Sporadic Strains Research Articles

Evaluation of sclB gene variation in Streptococcus pyogenes (Lancefield group A Streptococcus) and potential for subtyping

Variation of sclB gene sequences in group A Streptococcus (GAS) strains was evaluated for its potential use in subtyping the most common serotypes of Streptococcus pyogenes encountered in the UK. We sequenced a total of 188 strains, including randomly selected invasive GAS and outbreak-related strains. Variability was highest amongst M/emm 89 strains, whereas very little variation was observed amongst M/emm 1 and M/emm 28 GAS strains. Repeat patterns were identified in the collagen structure motif (CSM) of the M/emm 89 GAS strains. The sporadic strains were very diverse and encompassed most of the CSM patterns, whereas the outbreak-related strains were mainly clustered into two CSM groups. sclB gene cluster analysis distinguished outbreak strains from two different healthcare settings in the same geographical area. Sequence variations were assessed by the number of pentameric repeats (CAAAA) present at the 5' region of the sclB gene. The determination of sclB polymorphisms amongst GAS serotype M/emm 89 strains could be used as an important epidemiological marker to inform clinicians and outbreak control teams during outbreak investigations.

Isolation of Bacteriophage against Currently Circulating Strains of Acinetobacter baumannii

We successfully isolated bacteriophage active against clinical strains of Acinetobacter baumannii by enrichichment from activated sewage sludge using representatives of those strains. Purified bacteriophage suspensions obtained were tested on a range of clinical isolates that included representatives of multiple strains of each of the international clonal lineages, as well as minor and sporadic strains. Most representatives of the South East clone, a successful sublineage belonging to international clone II, and a representative of a further strain belonging to international clone II were susceptible to the phage, while further strains belonging to this lineage, as well as those from other lineages were not susceptible. Examination by transmission electron microscopy revealed bacteriophage of the Myoviridae family. Activated sewage sludge is a valuable source of bacteriophages active against some currently circulating strains of A. baumannii.

Diversity of 16S-23S rDNA Internal Transcribed Spacer (ITS) Reveals Phylogenetic Relationships in Burkholderia pseudomallei and Its Near-Neighbors

Length polymorphisms within the 16S-23S ribosomal DNA internal transcribed spacer (ITS) have been described as stable genetic markers for studying bacterial phylogenetics. In this study, we used these genetic markers to investigate phylogenetic relationships in Burkholderia pseudomallei and its near-relative species. B. pseudomallei is known as one of the most genetically recombined bacterial species. In silico analysis of multiple B. pseudomallei genomes revealed approximately four homologous rRNA operons and ITS length polymorphisms therein. We characterized ITS distribution using PCR and analyzed via a high-throughput capillary electrophoresis in 1,191 B. pseudomallei strains. Three major ITS types were identified, two of which were commonly found in most B. pseudomallei strains from the endemic areas, whereas the third one was significantly correlated with worldwide sporadic strains. Interestingly, mixtures of the two common ITS types were observed within the same strains, and at a greater incidence in Thailand than Australia suggesting that genetic recombination causes the ITS variation within species, with greater recombination frequency in Thailand. In addition, the B. mallei ITS type was common to B. pseudomallei, providing further support that B. mallei is a clone of B. pseudomallei. Other B. pseudomallei near-neighbors possessed unique and monomorphic ITS types. Our data shed light on evolutionary patterns of B. pseudomallei and its near relative species.

