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Integrative and conjugative elements (ICEs) are widespread autonomous mobile DNA, containing the genes necessary for their excision, conjugative transfer, and insertion into a new host cell. ICEs can carry additional genes that are non-essential for their transfer, but that can confer adaptive phenotypes to the host. Our aim here was to better characterize the presence, distribution and evolution of ICEs related to the well-described ICEclcamongPseudomonas aeruginosaclinical isolates, and to understand their potential role in spreading genes with adaptive benefit. We examined a total of 181P. aeruginosagenome sequences obtained from patient or hospital environment isolates. More than 90% of the isolates carried one or more ICEclc-like elements, with different degrees of conservation to the known ICEclc-lifestyle and transfer genes. ICE clones closely matched their host clonal phylogeny, but not exclusively, indicating that both clonal evolution and ICE-horizontal transfer are occurring in the hospital environment. Variable gene regions among the clinicalP. aeruginosaICEclc-type elements were notably enriched for heavy metal resistance genes, toxin-antitoxin systems, potential efflux systems and multidrug resistance proteins, a metalloprotease and for a variety of regulatory systems, but not for specific recognizable antibiotic resistance cassettes. Clonal persistence suggests adaptive benefits of these functional categories; and micro-patterns of gene gain and loss indicate ongoing ICE evolution within theP. aeruginosahosts.

Background Long-term outbreaks of multidrug-resistant Gram-negative bacilli related to hospital-building water systems have been described. However, successful mitigation strategies have rarely been reported. In particular, environmental disinfection or replacement of contaminated equipment usually failed to eradicate environmental sources of Pseudomonas aeruginosa. Methods We report the investigation and termination of an outbreak of P. aeruginosa producing VIM carbapenemase (PA-VIM) in the adult intensive care unit (ICU) of a Swiss tertiary care hospital with active case finding, environmental sampling and whole genome sequencing (WGS) of patient and environmental strains. We also describe the implemented control strategies and their effectiveness on eradication of the environmental reservoir. Results Between April 2018 and September 2020, 21 patients became either infected or colonized with a PA-VIM strain. For 16 of them, an acquisition in the ICU was suspected. Among 131 environmental samples collected in the ICU, 13 grew PA-VIM in sink traps and drains. WGS confirmed the epidemiological link between clinical and environmental strains and the monoclonal pattern of the outbreak. After removing sinks from patient rooms and implementation of waterless patient care, no new acquisition was detected in the ICU within 8 months after the intervention. Discussion Implementation of waterless patient care with removal of the sinks in patient rooms was successful for termination of a PA-VIM ICU outbreak linked to multiple environmental water sources. WGS provides highly discriminatory accuracy to investigate environment-related outbreaks.

Summary Background Extended-spectrum β-lactamase (ESBL)-producing Enterobacterales constitute a global burden for hospital infection, and the identification of carriers by screening patients at risk is recommended by several guidelines. Aim To evaluate the impact of rapid ESBL tests on the turnaround time (TAT) of screening. Methods Rectal swabs were analysed by culture and synergism tests for identification of non-Esherichia coli Enterobacterales that produce ESBLs (NEcESBL-producing Enterobacterales). The Rapid ESBL NP and NG CTX-M MULTI tests were performed on colonies grown on chromogenic media. The results of polymerase chain reaction and sequencing of ESBL genes were used as the gold standard. Results Among 473 analysed swabs, 75 (15.9%) grew NEcESBL-producing Enterobacterales, leading to 89 isolates. Sensitivities of the synergism, Rapid ESBL NP and NG CTX-M MULTI tests were 0.97 [95% confidence interval (CI) 0.88–0.99], 0.81 (95% CI 0.69–0.89) and 0.90 (95% CI 0.80–0.96), respectively. Specificities were 0.92 (95% CI 0.73–0.99), 0.85 (95% CI 0.64–0.95) and 0.96 (95% CI 0.78–1.00), respectively. Considering the 473 rectal swabs, ESBL screening using the synergism, Rapid ESBL NP and NG CTX-M MULTI tests was calculated. Sensitivities were 0.96 (95% CI 0.86–0.99), 0.81 (95% CI 0.68–0.90) and 0.91 (95% CI 0.79–0.97); specificities were 1.00 (95% CI 0.98–1.00), 0.99 (95% CI 0.98–1.00) and 1.00 (95% CI 0.99–1.00); positive predictive values were 0.96 (95% CI 0.86–0.99), 0.94 (95% CI 0.81–0.98) and 1.00 (95% CI 0.91–1.00); and negative predictive values were 1.00 (95% CI 0.98–1.00), 0.98 (95% CI 0.96–0.99) and 0.99 (95% CI 0.97–1.00), respectively. When no NEcESBL-producing Enterobacterales were observed, the mean TAT was 30 h. When NEcESBL-producing Enterobacterales were identified, the mean TATs were 74.7, 38.0 and 36.7 h for the synergism, Rapid ESBL NP and NG CTX-M MULTI tests, respectively. Conclusion The two rapid ESBL tests showed good performance and allowed a reduction in TAT for screening protocols to identify patients carrying ESBL-producing Enterobacterales.

