ABSTRACT
Echinocandins represent the first-line therapy of candidemia. Echinocandin resistance among Candida spp. is mainly due to acquired FKS mutations. In this study, we report the emergence of FKS-mutant Candida albicans/glabrata in Switzerland and provide the microbiological and clinical characteristics of 9 candidemic episodes. All patients were previously exposed to echinocandins (median 26 days; range 15-77). Five patients received initial echinocandin therapy with persistent candidemia in 4 of them. Overall mortality was 33%.
Subject(s)
Antifungal Agents/therapeutic use , Candida albicans/physiology , Candida glabrata/physiology , Candidemia/drug therapy , Drug Resistance, Fungal , Echinocandins/therapeutic use , Adult , Aged , Aged, 80 and over , Candida albicans/drug effects , Candida albicans/genetics , Candida glabrata/drug effects , Candida glabrata/genetics , Female , Humans , Male , Middle Aged , SwitzerlandABSTRACT
Auritidibacter ignavus is a Gram-stain-positive bacillus derived from otorrhea. Four strains derived from ear discharges in Canada and Switzerland, with features consistent with but distinguishable from Auritidibacter ignavus IMMIB L-1656T (accession number FN554542) by 16S rRNA gene sequencing (97.5â% similarity), were thought to represent a novel species of the genus Auritidibacter. Auritidibacter ignavus DSM 45359T (=IMMIB L-1656T) was acquired to compare with Canadian and Swiss strains by whole-genome sequencing (WGS). Unexpectedly, those isolates were observed to be consistent with A. ignavus DSM 45359T by WGS (ANIb scores >98â%), MALDI-TOF (Bruker), cellular fatty acid analysis and biochemically (some differences were observed). A nearly full 16S rRNA gene sequence could not be readily prepared from A. ignavus DSM 45359T, even after multiple attempts. A 16S rRNA gene chimeric consensus sequence created from the genome assembly of A. ignavus DSM 45359T had only 97.5â% similarity to that of A. ignavus IMMIB L-1656T, implying that 16S rRNA sequence accession number FN554542 could not be replicated. We concluded that our isolates of members of the genus Auritidibacter were consistent with A. ignavus DSM 45359T, did not represent a novel species, and that the sequence corresponding to FN554542 was not reproducible. By WGS, A. ignavus DSM 45359T had genome of 2.53×106 bp with a DNA G+C content of 59.34%, while genomes of Canadian and Swiss isolates ranged from 2.47 to 2.59×106 bp with DNA G+C contents of 59.3-59.52â%. A. ignavus NML 100628 (=NCTC 14178=LMG 30897) did not demonstrate a rodcoccus cycle. Emendation of Auritidibacter ignavus was proposed based on these results.
Subject(s)
Micrococcaceae/classification , Phylogeny , Aged , Bacterial Typing Techniques , Base Composition , Canada , DNA, Bacterial/genetics , Ear/microbiology , Fatty Acids/chemistry , Female , Humans , Male , Middle Aged , Nucleic Acid Hybridization , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , SwitzerlandABSTRACT
We present the whole-genome sequence of an isolate of Auritidibacter ignavus, associated with ear infections. This complete assembly was compared to genomes of four global isolates, which revealed a high diversity within the species.
Subject(s)
Actinobacteria/drug effects , Actinobacteria/genetics , Anti-Bacterial Agents/pharmacology , Genome, Bacterial/genetics , Microbial Sensitivity Tests , Whole Genome Sequencing , Actinobacteria/isolation & purification , Anaerobiosis , DNA, Bacterial/genetics , Genetic Variation , Humans , Mastitis/microbiology , Microbiota , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNAABSTRACT
OBJECTIVES: Echinocandins represent the first-line treatment of candidaemia. Acquired echinocandin resistance is mainly observed among Candida albicans and Candida glabrata and is associated with FKS hotspot mutations. The commercial Sensititre YeastOne™ (SYO) kit is widely used for antifungal susceptibility testing, but interpretive clinical breakpoints are not well defined. We determined echinocandins epidemiological cut-off values (ECV) for C. albicans/glabrata tested by SYO and assessed their ability to identify FKS mutants in a national survey of candidaemia. METHODS: Bloodstream isolates of C. albicans and C. glabrata were collected in 25 Swiss hospitals from 2004 to 2013 and tested by SYO. FKS hotspot sequencing was performed for isolates with an MIC≥ECV for any echinocandin. RESULTS: In all, 1277 C. albicans and 347 C. glabrata were included. ECV 97.5% of caspofungin, anidulafungin and micafungin were 0.12, 0.06 and 0.03 µg/mL for C. albicans, and 0.25, 0.12 and 0.03 µg/mL for C. glabrata, respectively. FKS hotspot sequencing was performed for 70 isolates. No mutation was found in the 52 'limit wild-type' isolates (MIC=ECV for at least one echinocandin). Among the 18 'non-wild-type' isolates (MIC>ECV for at least one echinocandin), FKS mutations were recovered in the only two isolates with MIC>ECV for all three echinocandins, but not in those exhibiting a 'non-wild-type' phenotype for only one or two echinocandins. CONCLUSION: This 10-year nationwide survey showed that the rate of echinocandin resistance among C. albicans and C. glabrata remains low in Switzerland despite increased echinocandin use. SYO-ECV could discriminate FKS mutants from wild-type isolates tested by SYO in this population.