A school outbreak of Shigella sonnei infection in China: Clinical features, antibiotic susceptibility and molecular epidemiology

To describe the clinical features of infection, and the antibiotic susceptibility of epidemic strains, and investigate plasmid maps and integrons of the isolates from an outbreak of Shigella sonnei infection at an elementary school in southwest China. Cross-sectional study. An elementary school and five hospitals in Chengdu in southwest China. There were 1,134 students in the school. 937 (82.6%) students had signs and symptoms. Of the 568 (60.6%, 568/937) hospitalized students, 93.3% 86.8%, 72.4%, and 28.9% of the hospitalized patients had diarrhea, fever, abdominal pain, and vomiting, respectively. S. sonnei strains were isolated from the stool samples of 36.0% (337/937) students. All of the outbreak isolates had the same high-level antimicrobial resistance and plasmid profiles, which were different from that of sporadic strains. All the outbreak S. sonnei isolates were positive for the integrin gene and contained class 2 integron; however, two outbreak isolates contained class 1 and class 2 integrons. Diarrhea, fever, and abdominal pain were the three most common clinical manifestations observed in patients infected with S. sonnei. High-level antibiotic resistance was observed among Shigella species.

Deciphering the multifactorial nature of Acinetobacter baumannii pathogenicity.

Background Acinetobacter baumannii is an emerging bacterial pathogen that causes a broad array of infections, particularly in hospitalized patients. Many studies have focused on the epidemiology and antibiotic resistance of A. baumannii, but little is currently known with respect to its virulence potential.Methodology/Principal FindingsThe aim of this work was to analyze a number of virulence-related traits of four A. baumannii strains of different origin and clinical impact for which complete genome sequences were available, in order to tentatively identify novel determinants of A. baumannii pathogenicity. Clinical strains showed comparable virulence in the Galleria mellonella model of infection, irrespective of their status as outbreak or sporadic strains, whereas a non-human isolate was avirulent. A combined approach of genomic and phenotypic analyses led to the identification of several virulence factors, including exoproducts with hemolytic, phospholipase, protease and iron-chelating activities, as well as a number of multifactorial phenotypes, such as biofilm formation, surface motility and stress resistance, which were differentially expressed and could play a role in A. baumannii pathogenicity.Conclusion/SignificanceThis work provides evidence of the multifactorial nature of A. baumannii virulence. While A. baumannii clinical isolates could represent a selected population of strains adapted to infect the human host, subpopulations of highly genotypically and phenotypically diverse A. baumannii strains may exist outside the hospital environment, whose relevance and distribution deserve further investigation.

A Field Guide to Pandemic, Epidemic and Sporadic Clones of Methicillin-Resistant Staphylococcus aureus

In recent years, methicillin-resistant Staphylococcus aureus (MRSA) have become a truly global challenge. In addition to the long-known healthcare-associated clones, novel strains have also emerged outside of the hospital settings, in the community as well as in livestock. The emergence and spread of virulent clones expressing Panton-Valentine leukocidin (PVL) is an additional cause for concern. In order to provide an overview of pandemic, epidemic and sporadic strains, more than 3,000 clinical and veterinary isolates of MRSA mainly from Germany, the United Kingdom, Ireland, France, Malta, Abu Dhabi, Hong Kong, Australia, Trinidad & Tobago as well as some reference strains from the United States have been genotyped by DNA microarray analysis. This technique allowed the assignment of the MRSA isolates to 34 distinct lineages which can be clearly defined based on non-mobile genes. The results were in accordance with data from multilocus sequence typing. More than 100 different strains were distinguished based on affiliation to these lineages, SCCmec type and the presence or absence of PVL. These strains are described here mainly with regard to clinically relevant antimicrobial resistance- and virulence-associated markers, but also in relation to epidemiology and geographic distribution. The findings of the study show a high level of biodiversity among MRSA, especially among strains harbouring SCCmec IV and V elements. The data also indicate a high rate of genetic recombination in MRSA involving SCC elements, bacteriophages or other mobile genetic elements and large-scale chromosomal replacements.