The recent increase of migration to Europe represents a risk of increased the prevalence of multidrug-resistant (MDR) bacteria. We conducted a cross-sectional study among asylum seekers admitted at two hospitals in Switzerland. Of the 59 patients included, 9 (14%) were colonised by a MDR bacteria, including 5 (8.5%) methicilin-resistant Staphylococcus aureus (MRSA) and 4 (6.8%) extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae. No patient carried both ESBL-producing bacteria and MRSA. None of the patients carried a vancomycin-resistant Enterococcus (VRE) or a carbapenem-resistant Enterobacteriaceae (CRE). Colonisation with MDR bacteria was not associated with hospitalisation abroad or recent arrival in Switzerland. Whole genome sequencing analysis allowed us to exclude transmission between patients. The prevalence of MDR bacteria carriage is moderate among asylum seekers in western Switzerland. Further surveillance studies are necessary to determine if there is a risk of dissemination of pathogens into the local population.

Since the introduction of antibiotics, successive waves of Staphylococcus aureus clones occurred, each one having characteristic susceptibility pattern to antibiotics and virulence factors. We report here the results of a molecular epidemiological surveillance of methicillin-resistant S. aureus (MRSA) in French-speaking Switzerland between 2006 and 2020 showing the emergence and disappearance of clones known for their international dissemination, and the sporadic appearance of other international clones. Since 2012, a marked decrease in the incidence of cases attributable to the biology of the clones and to the control measures taken in the hospitals has been observed. These results highlight the importance of continuous surveillance in order to better assess the burden of this multi-resistant pathogen in our region.Depuis l’introduction des antibiotiques, des vagues successives de clones de

Toxigenic Clostridioides difficile is responsible for up to one third of post antibiotic diarrhea and for more than 95% of pseudomembranous colitis. Nowadays, diagnosis relies on the documentation of the presence of the toxin in stools by specific antigenic or PCR tests. Stool cultures have been mostly abandoned, leading to the absence of isolates for further epidemiological analyses. Aliquots of stool samples, frozen for up to two years, were thawed and inoculated onto commercial C. difficile media. Eighteen stools were recovered from patients hospitalized in the pediatric ward where at that time a chain of transmission was suspected. Eleven stools were recovered from patients hospitalized in a medical ward over a three months period with no suspected transmission event. Up to 16 characteristic colonies were isolates per culture. PCR of toxins genes and molecular typing by Double Locus Sequence Typing (DLST) were performed on these colonies. Whole genome multi locus sequence typing (wgMLST) was performed on selected isolates. Among the 29 stool specimens, no growth was observed for four stools and only one colony grew for one stool. Except the latter, all 16 colonies of the 24 stools showed identical toxin genes profiles than the original stool. However, variant DLST genotypes was observed within 20% of investigated stools. The majority of variants were single locus variant due to an IN/DEL of the repeat in one of the two DLST locus. Despite this variation, results of molecular typing overrule the putative transmission chain in the pediatric ward and revealed undetected chains of transmission in the medical ward. These results were confirmed with wgMLST. The developed protocol allows prospective and retrospective molecular and genomic epidemiological investigation of C. difficile infections for infection control purpose.