Subject(s)
Antifungal Agents/pharmacology , Candida albicans/genetics , Candidiasis/microbiology , Drug Resistance, Fungal , Echinocandins/pharmacology , Candida glabrata , Echinocandins/administration & dosage , Humans , Microbial Sensitivity Tests , Mutation , Population Surveillance , Switzerland/epidemiologyABSTRACT
OBJECTIVES: Whole-genome sequencing (WGS) is a promising tool for identifying transmission pathways in outbreaks caused by multidrug-resistant bacteria. However, it is uncertain how the data produced by WGS can be best integrated into epidemiologic investigations. METHODS: We tested various genomic analyses to identify clonal groups in two distinct outbreaks of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae that occurred in Switzerland in 2013 and 2015. In blinded fashion, we sequenced 12 strains involved in the two outbreaks, respectively, and six that were epidemiologically unrelated. We analysed genomic commonalities from conserved genes to plasmid-borne antibiotic resistance genes (ARGs) and contrasted these results with available epidemiologic evidence. RESULTS: Using WGS, blinded analysts correctly identified the two clusters of strains from the two outbreaks. Nonetheless, the 2015 index strain was found to be slightly different (1-3 single nucleotide variants) from the strains recovered from secondary cases, likely because prior long-term carriage (3 years) by the index patient allowed for genetic mutations over time. Also, we observed occasional loss of ARG-bearing plasmidic fragments in outbreak-causing strains. CONCLUSIONS: Retrospective WGS analysis was successful in identifying clonal groups in both outbreaks. Still, data should be analysed with caution in cases of previous long-term carriage of the studied bacteria.
Subject(s)
Bacterial Proteins/metabolism , Cross Infection/epidemiology , Disease Outbreaks , Klebsiella Infections/epidemiology , Klebsiella pneumoniae/classification , Molecular Typing/methods , Whole Genome Sequencing/methods , beta-Lactamases/metabolism , Aged , Cluster Analysis , Cross Infection/microbiology , Disease Transmission, Infectious , Genotype , Humans , Klebsiella Infections/microbiology , Klebsiella pneumoniae/enzymology , Klebsiella pneumoniae/isolation & purification , Male , Molecular Epidemiology/methods , Retrospective Studies , Switzerland/epidemiologyABSTRACT
Toxigenic Corynebacterium diphtheriae is an important and potentially fatal threat to patients and public health. During the current dramatic influx of refugees into Europe, our objective was to use whole genome sequencing for the characterization of a suspected outbreak of C. diphtheriae wound infections among refugees. After conventional culture, we identified C. diphtheriae using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and investigated toxigenicity by PCR. Whole genome sequencing was performed on a MiSeq Illumina with >70×coverage, 2×250 bp read length, and mapping against a reference genome. Twenty cases of cutaneous C. diphtheriae in refugees from East African countries and Syria identified between April and August 2015 were included. Patients presented with wound infections shortly after arrival in Switzerland and Germany. Toxin production was detected in 9/20 (45%) isolates. Whole genome sequencing-based typing revealed relatedness between isolates using neighbour-joining algorithms. We detected three separate clusters among epidemiologically related refugees. Although the isolates within a cluster showed strong relatedness, isolates differed by >50 nucleotide polymorphisms. Toxigenic C. diphtheriae associated wound infections are currently observed more frequently in Europe, due to refugees travelling under poor hygienic conditions. Close genetic relatedness of C. diphtheriae isolates from 20 refugees with wound infections indicates likely transmission between patients. However, the diversity within each cluster and phylogenetic time-tree analysis suggest that transmissions happened several months ago, most likely outside Europe. Whole genome sequencing offers the potential to describe outbreaks at very high resolution and is a helpful tool in infection tracking and identification of transmission routes.
