Yossi Paitan

A national survey of the molecular epidemiology of Clostridium difficile in Israel: the dissemination of the ribotype 027 strain with reduced susceptibility to vancomycin and metronidazole.

Our goals were to study the molecular epidemiology and antimicrobial susceptibilities of C. difficile strains in Israel. Microbiology laboratories serving 6 general hospitals (GH) and 10 long-term care facilities (LTCF) were asked to submit all stool samples in January-February 2014 that tested positive for C. difficile. Toxigenic C. difficile isolates were recovered in 208 out of 217 samples (95.8%), of which 50 (23.6%) were from LTCFs. Ribotype 027 was the most common type overall, identified in 65 samples (31.8%), and was the predominant strain in the 3 GHs with the highest incidence of C. difficile infections. Other common strains were slpA types cr-02 (n = 45) and hr-02 (n = 18). The proportions of vancomycin and metronidazole MIC values >2mg/L were high in ribotype 027 (87.7% and 44.6%, respectively) and slpA-cr-02 strains (88.8% and 17.8%, respectively). This study demonstrates that the ribotype 027 strain has disseminated across Israel and is now the most common strain.

Interactions between the intestinal microbiota and bile acids in gallstones patients.

Cholecystectomy, surgical removal of the gallbladder, changes bile flow to the intestine and can therefore alter the bidirectional interactions between bile acids (BAs) and the intestinal microbiota. We quantified and correlated BAs and bacterial community composition in gallstone patients scheduled for cholecystectomy before and after the procedure, using gas-liquid chromatography and 16S rRNA amplicon sequencing, followed by quantitative real-time polymerase chain reaction of the phylum Bacteroidetes. Gallstone patients had higher overall concentrations of faecal BAs and a decreased microbial diversity, accompanied by a reduction in the beneficial genus Roseburia and an enrichment of the uncultivated genus Oscillospira, compared with controls. These two genera may thus serve as biomarkers for symptomatic gallstone formation. Oscillospira was correlated positively with secondary BAs and negatively with primary BAs, while the phylum Bacteroidetes showed an opposite trend. Cholecystectomy resulted in no substantial change in patients faecal BAs. However, bacterial composition was significantly altered, with a significant increase in the phylum Bacteroidetes. Given that cholecystectomy has been associated with a higher risk of colorectal cancer and that members of the Bacteroidetes are increased in that disease, microbial consequences of cholecystectomy should be further explored.

Pregnancy-Associated Listeriosis: Clinical Characteristics and Geospatial Analysis of a 10-Year Period in Israel

BACKGROUNDnListeria monocytogenes is a foodborne pathogen that causes life-threatening infections in elderly, immunocompromised, and pregnant women. In pregnancy it may cause fetal loss or a preterm delivery, and the neonate is prone to neonatal sepsis and death.nnnMETHODSnWe created a cohort of all L. monocytogenes cases during 10 years (1998-2007) in Israel, by a comprehensive review of cases in hospitals throughout the country and cases reported to the Ministry of Health.nnnRESULTSnOne hundred sixty-six pregnancy-related listeriosis cases were identified, resulting in a yearly incidence of 5-25 cases per 100 000 births. Presentation associated with fetal demise was more common in the second trimester (55.3%), and preterm labor (52.3%) and abnormal fetal heart rate monitoring (22.2%) were more common in the third trimester (P = .001). Fetal viability was low in the second trimester (29.2%) and much higher (95.3%) in the third trimester. Each additional week of pregnancy increased the survival chance by 33% (odds ratio, 1.331 [95% confidence interval, 1.189-1.489]). A single case of maternal mortality was identified. Listeria monocytogenes serotype 4b was more common in pregnancy-related than in non-pregnancy-related cases (79.5% vs 61.3%, P = .011). Pulsed-field gel electrophoresis analysis suggested that 1 pulsotype is responsible for 35.7% of the pregnancy cases between 2001 and 2007. This clone is closely related to the Italian gastroenteritis-associated HPB2262 and the invasive US Scott A L. monocytogenes strains.nnnCONCLUSIONSnOur survey emphasizes the high rate of pregnancy-related listeriosis in Israel and shows that specific clones might account for this.