The global spread of extended-spectrum β-lactamase (ESBL) is a matter of great concern given the high morbidity and mortality associated with invasive infections. The most frequent ESBLs are of the CTX-M type, followed by the TEM and SHV variants, being reported in all Enterobacterales species and

A recent hospital outbreak related to premoistened gloves used to wash patients exposed the difficulties of defining Burkholderia species in clinical settings. The outbreak strain displayed key B. stabilis phenotypes, including the inability to grow at 42°C; we used whole-genome sequencing to confirm the pathogen was B. stabilis. The outbreak strain genome comprises 3 chromosomes and a plasmid, sharing an average nucleotide identity of 98.4% with B. stabilis ATCC27515 BAA-67, but with 13% novel coding sequences. The genome lacks identifiable virulence factors and has no apparent increase in encoded antimicrobial drug resistance, few insertion sequences, and few pseudogenes, suggesting this outbreak was an opportunistic infection by an environmental strain not adapted to human pathogenicity. The diversity among outbreak isolates (22 from patients and 16 from washing gloves) is only 6 single-nucleotide polymorphisms, although the genome remains plastic, with large elements stochastically lost from outbreak isolates.

The molecular epidemiology of 38 non-duplicate toxigenic Clostridioides (previously Clostridium) difficile isolates from inpatients from a hospital in Brazil during a 6-year period (2012-2017) were investigated by multilocus sequence typing (MLST) and ribotyping. These isolates were classified into 20 sequence types (ST), six (30%) of which were novel, revealing a high diversity in a single hospital. Classic hypervirulent strains ST1/RT027 and ST11/RT078 were not identified, while ST42 (almost all RT106) was the most common type, being detected in 11 (28.9%) strains. Noteworthy, six (15.8%) isolates were classified into five STs from clade 2, four of which were new ST and RT. Our study suggests that possible hypervirulent strains other than ST1/RT027 might be inadvertently circulating in Brazilian hospitals and highlights the importance of permanent surveillance on circulating strains in a national scale.

Background: Methicillin-resistant Staphylococcus aureus (MRSA) is a common healthcare-associated pathogen that remains a major public health concern. Sequence type 228 (ST228) was first described in Germany and spread to become a successful MRSA clone in several European countries. In 2000, ST228 emerged in Lausanne and has subsequently caused several large outbreaks. Here, we describe the evolutionary history of this clone and identify the genetic changes underlying its expansion in Switzerland. Materials and Methods: We aimed to understand the phylogeographic and demographic dynamics of MRSA ST228/ST111 by sequencing 530 representative isolates of this clone that were collected from 14 European countries between 1997 and 2012. Results: The phylogenetic analysis revealed distinct lineages of ST228 isolates associated with specific geographic origins. In contrast, isolates of ST111, which is a single locus variant of ST228 sharing the same spa type t041, formed a monophyletic cluster associated with multiple countries. The evidence points to a German origin of the sampled population, with the basal German lineage being characterized by spa type t001. The highly successful Swiss ST228 lineage diverged from this progenitor clone through the loss of the aminoglycoside-streptothricin resistance gene cluster and the gain of mupirocin resistance. This lineage was introduced first in Geneva and was subsequently introduced into Lausanne. Conclusion: Our results reveal the radiation of distinct lineages of MRSA ST228 from a German progenitor, as the clone spread into different European countries. In Switzerland, ST228 was introduced first in Geneva and was subsequently introduced into Lausanne., SCOPUS: ar.j, info:eu-repo/semantics/published