Subject(s)
Bacterial Toxins/genetics , Corynebacterium diphtheriae/genetics , Diphtheria/epidemiology , Disease Outbreaks , Wound Infection/epidemiology , Adolescent , Adult , Africa/epidemiology , Bacterial Toxins/metabolism , Bacterial Typing Techniques , Corynebacterium diphtheriae/drug effects , Corynebacterium diphtheriae/isolation & purification , Diphtheria/drug therapy , Drug Resistance, Multiple, Bacterial/genetics , Female , Genes, Bacterial , Germany/epidemiology , Humans , Male , Multigene Family , Multilocus Sequence Typing , Phylogeny , Refugees , Switzerland/epidemiology , Syria/epidemiology , Wound Infection/drug therapy , Wound Infection/microbiology , Young AdultABSTRACT
Neisseria cinerea is a human commensal. The first known case of meningitis and bacteremia due to Neisseria cinerea following percutaneous glycerol instillation of the trigeminal ganglion is reported. Conventional phenotypic methods and complete 16S RNA gene sequencing accurately identified the pathogen. Difficulties in differentiation from pathogenic neisseriae are discussed.
Subject(s)
Bacteremia/diagnosis , Meningitis, Bacterial/diagnosis , Neisseria cinerea/isolation & purification , Neisseriaceae Infections/diagnosis , Anti-Bacterial Agents/pharmacology , Bacteremia/complications , Bacteremia/microbiology , Cluster Analysis , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Head/diagnostic imaging , Humans , Male , Meningitis, Bacterial/complications , Meningitis, Bacterial/microbiology , Microbial Sensitivity Tests , Middle Aged , Molecular Sequence Data , Neisseria cinerea/classification , Neisseria cinerea/drug effects , Neisseria cinerea/genetics , Neisseriaceae Infections/microbiology , Neisseriaceae Infections/pathology , Phylogeny , RNA, Ribosomal, 16S/genetics , Rhizotomy/adverse effects , Sequence Analysis, DNA , Tomography, X-Ray Computed , Trigeminal Neuralgia/therapyABSTRACT
A commercially available assay (eazyplex® SuperBug CRE) detecting the most common carbapenemase and ESBL types was evaluated directly on 50 urine samples. Eazyplex® correctly detected ESBL-encoding genes in all 30 urine samples with confirmed ESBL production (sensitivity 100%). Two specimens showed invalid and one specimen false-positive results (specificity 97.9%).
Subject(s)
Bacterial Proteins/urine , Enterobacteriaceae Infections/urine , Enterobacteriaceae/enzymology , Nucleic Acid Amplification Techniques/methods , beta-Lactamases/urine , Bacterial Proteins/genetics , Enterobacteriaceae/genetics , Enterobacteriaceae/isolation & purification , Enterobacteriaceae Infections/microbiology , Humans , Nucleic Acid Amplification Techniques/economics , Reagent Kits, Diagnostic , beta-Lactamases/geneticsABSTRACT
We report an imported case of louse-borne relapsing fever in a young adult Eritrean refugee who presented with fever shortly after arriving in Switzerland. Analysis of blood smears revealed spirochetes identified as Borrelia recurrentis by 16S rRNA gene sequencing. We believe that louse-borne relapsing fever may be seen more frequently in Europe as a consequence of a recent increase in refugees from East Africa travelling to Europe under poor hygienic conditions in confined spaces.
Subject(s)
Borrelia/isolation & purification , RNA, Ribosomal, 16S/genetics , Relapsing Fever/diagnosis , Animals , Borrelia/genetics , Ceftriaxone/administration & dosage , DNA, Bacterial/genetics , Doxycycline/administration & dosage , Eritrea , Humans , Refugees , Relapsing Fever/blood , Relapsing Fever/drug therapy , Switzerland , Travel , Treatment OutcomeABSTRACT
INTRODUCTION: In immunosuppressed hosts, rapid identification of microorganisms of bloodstream infections is crucial to ensuring effective antimicrobial therapy. Conventional culture requires up to 72 h from sample collection to pathogen identification. METHODS: We used the SepsiTyper Kit and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF; Microflex, Bruker) directly from positive blood culture (BacT/ALERT 3D, FN/FA vials; bioMérieux) in comparison to standard culture methodology (VITEK 2; bioMérieux) for species identification. RESULTS: A total of 62 consecutive positive blood cultures from immunosuppressed patients (solid organ or hematopoietic transplant recipients, or with febrile neutropenia) were analyzed. Culture yielded gram-negative bacteria (GNB) in 27/62 (43.5%) and gram-positive (GPB) in 35/62 (56.5%) vials. For GNB, the predominant species identified by MALDI-TOF and confirmed by VITEK were Escherichia coli (16/16 correctly identified) and Enterobacter cloacae (4/4), with a sensitivity and specificity of 92.6% and 100%, respectively. For GPB, predominant species were Staphylococcus aureus (3/3), coagulase-negative staphylococci (12/24), and Enterococcus faecium (6/6) with a sensitivity of 100%, 60%, and 100%, respectively. The median time from blood collection to species identification was 27.4 h with MALDI-TOF identification and 46.6 h with conventional methodology. CONCLUSION: Using MALDI-TOF directly from positive blood cultures allowed a shorter time to identification with high sensitivity and specificity in immunosuppressed patients.