Evaluation of single and double-locus real-time PCR assays for methicillin-resistant Staphylococcus aureus (MRSA) surveillance

BackgroundMethicillin-resistant Staphylococcus aureus (MRSA) is a human pathogen, representing an infection control challenge. Conventional MRSA screening takes up to three days, therefore development of rapid detection is essential. Real time-PCR (rt-PCR) is the fastest method fulfilling this task. All currently published or commercially available rt-PCR MRSA assays relay on single or double-locus detection. Double-locus assays are based on simultaneous detection of mecA gene and a S. aureus-specific gene. Such assays cannot be applied on clinical samples, which often contain both coagulase-negative staphylococci (CoNS) and S. aureus, either of which can carry mecA. Single-locus assays are based on detection of the staphylococcal cassette chromosome mec (SCCmec) element and the S. aureus-specific orfX gene, assuming that it is equivalent to mecA detection.FindingsParallel evaluation of several published single and double-locus rt-PCR MRSA assays of 150 pure culture strains, followed by analysis of 460 swab-derived clinical samples which included standard identification, susceptibility testing, followed by PCR detection of staphylococcal suspected isolates and in-PCR mixed bacterial populations analysis indicated the following findings.Pure cultures analysis indicated that one of the single-locus assay had very high prevalence of false positives (Positive predictive value = 77.8%) and was excluded from further analysis. Analysis of 460 swab-derived samples indicated that the second single-locus assay misidentified 16 out of 219 MRSAs and 13 out of 90 methicillin-sensitive S. aureuss (MSSA) were misidentified as MRSAs. The double-locus detection assay misidentified 55 out of 90 MSSAs. 46 MSSA containing samples were misidentified as MRSA and 9 as other than S. aureus ending with low positive predicted value (<85%) and very low specificity (<62%).ConclusionThe results indicate that high prevalence of false-positive and false-negative reactions occurs in such assays.

Persistent Helicobacter canis Bacteremia in a Patient with Gastric Lymphoma

A 78-year-old man with gastric diffuse large B cell lymphomapresented with persistent Helicobacter canis bacteremia whilereceiving chemotherapy. An examination of his medicalhistory revealed a close exposure to dogs. The patientrecovered after 4 weeks of antibiotic therapy. Immunocompromisedpersons who maintain close contacts with dogs maybe at risk for this infection.

MRSA SCCmec epidemiology in Israel: development and implementation of an MRSA SCCmec typing strategy

Staphylococcal cassette chromosome mec (SCCmec) typing is essential for investigating the molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA). Published assays were often found to be limited in their ability to characterize isolates that were not collected locally. We aimed to develop, test, and implement a molecular method which would enable the SCCmec classification of a large collection of MRSA isolates in a routine clinical laboratory. A multistep working algorithm consisting of two main steps and four additional supplementary steps was developed, using previously reported primers. A total of 1,008 isolates obtained locally, by both clinical and screening cultures, were tested. The majority of isolates (82.54%) could be classified using two main reactions. Overall, our MRSA SCCmec typing strategy was able to classify 917/1,008 (90.97%) of the MRSA isolates. The most predominant was type II SCCmec (41%); a high prevalence of type V SCCmec (16.37%) was also found. PVL gene carriage was found among two type IV SCCmec isolates only. We present a logistically feasible, multistep, MRSA SCCmec typing algorithm which can be used to type a large collection of MRSA isolates. The distinctly higher prevalence of SCCmec type V might reflect a unique MRSA distribution pattern in Israel.

Evaluation of the NanoCHIP® Infection Control Panel test for direct detection and screening of methicillin-resistant Staphylococcus aureus (MRSA), Klebsiella pneumoniae carbapenemase (KPC)-producing bacteria and vancomycin-resistant Enterococcus (VRE).