Since the late 1990s, changes in the epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) were recognized with the emergence of community-associated MRSA (CA-MRSA). CA-MRSA belonging to clonal complex 152 (CC152), carrying the small staphylococcal cassette chromosome mec (SCCmec) type V and encoding the Panton-Valentine leukocidin (PVL), has been observed in Europe. The aim of this study was to investigate its origin, evolution, and dissemination. Whole-genome sequencing was performed on a global collection of 149 CC152 isolates spanning 20 years (93 methicillin-susceptible S. aureus [MSSA] and 56 MRSA isolates). Core genome phylogeny, Bayesian inference, in silico resistance analyses, and genomic characterization were applied. Phylogenetic analysis revealed two major distinct clades, one dominated by MSSA and the other populated only by MRSA. The MSSA isolates were predominately from sub-Saharan Africa, whereas MRSA was almost exclusively from Europe. The European MRSA isolates all harbored an SCCmec type V (5C2&5) element, whereas other SCCmec elements were sporadically detected in MRSA from the otherwise MSSA-dominated clade, including SCCmec types IV (2B), V (5C2), and XIII (9A). In total, 93% of the studied CC152 isolates were PVL positive. Bayesian coalescent inference suggests an emergence of the European CC152-MRSA in the 1990s, while the CC152 lineage dates back to the 1970s. The CA-MRSA CC152 clone mimics the European CC80 CA-MRSA lineage by its emergence from a PVL-positive MSSA ancestor from North Africa or Europe. The CC152 lineage has acquired SCCmec several times, but acquisition of SCCmec type V (5C2&5) seems associated with expansion of MRSA CC152 in Europe.IMPORTANCE Understanding the evolution of CA-MRSA is important in light of the increasing importance of this reservoir in the dissemination of MRSA. Here, we highlight the story of the CA-MRSA CC152 lineage using whole-genome sequencing on an international collection of CC152. We show that the evolution of this lineage is novel and that antibiotic usage may have the potential to select for the phage-encoded Panton-Valentine leukocidin. The diversity of the strains correlated highly to geography, with higher level of resistance observed among the European MRSA isolates. The mobility of the SCCmec element is mandatory for the emergence of novel MRSA lineages, and we show here distinct acquisitions, one of which is linked to the successful clone found throughout Europe today.

Whole genome sequencing (WGS) enables high resolution typing of bacteria up to the single nucleotide polymorphism (SNP) level. WGS is used in clinical microbiology laboratories for infection control, molecular surveillance and outbreak analyses. Given the large palette of WGS reagents and bioinformatics tools, the Swiss clinical bacteriology community decided to conduct a ring trial (RT) to foster harmonization of NGS-based bacterial typing. The RT aimed at assessing methicillin-susceptible Staphylococcus aureus strain relatedness from WGS and epidemiological data. The RT was designed to disentangle the variability arising from differences in sample preparation, SNP calling and phylogenetic methods. Nine laboratories participated. The resulting phylogenetic tree and cluster identification were highly reproducible across the laboratories. Cluster interpretation was, however, more laboratory dependent, suggesting that an increased sharing of expertise across laboratories would contribute to further harmonization of practices. More detailed bioinformatic analyses unveiled that while similar clusters were found across laboratories, these were actually based on different sets of SNPs, differentially retained after sample preparation and SNP calling procedures. Despite this, the observed number of SNP differences between pairs of strains, an important criterion to determine strain relatedness given epidemiological information, was similar across pipelines for closely related strains when restricting SNP calls to a common core genome defined by S. aureus cgMLST schema. The lessons learned from this pilot study will serve the implementation of larger-scale RT, as a mean to have regular external quality assessments for laboratories performing WGS analyses in a clinical setting.

Pseudomonas aeruginosa is one of the main pathogens responsible for nosocomial infections, particularly in Intensive Care Units (ICUs). Due to the complexity of P. aeruginosa ecology, only powerful typing methods can efficiently allow its surveillance and the detection during expanding outbreaks. An increase in P. aeruginosa incidence was observed in the ICUs of the Lausanne University Hospital between 2010 and 2014. All clinical and environmental isolates retrieved during this period were typed with Double locus sequence typing (DLST), which detected the presence of three major genotypes: DLST 1–18, DLST 1–21, and DLST 6–7. DLST 1–18 (ST1076) isolates were previously associated with an epidemiologically well-described outbreak in the burn unit. Nevertheless, DLST 1–21 (ST253) and DLST 6–7 (ST17) showed sporadic occurrence with only few cases of possible transmission between patients. Whole genome sequencing (WGS) was used to further investigate the epidemiology of these three major P. aeruginosa genotypes in the ICUs. WGS was able to differentiate between outbreak and non-outbreak isolates and confirm suspected epidemiological links. Additionally, whole-genome single nucleotide polymorphisms (SNPs) results considered isolates as closely related for which no epidemiological links were suspected, expanding the epidemiological investigation to unsuspected links. The combination of a first-line molecular typing tool (DLST) with a more discriminatory method (WGS) proved to be an accurate and cost-efficient typing strategy for the investigation of P. aeruginosa epidemiology in the ICUs.