Subject(s)
Bacteremia/diagnosis , Communicable Diseases/diagnosis , Gram-Negative Bacteria/isolation & purification , Gram-Positive Bacteria/isolation & purification , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Cohort Studies , Communicable Diseases/microbiology , Humans , Immunocompromised Host , Sensitivity and Specificity , Time FactorsABSTRACT
BACKGROUND: Detection of fungal DNA from formalin-fixed, paraffin-embedded (FFPE) tissue is challenging due to degradation of DNA and presence of PCR inhibitors in these samples. We analyzed FFPE samples of 26 patients by panfungal PCR and compared the results to the composite diagnosis according to the European Organization for Research and Treatment of Cancer (EORTC) criteria. Additionally we analyzed the quality of human and fungal DNA and their level of age-dependent degradation, as well as the existence of PCR inhibition in these tissue samples. METHODS: We evaluated two 45-cycle panfungal PCR tests that target the internal transcribed spacer 2 (ITS2) as well as the ITS1-5.8S-ITS2 (ITS1-2) region. The PCRs were applied to 27 FFPE specimens from 26 patients with proven invasive fungal disease (IFD), and one patient with culture and histologically negative but PCR-positive fungal infection collected at our institution from 2003 to 2010. Quality of DNA in FFPE tissue samples was evaluated using fragments of the beta-globin gene for multiplex PCR, inhibition of PCR amplification was evaluated by spiking of C. krusei DNA to each PCR premix. RESULTS: In 27 FFPE samples the ITS2 PCR targeting the shorter fragment showed a higher detection rate with a sensitivity of 53.8% compared to the ITS1-2 fragment (sensitivity 38%). Significant time-dependent degradation of human DNA in FFPE sample extracts was detected based on partial beta-globin gene amplification which was not in correlation to successful panfungal PCR identification of fungal organisms. The analytical sensitivity of both assays compared with culture was 60 CFU/ml of a Candida krusei reference strain. The performance of the two tests in an Aspergillus proficiency panel of an international external quality assessment programme showed considerable sensitivity. CONCLUSION: Panfungal diagnostic PCR assays applied on FFPE specimens provide accurate identification of molds in highly degraded tissue samples and correct identification in samples stored up to 7 years despite sensitivity limitations, mainly caused by partial PCR inhibition and DNA degradation by formalin.
Subject(s)
Aspergillosis/diagnosis , DNA, Fungal/isolation & purification , Polymerase Chain Reaction/methods , Aspergillosis/microbiology , Aspergillus/genetics , DNA, Fungal/genetics , Fixatives/chemistry , Formaldehyde/chemistry , Humans , Molecular Diagnostic Techniques , Mycological Typing Techniques , Paraffin Embedding , Sensitivity and Specificity , Tissue FixationABSTRACT
The species Corynebacterium pyruviciproducens was described in 2010 based on the features of a single strain. In this report, we describe the chemotaxonomic and phenotypic characteristics of 11 C. pyruviciproducens clinical strains isolated in Switzerland and Canada in comparison to the strain 06-17730(T). Heterogeneities within the type strain were found in the 16S rRNA gene and in biochemical markers. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identification of this species could not be achieved since currently this bacterial species is not included in the corresponding database. Reliable identification is obtained only with sequence-based identification tools. Results of antimicrobial susceptibility testing of this species with an extended panel of antimicrobials are presented here for the first time.
