A pseudo-outbreak of MRSA due to laboratory contamination related to MRSA carriage of a laboratory staff member.

BACKGROUND: Methicillin resistant Staphylococcus aureus (MRSA) is a major burden for hospitals globally. However, in the Netherlands, the MRSA prevalence is relatively low due to the 'search and destroy' policy. Routine multiple-locus variable-number of tandem repeat analysis (MLVA) of MRSA isolates supports outbreak detection. However, whole genome multiple locus sequence typing (wgMLST) is superior to MLVA in identifying (pseudo-)outbreaks with MRSA. The present study describes a pseudo-outbreak of MRSA at the bacteriology laboratory of a large Dutch teaching hospital. METHODS: All staff members of the bacteriology laboratory of the Elisabeth-TweeSteden hospital were screened for MRSA carriage, after a laboratory contamination with MRSA was suspected. Clonal relatedness between the index isolate and the MRSA isolates from laboratory staff members and all previous MRSA isolates from the Elisabeth-TweeSteden hospital with the same MLVA-type as the index case was examined based on wgMLST using whole genome sequencing. RESULTS: One of the staff members was identified as the probable source of the laboratory contamination, because of carriage of a MRSA possessing the same MLVA-type as the index case. Eleven other isolates with the same molecular characteristics were found in the database, of which seven were retrospectively suspected of contamination. Clonal relatedness was found between ten isolates, including the isolate found in the staff member and the MRSA found in the index patient with a maximum of eleven alleles difference. All isolates were epidemiologically linked through the laboratory staff member, who had worked on all these cultures. CONCLUSIONS: The present study describes a MRSA pseudo-outbreak over a 2.5-year period due to laboratory contamination caused by a MRSA carrying laboratory staff member involving nine patients. In case of unexpected bacteriological findings, the possibility of a laboratory contamination should be considered.

SARS-CoV-2 Alpha-Variant Outbreak Amongst a Partially Vaccinated Long-Term Care Facility Population in The Netherlands-Phylogenetic Analysis and Infection Control Observations.

Despite extensive vaccination and booster programs, SARS-CoV-2 outbreaks in long-term care facilities (LTCF) continue to occur. We retrospectively describe a SARS-CoV-2 outbreak amongst a partially vaccinated LTCF population in The Netherlands which occurred in March 2021. The facility comprised three floors functioning as separate wards. Nasopharyngeal swabs for SARS-CoV-2 qRT-PCR were obtained from residents and staff presenting with COVID-19-like symptoms and from all residents and staff during two point prevalence screenings (PPS). Samples meeting technical criteria were included for phylogenetic analysis. Positive SARS-CoV-2 qRT-PCR were obtained from 11 (18%) of 61 residents and 8 (7%) of 110 staff members between March 8 and March 25. Seven (37%) cases and five (63%) vaccinated cases were diagnosed through PPS. Cases were found on all wards. Phylogenetic analysis (n = 11) showed a maximum difference of four nucleotides between sequences on the outer branches of the tree, but identified two identical sequences on the root differing maximum two nucleotides from all other sequences, suggesting all did belong to the same cluster. Our results imply that PPS is useful in containing SARS-CoV-2 outbreaks amongst (vaccinated) LTCF populations, as an entire LTCF might behave as a single epidemiological unit and it is preferable to maximize the number of samples included for phylogenetic analysis.

Duration of rectal colonization with extended-spectrum beta-lactamase-producing Escherichia coli: results of an open, dynamic cohort study in Dutch nursing home residents (2013-2019).