Identification of multi-resistant strains of Acinetobacter baumannii from an ICU in Greece using sequence-based typing and PFGE

Acinetobacter baumannii has emerged as an important nosocomial pathogen in many European countries, including Greece. In this study, we analysed 20 multi-resistant A. baumannii strains, derived from the First intensive care unit (ICU) of the General Hospital “G. Papanikolaou”, in order to investigate their epidemiology. Samples were taken from the pharynx and perineum of ICU patients for determination of their carrier status. Multilocus sequence typing (MLST)-based on the three-genes scheme (ompA, csuE and bla OXA-51-like) and pulsed field gel electrophoresis (PFGE) were the methods used to examine these isolates, after identification with VITEK 2. Using sequence-based typing, 16 out of 20 isolates (80%) were found to belong to the group ST 1 (EU-II), one (5%) belonged to ST 2 (EU-I) and three (15%) were ND (not determined) or sporadic strains. Using PFGE, nine strains were type Α, two were type Β and some strains could not be identified. ST group 1 prevailed (80%) among the other two groups. Both methods appear to yield similar results, though MLST seems to have more advantages. Sequence-based typing along with PFGE provides us with a powerful tool for identifying multi-resistant A. baumannii strains, which are more likely to induce problems in ICUs.

P96 Haplotype variability in Pseudomonas aeruginosa (Psa) strains in the adult CF population

<h3>Introduction</h3> Morphological type variation in Psa is thought to aid its survival in hostile environments, including the CF lung. Previous studies using PGFE have shown wide heterogeneity in LES strain, despite this, little is known about their phenotypic diversity (haplotypes). To look at this further, we compared the haplotypes of the most successful and prevalent UK transmissible Psa (the Liverpool epidemic strain, LES) with those of sporadic strains and assessed their response to antibiotic pressure. <h3>Methods</h3> Sputum from two groups of adult CF patients chronically infected (for at least 4 years) with sporadic single Psa strains or LES was analysed at the beginning and end of an intravenous antibiotic-treated exacerbation, where every patient had subjective and spirometric improvement, and also for LES patients over a period of time (at least 4 months) when they were in a stable state. From each sample, 40 single Psa colonies were selected (with every morphological type proportionately represented), and colony morphology, susceptibility to six antibiotics (ciprofloxacin, ceftazidime, colomycin, meropenem, tobramycin, piperacillin/tazobactam), hypermutability (rate of spontaneous mutation to rifampicin resistance) and auxotrophy (ability to grow on glucose M9 media) determined. Each Psa colony could potentially exhibit any of nine combinations: antibiotic susceptibility patterns, auxotrophy, hypermutability, and six colony morphologies. The resulting haplotypes were compared for LES and unique strains using ‘e-burst’ software. <h3>Results</h3> Overall, 151 unique haplotypes were defined (96 LES, 75 sporadic, 20 shared), with LES demonstrating the greater number (X²=4.67, p&lt;0.03). Following antibiotic pressure, there was an alteration in haplotypes which was similar in both groups (LES 54%, sporadic 64%, p=0.28): but during the stable state LES demonstrated a significantly greater change in haplotypes (89%, p=0.004). <h3>Conclusion</h3> A change in haplotypes occurs in all CF Psa strains during treatment for clinical exacerbations, presumably as a defence mechanism against the challenge of hostile antibiotic therapy. However, the enhanced haplotype variability of transmissible strains with time when there is no antibiotic pressure may be a strategy that confers a survival advantage compared to sporadic strains: studies are under way to explore this further.

Application of phage typing and pulsed-field gel electrophoresis to analyse Salmonella enterica isolates from a suspected outbreak in Lagos, Nigeria

Inadequate potable water supply and poor sanitation predispose to food- and water-borne diseases associated with Salmonella enterica serovars in developing countries. In this study the possible source of an unprecedented upsurge of Salmonella-associated community gastroenteritis was traced using both phage-typing and pulsed-field gel electrophoresis (PFGE). Nineteen Salmonella Typhimurium (three sporadic isolates included) and 13 Salmonella Enteritidis isolates from clinical, animal, and environmental samples were subjected to antimicrobial susceptibility testing, phage-typing, and PFGE analysis using standard procedures. Eleven (68.8%) of the 16 outbreak-related multidrug resistant S. Typhimurium belonged to DT 71 phage type with cluster PFGE type X3, representing the most prevalent strain identified among human, animal, and environmental isolates. The remaining five (31.2%) outbreak-related strains reacted but did not conform with clear phage types (RDNC) with cluster PFGE types X1 and X2 (96.8% similarity). Sporadic strains were untypable and belonged to X4 PFGE type. However, the evaluated S. Enteritidis strains that were multidrug resistant without a definite phage type belonged to PFGE cluster type X1e and were identified among the water and human strains. None of the Typhimurium and Enteritdis isolates was resistant to the fluoroquinolone antibiotics that were evaluated. This study emphasizes the epidemiological usefulness of PFGE typing in the detection of emerging strains of multipledrug resistant Salmonella, particularly S. Typhimurium DT71, that pose serious health implications in our environment. The study provides epidemiological links between environmental reservoirs and human infection in this community.