Subject(s)
Corynebacterium Infections/microbiology , Corynebacterium/classification , Corynebacterium/isolation & purification , Bacterial Typing Techniques , Canada , Cluster Analysis , Corynebacterium/genetics , Corynebacterium/physiology , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Humans , Molecular Sequence Data , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , SwitzerlandABSTRACT
We report the epidemiological and clinical features of the first outbreak of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-KP) type 2 in Switzerland. The outbreak took place in the medical intensive care unit (MICU) of our tertiary care hospital and affected three severely ill patients. After the implementation of strict infection control measures, no further patients colonised with KPC-KP could be detected by the screening of exposed patients. Successful treatment of patients infected with KPC-KP consisted of a combination therapy of meropenem, colistin and tigecycline.
Subject(s)
Disease Outbreaks , Infection Control/methods , Klebsiella Infections/epidemiology , Klebsiella Infections/microbiology , Klebsiella pneumoniae/isolation & purification , beta-Lactamases/metabolism , Adult , Aged , Anti-Bacterial Agents/therapeutic use , Colistin/therapeutic use , Electrophoresis, Gel, Pulsed-Field , Genotype , Humans , Intensive Care Units , Klebsiella Infections/pathology , Klebsiella Infections/prevention & control , Klebsiella pneumoniae/classification , Klebsiella pneumoniae/enzymology , Klebsiella pneumoniae/genetics , Male , Meropenem , Middle Aged , Minocycline/analogs & derivatives , Minocycline/therapeutic use , Molecular Typing , Switzerland/epidemiology , Tertiary Care Centers , Thienamycins/therapeutic use , Tigecycline , Treatment Outcome , beta-Lactamases/geneticsABSTRACT
We prospectively analyzed 34 clinical biopsy samples from 23 patients with a suspected invasive fungal infection by fungal culture, histology and a panfungal PCR followed by sequencing. Results were compared to the composite diagnosis according the European Organization for Research and Treatment of Cancer (EORTC) criteria. In 34 samples, culture, histology and panfungal PCR were positive in 35%, 38% and 62%, respectively. On the sample level the panfungal PCR revealed a sensitivity of 69% and a specificity of 62.5% compared to proven IFI according postoperative EORTC criteria. On patient level, the sensitivity of the PCR approach was 100%, specificity 62.5%.
Subject(s)
Clinical Laboratory Techniques/methods , DNA, Fungal/isolation & purification , Molecular Diagnostic Techniques/methods , Mycology/methods , Mycoses/diagnosis , Polymerase Chain Reaction/methods , Sequence Analysis, DNA/methods , Adult , Aged , DNA, Fungal/chemistry , DNA, Fungal/genetics , Female , Humans , Male , Middle Aged , Prospective Studies , Sensitivity and SpecificityABSTRACT
Little is known about the clinical significance and laboratory diagnosis of Actinomyces funkei. In this report we describe six clinical cases where A. funkei was isolated from purulent, polymicrobial infections. Conventional identification procedures were compared with molecular methods including matrix-assisted laser desorption/ionization time-of-flight mass spectrometry technique. Analysis of the full 16S rRNA gene sequence of the six investigated strains revealed differences from the A. funkei type strain. DNA-DNA hybridization showed that the clinical strains represent a novel 16S rRNA gene variant within the species of A. funkei.
Subject(s)
Actinomyces/classification , Actinomyces/isolation & purification , Actinomycosis/microbiology , Suppuration/microbiology , Actinomyces/chemistry , Actinomyces/genetics , Adult , Aged , Aged, 80 and over , Bacteriological Techniques , Cluster Analysis , Coinfection/microbiology , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Female , Humans , Male , Middle Aged , Molecular Sequence Data , Nucleic Acid Hybridization , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Spectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationABSTRACT
Corynebacterium tuberculostearicum is a lipophilic corynebacterium validly characterized in 2004. We provide clinical information on 18 patients from whom this organism was isolated. The majority of the patients were hospitalized and had a history of prolonged treatment with broad-spectrum antimicrobials. In 7 (38.9%) of the 18 cases, the isolates were found to be clinically relevant. The present report also includes detailed data on the biochemical and molecular identification of C. tuberculostearicum, as well as its identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Our data demonstrate that routine biochemical tests do not provide reliable identification of C. tuberculostearicum. MALDI-TOF MS represents a helpful tool for the identification of this species, since all of the strains matched C. tuberculostearicum as the first choice and 58.3% (7/12) of the strains processed with the full extraction protocol generated scores of >2.000. Nevertheless, partial 16S rRNA gene sequencing still represents the gold standard for the identification of this species. Due to the challenging identification of C. tuberculostearicum, we presume that this organism is often misidentified and its clinical relevance is underestimated. The antimicrobial susceptibility profile of C. tuberculostearicum presented here reveals that 14 (87.5%) of the 16 strains analyzed exhibited multidrug resistance.