BACKGROUND: In 2016, a study in a Dutch nursing home showed prolonged colonization duration of extended-spectrum ß-lactamase-producing (ESBL)-ST131 compared to ESBL-non-ST131. In this study, we assessed the duration of rectal ESBL-producing E. coli (ESBL-EC) colonization in residents in the same nursing home for an extended period of six years. We aimed to estimate the influence of a possible bias when follow up is started during an outbreak. METHODS: Between 2013 and 2019, repetitive point prevalence surveys were performed by culturing rectal or faecal swabs from all residents. Kaplan-Meier survival analysis was performed to calculate the median time to clearance of ESBL-EC with a log-rank analysis to test for differences between ESBL-ST131 and ESBL-non-ST131. RESULTS: The study showed a median time to clearance of 13.0 months (95% CI 0.0-27.9) for ESBL-ST131 compared to 11.2 months (95% CI 4.8-17.6) for ESBL-non-ST131 (p = 0.044). In the subgroup analysis of residents who were ESBL-EC positive in their first survey, the median time to clearance for ST131 was 59.7 months (95% CI 23.7-95.6) compared to 16.2 months (95% CI 2.1-30.4) for ESBL-non-ST131 (p = 0.036). In the subgroup analysis of residents who acquired ESBL-EC, the median time to clearance for ST131 was 7.2 months (95% CI 2.1-12.2) compared to 7.9 months (95% CI 0.0-18.3) for ESBL-non-ST131 (p = 0.718). The median time to clearance in the ESBL-ST131 group was significantly longer in residents who were ESBL-ST131 colonised upon entering the study than in residents who acquired ESBL-ST131 during the study (p = 0.001). CONCLUSION: A prolonged colonization with ESBL-ST131 was only found in the subgroup who was ESBL-EC positive upon entering the study. The prolonged duration with ESBL-ST131 in the previous study was probably biased by factors that occured during (the start of) the outbreak.

Implementation of the Infection Risk Scan (IRIS) in nine hospitals in the Belgian-Dutch border region (i-4-1-Health project).

BACKGROUND: A tool, the Infection Risk Scan has been developed to measure the quality of infection control and antimicrobial use. This tool measures various patient-, ward- and care-related variables in a standardized way. We describe the implementation of this tool in nine hospitals in the Dutch/Belgian border area and the obtained results. METHODS: The IRIS consists of a set of objective and reproducible measurements: patient comorbidities, (appropriate) use of indwelling medical devices, (appropriate) use of antimicrobial therapy, rectal carriage of Extended-spectrum beta-lactamase producing Enterobacterales and their clonal relatedness, environmental contamination, hand hygiene performance, personal hygiene of health care workers and presence of infection prevention preconditions. The Infection Risk Scan was implemented by an expert team. In each setting, local infection control practitioners were trained to achieve a standardized implementation of the tool and an unambiguous assessment of data. RESULTS: The IRIS was implemented in 34 wards in six Dutch and three Belgian hospitals. The tool provided ward specific results and revealed differences between wards and countries. There were significant differences in the prevalence of ESBL-E carriage between countries (Belgium: 15% versus The Netherlands: 9.6%), environmental contamination (median adenosine triphosphate (ATP) level Belgium: 431 versus median ATP level The Netherlands: 793) and calculated hand hygiene actions based on alcohol based handrub consumption (Belgium: 12.5/day versus The Netherlands: 6.3/day) were found. CONCLUSION: The Infection risk Scan was successfully implemented in multiple hospitals in a large cross-border project and provided data that made the quality of infection control and antimicrobial use more transparent. The observed differences provide potential targets for improvement of the quality of care.

Distinguishing blaKPC Gene-Containing IncF Plasmids from Epidemiologically Related and Unrelated Enterobacteriaceae Based on Short- and Long-Read Sequence Data.