Five dogs with chronic-recurring diarrhea were positive for Clostridioides difficile infection (CDI), but were unresponsive to treatment with metronidazole. One of these animals was subjected to a colonoscopy, which revealed eosinophilic infiltration of the colon. All five animals completely recovered after dietary changes. The present work suggests that CDI might occur in dogs with other intestinal alterations. In addition, this report suggests that dysbiosis should be considered in animals that have chronic-recurring diarrhea and test positive for C. difficile., Highlights • C. difficile infection (CDI) in dogs are still largely unknown. • Five dogs with chronic-recurring diarrhea were positive for CDI. • All animals completely recovered after dietary changes. • Dysbiosis should be considered in dogs with chronic-recurring diarrhea and CDI.

Whole-genome sequencing (WGS) has emerged as a powerful molecular typing method for outbreak analysis enabling the rapid discrimination between outbreak and non-outbreak isolates. However, such analysis can be challenging in the absence of closely related reference genomes. In this study, we assessed the use of WGS in investigating an outbreak of a relatively understudied bacterial pathogen with no publicly available closely related reference genome. Eleven Burkholderia cepacia complex (Bcc) isolates (seven from patients and four from disposable dermal gloves packages) that were collected during an outbreak were sequenced using the Illumina MiSeq platform. Our results showed that mapping the 11 sequenced Bcc outbreak isolates against a genetically distant reference genome yield loses coverage (31.6-48.3%) and a high number of detected false single-nucleotide polymorphisms (SNPs) (1123-2139). Therefore, a reference genome consensus from an outbreak clinical isolate was generated by combining both de novo assembly and mapping approaches. Based on this approach, we were able to demonstrate that the Bcc outbreak isolates were closely related and were phylogenetically distinct from the 11 publically available Bcc genomes. In addition, the pairwise SNP distance analysis detected only 1 to 6 SNPs differences among the outbreak isolates, confirming that contaminated disposable dermal gloves were the cause of the outbreak.

Vancomycin-resistant Enterococcus faecium (VREfm) emerged as an important cause of nosocomial infections worldwide. Previous studies based on molecular typing revealed that VREfm outbreaks are mainly associated with a particular genetic lineage, namely clonal complex 17 (CC17), which harbours either vanA or vanB gene cluster. The University Hospital of Lausanne faced several VREfm episodes of transmissions between 2014 and 2017. In this study, we used whole-genome sequencing (WGS) to investigate the relatedness of 183 VREfm isolates collected from 156 patients. Sequence types (ST) 17, ST80 and ST117 were the most predominant clones. Based on epidemiological data, 10 outbreaks were identified, which were caused by at least 13 distinct genotypes. The majority of isolates involved in outbreaks (91%) differed by only 0 to 3 SNPs. Four outbreaks involved more than one genotype and half of the cases considered as sporadic were possibly linked to an outbreak. By sequencing all isolates, we were able to better understand our local epidemiology of VREfm. The polyclonal structure observed between the different outbreaks strains, the high level of recombination detected in isolates, the time elapsed between admission and the first VREfm detection and the negative screening at admission support the hypothesis of the emergence of new VREfm clones within the hospitalised population.

Pseudomonas aeruginosa is one of the major Gram-negative pathogens responsible for hospital-acquired infections. Here, we present high-quality genome sequences of isolates from three P. aeruginosa genotypes retrieved from patients hospitalized in intensive care units., Pseudomonas aeruginosa is one of the major Gram-negative pathogens responsible for hospital-acquired infections. Here, we present high-quality genome sequences of isolates from three P. aeruginosa genotypes retrieved from patients hospitalized in intensive care units. PacBio reads were assembled into a single contig, which was afterward corrected using Illumina HiSeq reads.