Subject(s)
Corynebacterium Infections/microbiology , Corynebacterium/drug effects , Corynebacterium/isolation & purification , Drug Resistance, Multiple, Bacterial , Adolescent , Adult , Aged , Aged, 80 and over , Bacterial Typing Techniques , Bacteriological Techniques/methods , Corynebacterium/chemistry , Corynebacterium/classification , Corynebacterium Infections/pathology , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Female , Genotype , Hospitalization/statistics & numerical data , Humans , Male , Middle Aged , Molecular Diagnostic Techniques/methods , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Young AdultABSTRACT
The management of the ongoing lymphogranuloma venereum epidemic in industrialized Western countries caused by Chlamydia trachomatis variant L2b still needs improvements in diagnosis, therapy and prevention. We therefore developed the first rapid C. trachomatis variant L2b-specific polymerase chain reaction to circumvent laborious ompA gene sequencing.
Subject(s)
Bacteriological Techniques/methods , Chlamydia trachomatis/classification , Chlamydia trachomatis/isolation & purification , Lymphogranuloma Venereum/diagnosis , Lymphogranuloma Venereum/microbiology , Molecular Diagnostic Techniques/methods , Polymerase Chain Reaction/methods , Bacterial Outer Membrane Proteins/genetics , Base Sequence , Chlamydia trachomatis/genetics , Cross Reactions , DNA Primers/genetics , Europe , Humans , Male , Molecular Sequence Data , Sensitivity and Specificity , Sequence Alignment , Sequence Analysis, DNAABSTRACT
We report four epidemiologically unrelated cases of KPC-carrying Klebsiella pneumoniae identified in Switzerland between May 2009 and November 2010. Three cases were transferred from Italy (two KPC-3, one KPC-2) and one from Greece (KPC-2). Resistance to colistin and doxycycline emerged in one KPC-3-carrying K. pneumoniae strain during therapy. These results demonstrate ongoing dissemination of KPC throughout Europe. Rapid and reliable identification of KPC and implementation of control measures is essential to limit spread.
Subject(s)
Bacterial Proteins/genetics , Klebsiella Infections/microbiology , Klebsiella pneumoniae/classification , Klebsiella pneumoniae/enzymology , beta-Lactamases/genetics , Aged , Bacterial Proteins/metabolism , Disease Outbreaks , Drug Resistance, Multiple, Bacterial/genetics , Female , Greece , Humans , Italy , Klebsiella Infections/drug therapy , Klebsiella Infections/genetics , Klebsiella pneumoniae/drug effects , Klebsiella pneumoniae/genetics , Klebsiella pneumoniae/isolation & purification , Male , Microbial Sensitivity Tests , Middle Aged , Polymerase Chain Reaction , Species Specificity , Switzerland/epidemiology , Treatment Outcome , beta-Lactamases/metabolismABSTRACT
The emergence of methicillin-resistant Staphylococcus aureus (MRSA) has become an increasing problem worldwide in recent decades. Molecular typing methods have been developed to identify clonality of strains and monitor spread of MRSA. We compared a new commercially available DiversiLab (DL) repetitive element PCR system with spa typing, spa clonal cluster analysis, and pulsed-field gel electrophoresis (PFGE) in terms of discriminatory power and concordance. A collection of 106 well-defined MRSA strains from our hospital was analyzed, isolated between 1994 and 2006. In addition, we analyzed 6 USA300 strains collected in our institution. DL typing separated the 106 MRSA isolates in 10 distinct clusters and 8 singleton patterns. Clustering analysis into spa clonal complexes resulted in 3 clusters: spa-CC 067/548, spa-CC 008, and spa-CC 012. The discriminatory powers (Simpson's index of diversity) were 0.982, 0.950, 0.846, and 0.757 for PFGE, spa typing, DL typing, and spa clonal clustering, respectively. DL typing and spa clonal clustering showed the highest concordance, calculated by adjusted Rand's coefficients. The 6 USA300 isolates grouped homogeneously into distinct PFGE and DL clusters, and all belonged to spa type t008 and spa-CC 008. Among the three methods, DL proved to be rapid and easy to perform. DL typing qualifies for initial screening during outbreak investigation. However, compared to PFGE and spa typing, DL typing has limited discriminatory power and therefore should be complemented by more discriminative methods in isolates that share identical DL patterns.