Fast and simple epidemiological typing of Pseudomonas aeruginosa using the double-locus sequence typing (DLST) method.

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

Changing molecular epidemiology of methicillin-resistant Staphylococcus aureus in an Algerian hospital.

INTRODUCTION: Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of both hospital- and community-acquired infections worldwide. However, data about the molecular epidemiology of MRSA in North Africa are still scarce. METHODOLOGY: All MRSA isolates recovered between January 2006 and July 2011 from one Algerian hospital were genetically and phenotypically characterized. RESULTS: The predominance of a European community-associated-MRSA (CA-MRSA) clone (ST80-SCCmec IV-PVL positive) was revealed by this analysis. CONCLUSION: Our data suggest that a CA-MRSA clone recently invaded the hospital setting in Algiers and replaced a typical hospital-associated pandemic clone such as the Brazilian clone (ST239-SCCmec IIImercury-PVL negative)

Molecular Epidemiology of Pseudomonas aeruginosa in the Intensive Care Units – A Review

Pseudomonas aeruginosa is one of the leading nosocomial pathogens in intensive care units (ICU). This opportunist pathogen is commonly recovered from moist environments, and is also found colonizing 2.6 to 24% of hospitalized patients. We reviewed the recent literature that used highly discriminatory typing methods to precisely identify the reservoirs and modes of transmission of this microorganism in the ICU setting. In most ICUs, the endogenous flora was suspected to be the main source of infection compared to exogenous sources (other patients, the contaminated environment such as sinks or taps). However, the percentage of endogenous versus exogenous sources might vary considerably from one setting to another. Reasons for this include the compliance of health care workers to infection control measures, the contamination of the environment, and probably also the biology of the pathogen (intrinsic fitness factors). As P. aerugi-nosa is ubiquitous in the environment and colonizes up to 15% of hospitalized patients, eradication of the reservoir is difficult, if not impossible. Therefore, efforts should primarily focus on reinforcement of infection control measures to limit its transmission

MRSA screening by the Xpert MRSA PCR assay: pooling samples of the nose, throat, and groin increases the sensitivity of detection without increasing the laboratory costs.

The performance of the Xpert MRSA polymerase chain reaction (PCR) assay on pooled nose, groin, and throat swabs (three nylon flocked eSwabs into one tube) was compared to culture by analyzing 5,546 samples. The sensitivity [0.78, 95 % confidence interval (CI) 0.73-0.82] and specificity (0.99, 95 % CI 0.98-0.99) were similar to the results from published studies on separated nose or other specimens. Thus, the performance of the Xpert MRSA assay was not affected by pooling the three specimens into one assay, allowing a higher detection rate without increasing laboratory costs, as compared to nose samples alone

Draft Genome Sequences of Two Carbapenemase-Producing Acinetobacter baumannii Clinical Strains Isolated from Albanian and Togolese Patients.

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

Evaluation of three consecutive versions of a commercial rapid PCR test to screen for methicillin-resistant Staphylococcus aureus.

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. 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. 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 < 0.00001). These significant differences in performance show the importance of evaluating each new version of a commercial test

Automated Incubation and Digital Image Analysis of Chromogenic Media Using Copan WASPLab Enables Rapid Detection of Vancomycin-Resistant Enterococcus.

Objective: The aim of the present study was to assess whether the WASPLab automation enables faster detection of vancomycin-resistant Enterococcus (VRE) on chromogenic VRE-specific plates by shortening the incubation time. Methods: Ninety different VRE culture negative rectal ESwab specimens were spiked with various concentrations (ranging from 3 × 10 <sup>2</sup> to 3 × 10 <sup>7</sup> CFU/ml) of 10 Enterococcus faecium strains (vancomycin MICs ranging from 32 to >256 mg/l), 3 E. faecium VanB strains (vancomycin MICs: 4, 8, and 16 mg/l), and 2 E. faecium VanB strains displaying vancomycin heteroresistance (vancomycin MICs: 64 and 96 mg/l). Results: Besides the two strains exhibiting vancomycin heteroresistance, all the other 13 VRE strains included in this study were detected as early as 24 h on the WASPLab even if the inoculum was low (3 × 10 <sup>3</sup> CFU/ml). When the vancomycin MICs were high, all strains were detected as early as at 18 h. However, 30 h was a conservative time point for finalizing the analysis of chromogenic cultures. Conclusion: These results suggested that the WASPLab automated incubation could allow decreasing the initial incubation time to 18 h, followed by an intermediate time at 24 h and a final incubation period of 30 h for VRE culture screening, to deliver rapid results without affecting the analytical sensitivity

High-Quality Complete Genome Sequences of Three Pseudomonas aeruginosa Isolates 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