Facing multidrug resistant (MDR) bacterial pathogens is one of the most important challenges for our society. The spread of highly virulent and resistant pathogens can be described using molecular typing technologies; in particular, whole genome sequencing (WGS) data can be used for molecular typing purposes with high resolution. WGS data analysis can explain the spatiotemporal patterns of pathogen transmission. However, the transmission between compartments (human, animal, food, environment) is very complex. Interoperable and curated metadata are a key requirement for fully understanding this complexity. In addition, high quality sequence data are a key element between centres using WGS data for diagnostic and epidemiological applications. We aim to describe steps to improve WGS data analysis and to implement a molecular surveillance platform allowing integration of high resolution WGS typing data and epidemiological data.

Objectives Screening for methicillin-resistant Staphylococcus aureus (MRSA) is part of many recommendations to control MRSA. Several rapid PCR tests are available commercially and updated versions are constantly released. We aimed to evaluate the performance of three consecutive versions (G3, Gen3 and NxG) of the XpertMRSA test. Methods Routine samples for MRSA screening were simultaneously tested by culture and rapid PCR. The three versions of XpertMRSA were used successively and compared with culture. Results A total of 3512, 2794 and 3288 samples were analysed by culture and by the G3, Gen3 and NxG XpertMRSA versions, respectively. The rates of positive-by-culture in the three groups were 5.0%, 4.7% and 4.3%, respectively. The sensitivity improved over time (71.4, 95% CI 64.0–77.9; 82.3, 95% CI 74.4–88.2; and 84.3%, 95% CI 77.0–89.7, respectively), but not significantly. The specificity (98.4, 95% CI 97.9–98.8; 96.8, 95% CI 96.0–97.4; and 99.1, 95% CI 98.7–99.4, respectively) and the positive likelihood ratios (45.7, 95% CI 34.4–60.8; 25.6, 95% CI 20.5–32.0; and 97.1, 95% CI 66.3–142.4) were significantly lower in the Gen3 version (p Conclusions These significant differences in performance show the importance of evaluating each new version of a commercial test.

Limiting the emergence and spread of multi-resistant bacteria is a global concern and the management of colonized patient represents a real challenge, especially in the hospital setting, where risks of acquisition and transmission are increased. Switzerland is not protected from undesirable trends : for instance, recent outbreaks of vancomycin-resistant enterococci (VRE) have been reported in several hospitals in western Switzerland. Since 2011, more than 250 patients have been tested positive during these outbreak episodes and the molecular analysis of the documented strains shows an unexpected diversity, including both sporadic and epidemic strains. This emerging threat requires strict monitoring, prevention and infection control strategies in our healthcare facilities.Limiter l’émergence et la diffusion des bactéries multirésistantes (BMR) est une urgence mondiale et la gestion des patients porteurs représente un véritable défi, notamment en milieu hospitalier, où les risques d’acquisition et de transmission de ces germes sont multipliés. La Suisse n’est pas épargnée par ce phénomène. En témoignent les épidémies récentes à entérocoques résistant à la vancomycine (ERV) dans plusieurs hôpitaux de Suisse romande. Depuis 2011, plus de 250 patients ont été dépistés positifs durant ces épisodes et l’analyse moléculaire par séquençage complet de génome montre une diversité inattendue des souches, qu’elles soient sporadiques ou à potentiel épidémique. Cette menace émergente, bien réelle, implique une stratégie de surveillance, prévention et contrôle de l’infection stricte dans nos établissements de soins.

Features of Clostridioides difficile transmission in swine and the role of rodents as C. difficile reservoir are not clear. To investigate if rodents can carry strains of C. difficile that are genetically similar to those isolated from swine, 97 fecal samples from neonatal piglets and 41 intestinal contents from rodents were collected in two farms. All samples were subjected to C. difficile culture and the presence of A/B toxins in piglet feces were accessed by commercial enzyme imunoassay (EIA). C. difficile isolates were typed by double- (DLST) and multi-locus sequence typing (MLST). C. difficile was isolated from 15.5% of piglets and 31.7% of rodents. Most isolates were identified as DLST type 4-4 and 17-5 (both are ST11), which were found in both rodents and piglets. Results of this study suggested that rodents may have a role on the transmission and spread of C. difficile strains to swine.

