresistance (different susceptibility of the isolated strains in a single stomach) resulted in 36% of patients with pangastritis. Indeed, the concomitant presence of H. pylori strains in the same subject, either susceptible or resistant or vice versa, may interfere with the eradication outcomes. In our study, antibiotic resistant H. pylori typically develops from pre-existing susceptible strains rather than from co-infection with a different and unrelated strain. In fact, each pair of isolates detected in our 4 patients with heteroresistance belonged to the same genotype (cagA+ s1m2 in patient 1 and cagA+ s1m1 in patients 2, 3 and 4). In conclusion, H. pylori antibiotic resistance does present several issues in pluritreated patients owing to the rapid emergence of multi-resistant strains.