Limited information is available on whether blaKPC-containing plasmids from isolates in a hospital outbreak can be differentiated from epidemiologically unrelated blaKPC-containing plasmids based on sequence data. This study aimed to evaluate the performance of three approaches to distinguish epidemiologically related from unrelated blaKPC-containing pKpQiL-like IncFII(k2)-IncFIB(pQiL) plasmids. Epidemiologically related isolates were subjected to short- and long-read whole-genome sequencing. A hybrid assembly was performed, and plasmid sequences were extracted from the assembly graph. Epidemiologically unrelated plasmid sequences were extracted from GenBank. Pairwise comparisons of epidemiologically related and unrelated plasmids based on SNPs using snippy and of phylogenetic distance using Roary and using a similarity index that penalizes size differences between plasmids (Stoesser index) were performed. The percentage of pairwise comparisons misclassified as genetically related or as clonally unrelated was determined using different genetic thresholds for genetic relatedness. The ranges of number of SNPs, Roary phylogenetic distance, and Stoesser index overlapped between the epidemiologically related and unrelated plasmids. When a genetic similarity threshold that classified 100% of epidemiologically related plasmid pairs as genetically related was used, the percentages of plasmids misclassified as epidemiologically related ranged from 6.7% (Roary) to 20.8% (Stoesser index). Although epidemiologically related plasmids can be distinguished from unrelated plasmids based on genetic differences, blaKPC-containing pKpQiL-like IncFII(k2)-IncFIB(pQiL) plasmids show a high degree of sequence similarity. The phylogenetic distance as determined using Roary showed the highest degree of discriminatory power between the epidemiologically related and unrelated plasmids.

Management of a hospital-wide vancomycin-resistant Enterococcus faecium outbreak in a Dutch general hospital, 2014-2017: successful control using a restrictive screening strategy.

BACKGROUND: The emergence of vancomycin resistant enterococci poses a major problem in healthcare settings. Here we describe a hospital-wide outbreak of vancomycin-resistant Enterococcus faecium in a general hospital in The Netherlands in the period December 2014-February 2017. Due to late detection of the outbreak, a large cohort of approximately 25,000 (discharged) patients was classified as 'VRE suspected'. Hereupon a mitigated screening and isolation policy, as compared with the national guideline, was implemented to control the outbreak. METHODS: After the outbreak was identified, a screening policy consisting of a single rectal swab culture (with enrichment broth) to discontinue isolation and removing 'VRE suspected' label in the electronic patient files for readmitted VRE suspected patients, was implemented. In addition to the on admission screening, periodic hospital-wide point prevalence screening, measures to improve compliance with standard infection control precautions and enhanced environmental cleaning were implemented to control the outbreak. RESULTS: Between September 2014 and February 2017, 140 patients were identified to be colonised by vanA mediated vancomycin-resistant Enterococcus faecium (VREfm). Two of these patients developed bacteraemia. AFLP typing showed that the outbreak was caused by a single clone. Extensive environmental contamination was found in multiple wards. Within nine months after the detection of the outbreak no new VRE cases were detected. CONCLUSION: We implemented a control strategy based on targeted screening and isolation in combination with implementation of general precautions and environmental cleaning. The strategy was less stringent than the Dutch national guideline for VRE control. This strategy successfully controlled the outbreak, while it was associated with a reduction in the number of isolation days and the number of cultures taken.

Evaluation of an in vitro model with a novel statistical approach to measure differences in bacterial survival of extended-spectrum ß-lactamase-producing Escherichia coli on an inanimate surface.

Background: The role of environmental contamination in the transmission of Enterobacteriaceae is increasingly recognized. However, factors influencing the duration of survival in the environment have not yet been extensively studied. In this study, we developed and evaluated an in vitro model with a novel statistical approach to accurately measure differences in bacterial survival, that can be used to model the effects of multiple factors/conditions in future experiments. Methods: Two extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli (E. coli) isolates were used for this in vitro experiment: a CTX-M-15-producing E. coli sequence type (ST) 131 and a CTX-M-1-producing E. coli ST10 isolate. Each strain was 1:1 diluted in sterile water, sterile saline or sheep blood. Cover glasses (18 × 18 mm) were inoculated with the dilution and subsequently kept at room temperature. Bacterial survival on the glasses was determined hourly during the first day, once daily during the following 6 days, and from day 7 on, once weekly up to 100 days. The experiment was repeated six times for each strain, per suspension fluid. Results: Viable bacteria could be detected up to 70 days. A biphasic survival curve for all suspension fluids was observed, whereby there was a rapid decrease in the number of viable bacteria in the first 7 h, followed by a much slower decrease in the subsequent days. Conclusions: We found a difference in survival probability between E. coli ST10 and ST131, with a higher proportion of viable bacteria remaining after 7 h for ST131, particularly in sheep blood.