Bacterial pellets from Enterobacteriaceae positive blood cultures prepared using ammonium chloride were tested for rapid detection of β-lactamase using the commercial βLACTA test and read after 30 minutes. During 7 months, 137 bacterial pellets were tested prospectively. βLACTA test exhibited a sensitivity of 75% and a specificity of 100% for the detection of third-generation cephalosporin resistance. False negative tests were mainly observed with hyperproduced chromosomal or plasmid-borne AmpC.

OBJECTIVEThe risk of carrying methicillin-resistant Staphylococcus aureus (MRSA) is higher among nursing home (NH) residents than in the general population. However, control strategies are not clearly defined in this setting. In this study, we compared the impact of standard precautions either alone (control) or combined with screening of residents and decolonization of carriers (intervention) to control MRSA in NHs.DESIGNCluster randomized controlled trialSETTINGNHs of the state of Vaud, SwitzerlandPARTICIPANTSOf 157 total NHs in Vaud, 104 (67%) participated in the study.INTERVENTIONStandard precautions were enforced in all participating NHs, and residents underwent MRSA screening at baseline and 12 months thereafter. All carriers identified in intervention NHs, either at study entry or among newly admitted residents, underwent topical decolonization combined with environmental disinfection, except in cases of MRSA infection, MRSA bacteriuria, or deep skin ulcers.RESULTSNHs were randomly allocated to a control group (51 NHs, 2,412 residents) or an intervention group (53 NHs, 2,338 residents). Characteristics of NHs and residents were similar in both groups. The mean screening rates were 86% (range, 27%–100%) in control NHs and 87% (20%–100%) in intervention NHs. Prevalence of MRSA carriage averaged 8.9% in both control NHs (range, 0%–43%) and intervention NHs (range, 0%–38%) at baseline, and this rate significantly declined to 6.6% in control NHs and to 5.8% in intervention NHs after 12 months. However, the decline did not differ between groups (P=.66).CONCLUSIONUniversal screening followed by decolonization of carriers did not significantly reduce the prevalence of the MRSA carriage rate at 1 year compared with standard precautions.Infect Control Hosp Epidemiol 2015;00(0): 1–8

We report here the draft genome sequences of two multidrug-resistant Acinetobacter baumannii clinical strains, H31499 and H31506, which were isolated at the Lausanne University Hospital in 2015 from an Albanian and a Togolese patient, respectively.

We report here the draft genome sequences of two multidrug-resistant Acinetobacter baumannii clinical strains, H31499 and H31506, which were isolated at the Lausanne University Hospital in 2015 from an Albanian and a Togolese patient, respectively.

Methicillin-resistant Staphylococcus aureus (MRSA) were first isolated in 1961, soon after the introduction of methicillin for therapeutic treatments. Since then, the rate of MRSA isolates among S. aureus has continuously increased to reach 60% in some healthcare institutions. The resistance to methicillin is conferred by the acquisition of the mecA gene, which is located on a large mobile genetic element called the Staphylococcal chromosome cassette mec (SCCmec), and, so far 11 types of SCCmec elements have been described (types I–XI). The population structure of S. aureus has been shown to be highly clonal, and previous genomic comparisons showed that about 75% of the S. aureus genome is highly conserved (core genome), while the remaining 25% varies significantly among strains (accessory genome). The accessory genome consists mostly of mobile genetic elements (MGEs), such as bacteriophages, pathogenicity islands, genomic islands, plasmids, transposons, and the SCCmec element. The importance of understanding the patterns of evolution of MGEs is illustrated by the SCCmec element, which has been acquired and/or transferred on multiple occasions during the evolution of the species. The study of the population genetics of S. aureus has been addressed using multilocus sequence typing. Based on these data, the population structure of S. aureus was classified into related groups of strains defined as clonal complexes and their isolated sequence types. Extensive typing showed that the S. aureus population associated with humans consists of 10 major lineages and most MRSA belong to 6 of them. The presence of the same clones in different geographical regions suggested their rapid dissemination. Moreover, the epidemiology of MRSA is highly dynamic, and clonal replacement of predominant clones within a given locale has been widely documented. Although the reasons why some clones replace others are unclear, the emergence and replacement of clones might have significant consequences for public health, as different clones possess differing resistance and virulence attributes.