PurposeRapid detection of infection control targets is needed and several bacterial target assays are commercially available. Detection of patients colonized with Klebsiella pneumoniae carbapenemase-producing Enterobacteriaceae (KPC-CRE), methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) comprises an essential part of infection control programs. This study evaluated the performance and feasibility of a novel molecular-based diagnostic screening test, the NanoCHIP® Infection Control Panel (ICP) assay (Savyon Diagnostics, Israel), which enables simultaneous detection of KPC-CRE, MRSA and VRE directly from swab samples and compares its sensitivity and specificity to culture.MethodsProspective direct swab analysis of 338 (70 CRE, 198 MRSA and 70 VRE) screening swab samples.ResultsIncluding all targets and all valid samples, the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the NanoCHIP® ICP assay were 91.1, 99.5, 99.1 and 94.9xa0%, respectively.ConclusionsAs far as we know, this is the first report regarding a single molecular-based system that detects all three targets (CRE-KPC, MRSA and VRE) simultaneously, directly from swab samples, using the same reaction and platform. Overall, the assay was easy to perform, enabling medium- to high-throughput screening. Same day results enable efficient infection control interventions, such as carrier isolation.

Comparative performance study of six commercial molecular assays for rapid detection of toxigenic Clostridium difficile

OBJECTIVESnRapid and accurate detection of Clostridium difficile in stool affects patient treatment and containment efforts. Detection of C.xa0difficile toxin genes using nucleic acid amplification techniques (NAAT) is part of a multistep algorithm. Our objective was to directly compare the diagnostic accuracy and applicability of six commercial C.xa0difficile NAAT.nnnMETHODSnTwo hundred ten specimens were analysed in parallel by six commercial NAAT. Toxigenic culture was used as a reference method.nnnRESULTSnWe analysed 98 positive and 112 negative samples. The Xpert C.xa0difficile had 99% sensitivity (95% confidence interval (CI) 94.45-99.97), followed by Simplexa C.xa0difficile Universal Direct 95% (95% CI 88.49-98.32), Illumigene C.xa0difficile, and Quidel AmpliVue C.xa0difficile, both 93% (95% CI 85.84-97.08), and BDmax Cdiff and GenomEra C.xa0difficile, both 92% (95% CI 84.55-96.41). All assays had very high specificity (>99%). Invalid results requiring retesting were the highest in GenomEra (6.7%; 14/210) and BDmax (4.3%; 9/210), followed by AmpliVue (1.4%; 3/210) and Xpert (0.96%; 2/210). No retesting was required with Simplexa and Illumigene. The turnaround time was the shortest for the Illumigene and Xpert and the longest for BDmax, mostly due to the different reaction times of assays. Total hands-on time was comparable for all six assays.nnnCONCLUSIONSnAll assays had high sensitivity and specificity. The differences in turnaround time, repeat testing rates and platform characteristics could help laboratories decide which assay would integrate better in their setting and to better select a molecular platform for C.xa0difficile detection.

Gram-Negative Pathogens: Overview of Novel and Emerging Resistant Pathogens and Drugs

The rising prevalence of multiresistant Gram-negative bacterial infections has become a major clinical problem, as currently such infections comprise the majority of untreatable bacterial infections. The variety of resistance and transfer mechanisms and their rapid spread among Gram-negative bacteria constitutes a global infection control challenge, and an urgent need for development of new antimicrobials. Unfortunately, infection rates with multiresistant nonfermenters, such as Pseudomonas aeruginosa, Acinetobacter baumannii, or extended-spectrum β-lactamase producing Enterobacteriaceae and carbapenem resistant Enterobacteriaceae such as Klebsiella pneumoniae, are growing progressively while the pace of antibiotic drug development has slowed considerably during the last decade. This chapter reviews the main emerging Gram-negative resistant pathogens, their various resistance mechanisms, prevalence, risk factors, and summarizes the novel drugs being developed against them.

Current Trends in Antimicrobial Resistance of Escherichia coli

Escherichia coli is the most common Gram-negative bacterial pathogen, presenting both a clinical and an epidemiological challenge. In the last decade, several successful multidrug-resistant high-risk strains, such as strain E. coli ST131 have evolved, mainly due to the growing selective pressure of antimicrobial use. These strains present enhanced fitness and pathogenicity, effective transmission and colonization abilities, global distribution due to efficient dissemination, and resistance to various antimicrobial resistances. Here, we describe the emerging trends and epidemiology of resistant E. coli, including carbapenemase-producing E. coli, E. coli ST131 and colistin resistant E. coli.