Prevalence of nasal carriage of methicillin-resistant Staphylococcus aureus in patients at hospital admission in The Netherlands, 2010-2017: an observational study.

OBJECTIVES: We determined the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) nasal carriage upon hospital admission, among patients who were screened preoperatively for nasal S. aureus carriage between 2010 and 2017. We also aimed to evaluate the prevalence of MRSA carriers without the standard risk factors. METHODS: We conducted an observational study to determine the prevalence of MRSA nasal carriage among patients who were screened preoperatively for nasal S. aureus carriage between 2010 and 2017. Samples of cardiothoracic patients were tested by polymerase chain reaction (PCR), other samples were cultured using chromogenic agar plates. A Poisson regression model with robust error variance was used to assess whether there was a trend in the prevalence of MRSA over time. RESULTS: In total, 31 093 nasal swabs were obtained from 25 660 patients. Three-hundred and seventy-five swabs (1.2%) had an invalid result. Therefore, 30 718 swabs (98.8%) were included in our analysis. Overall, S. aureus was detected in 7981/30 718 patients (26.0% 95% CI 25.5-26.5%) of whom 41 were MRSA (0.13% 95% CI 0.10-0.18%). The MRSA prevalence varied from 0.03% to 0.17% over the years without evidence of a changing trend over time (p = 0.40). Results of the questionnaire revealed that 30 of the 41 patients (73.2%) had no known risk factors for MRSA carriage (0.10%; 95% CI 0.07-0.14%). CONCLUSION: Our study revealed a sustained low prevalence of MRSA carriage upon hospital admission over 7 years. This supports the effectiveness of the Dutch Search and Destroy policy, in combination with a restrictive antibiotic prescription policy.

Next-Generation Sequence Analysis Reveals Transfer of Methicillin Resistance to a Methicillin-Susceptible Staphylococcus aureus Strain That Subsequently Caused a Methicillin-Resistant Staphylococcus aureus Outbreak: a Descriptive Study.

Resistance to methicillin in Staphylococcus aureus is caused primarily by the mecA gene, which is carried on a mobile genetic element, the staphylococcal cassette chromosome mec (SCCmec). Horizontal transfer of this element is supposed to be an important factor in the emergence of new clones of methicillin-resistant Staphylococcus aureus (MRSA) but has been rarely observed in real time. In 2012, an outbreak occurred involving a health care worker (HCW) and three patients, all carrying a fusidic acid-resistant MRSA strain. The husband of the HCW was screened for MRSA carriage, but only a methicillin-susceptible S. aureus (MSSA) strain, which was also resistant to fusidic acid, was detected. Multiple-locus variable-number tandem-repeat analysis (MLVA) typing showed that both the MSSA and MRSA isolates were MT4053-MC0005. This finding led to the hypothesis that the MSSA strain acquired the SCCmec and subsequently caused an outbreak. To support this hypothesis, next-generation sequencing of the MSSA and MRSA isolates was performed. This study showed that the MSSA isolate clustered closely with the outbreak isolates based on whole-genome multilocus sequence typing and single-nucleotide polymorphism (SNP) analysis, with a genetic distance of 17 genes and 44 SNPs, respectively. Remarkably, there were relatively large differences in the mobile genetic elements in strains within and between individuals. The limited genetic distance between the MSSA and MRSA isolates in combination with a clear epidemiologic link supports the hypothesis that the MSSA isolate acquired a SCCmec and that the resulting MRSA strain caused an outbreak.