The antibiotic susceptibility and molecular epidemiology of Panton-Valentine leukocidin (PVL)-positive meticillin-resistant Staphylococcus aureus (MRSA) isolates reported from 17 countries in the Americas, Europe and, Australia-Asia were analysed. Among a total of 3236 non-duplicate isolates, the lowest susceptibility was observed to erythromycin in all regions. Susceptibility to ciprofloxacin showed large variation (25%, 75% and 84% in the Americas, Europe and Australia-Asia, respectively). Two vancomycin-intermediate PVL-positive MRSA isolates were reported, one from Hong Kong and the other from The Netherlands. Resistance to trimethoprim/sulfamethoxazole and linezolid was

In 2010-11, a trial conducted in nursing homes showed no benefit of meticillin-resistant Staphylococcus aureus (MRSA) universal screening and decolonization over standard precautions to reduce the prevalence of MRSA carriage. Accordingly, no routine screening was performed from 2012. A five-year follow-up shows no new evidence supporting the intervention. Recommendations issued after trial (no screening and decolonization of MRSA residents) were retained.

Although the molecular typing of Pseudomonas aeruginosa is important to understand the local epidemiology of this opportunistic pathogen, it remains challenging. Our aim was to develop a simple typing method based on the sequencing of two highly variable loci. Single-strand sequencing of three highly variable loci (ms172, ms217, and oprD) was performed on a collection of 282 isolates recovered between 1994 and 2007 (from patients and the environment). As expected, the resolution of each locus alone [number of types (NT) = 35-64; index of discrimination (ID) = 0.816-0.964] was lower than the combination of two loci (NT = 78-97; ID = 0.966-0.971). As each pairwise combination of loci gave similar results, we selected the most robust combination with ms172 [reverse; R] and ms217 [R] to constitute the double-locus sequence typing (DLST) scheme for P. aeruginosa. This combination gave: (i) a complete genotype for 276/282 isolates (typability of 98%), (ii) 86 different types, and (iii) an ID of 0.968. Analysis of multiple isolates from the same patients or taps showed that DLST genotypes are generally stable over a period of several months. The high typability, discriminatory power, and ease of use of the proposed DLST scheme makes it a method of choice for local epidemiological analyses of P. aeruginosa. Moreover, the possibility to give unambiguous definition of types allowed to develop an Internet database ( http://www.dlst.org ) accessible by all.

During a 1-year period, 87 methicillin-resistant Staphylococcus aureus isolates were collected from 4 major Cuban hospitals for epidemiological analysis. The majority (86%) were related to the community-associated USA300 clone, whereas the remaining belonged to a new clone ST72-V. Interestingly, no hospital-associated clone was found in these Cuban hospitals.

Summary Background Pseudomonas aeruginosa is a leading cause of healthcare-associated infections in the intensive care unit (ICU). Aim To investigate an unexplained increase in the incidence of P. aeruginosa recovered from clinical samples in the ICU over a two-year period. Methods After unsuccessful epidemiological investigation by conventional tools, P. aeruginosa clinical isolates of all patients hospitalized between January 2010 and July 2012 were typed by a novel double-locus sequence typing (DLST) method and compared to environmental isolates recovered during the investigation period. Findings In total, 509 clinical isolates from 218 patients and 91 environmental isolates were typed. Thirty-five different genotypic clusters were found in 154 out of 218 patients (71%). The largest cluster, DLST 1-18, included 23 patients who were mostly hospitalized during overlapping periods in the burn unit. Genotype DLST 1-18 was also recovered from floor traps, shower trolleys and the shower mattress in the hydrotherapy rooms, suggesting environmental contamination of the burn unit as the source of the outbreak. After implementation of appropriate infection control measures, this genotype was recovered only once in a clinical sample from a burned patient and twice in the environment, but never thereafter during a 12-month follow-up period. Conclusion The use of a novel DLST method allowed the genotyping of a large number of clinical and environmental isolates, leading to the identification of the environmental source of a large unrecognized outbreak in the burn unit. Eradication of the outbreak was confirmed after implementation of a continuous epidemiological surveillance of P. aeruginosa clones in the ICU.