Defining sporadic Creutzfeldt-Jakob disease strains and their transmission properties

The biological determinants of the phenotypic variation in sporadic Creutzfeldt-Jakob disease (sCJD) are unknown. To categorize sCJD cases, the prion protein (PrP) codon 129 genotype and the biochemical characteristics of the disease-associated form of PrP (PrP(Sc)) can be combined to form six subgroups (MM1, MM2, MV1, MV2, VV1, and VV2). This classification largely correlates with the known variation in the clinical and pathological features of sCJD, with the MM1 and MV1 cases representing the "classic" phenotype of sCJD. To address how this classification relates to different strains of sCJD we have inoculated each subgroup of sCJD to a panel of mice expressing different forms of the human PRNP gene (129MM, 129VV, and 129MV). We have established that all subtypes are transmissible to at least one genotype of mouse, and both agent and host factors determine transmission efficiency and the form of PrP(Sc) deposited in the brain. Moreover, we have identified four distinct strains of sCJD using our in vivo strain typing panel.

Clinical Outcome for Cystic Fibrosis Patients Infected With Transmissible Pseudomonas aeruginosa: An 8-Year Prospective Study

Although there is now compelling evidence for cross-infection by strains of Pseudomonas aeruginosa at some specialist (cystic fibrosis [CF]) centers, the clinical impact of infection by transmissible strains is unclear. In an 8-year prospective study, we compared the clinical outcome of two groups of patients with CF infected by transmissible (n = 28) and sporadic strains (n = 52) of P aeruginosa. There were no differences between the two groups in survival, annual changes in spirometry, or BMI. There were differences in requirements for IV antibiotic treatment (mean [SD]: 29.3 [21.9] days vs 53.1 [32.5] days) and hospitalization (median [range]: 11.6 [1.1, 49.3] days vs 23.3 [5.5, 103.6] days) between patients infected with sporadic and transmissible strains of P aeruginosa, respectively. We conclude that infection by transmissible P aeruginosa does not increase mortality but is associated with increased health-care and antibiotic use for patients with CF.

Emerging multidrug resistant Mycobacterium tuberculosis strains of the Beijing genotype circulating in Russia express a pattern of biological properties associated with enhanced virulence

The epidemiologically important Mycobacterium tuberculosis Beijing genotype strains, highly endemic in East Asia, have become an emerging infection in certain geographic areas, including Russia, because of its increasing prevalence and association with multidrug resistance (MDR). The aim was to verify whether MDR Beijing strains circulating in the emerging regions present some biological particularities that could contribute to their success in causing disease in comparison with the sporadic strains from locations with low prevalence of the Beijing genotype. We evaluated virulence-associated characteristics of the MDR Beijing strains isolated in Russia and compared them with those of the drug-resistant and susceptible Beijing strains from Brazil and reference H37Rv strain. We found that Russian MDR strains demonstrated an increased bacterial fitness and growth in THP-1 macrophage-like cells, as well as a higher capacity to induce non-protective cytokine synthesis and necrotic macrophage death. By contrast, the biological properties of the strains isolated in Brazil largely resembled those of the H37Rv strain, with the exception of the drug-resistant isolates that presented significantly reduced fitness. The data demonstrate that the emerging MDR strains of the Beijing genotype circulating in Russia do express a pattern of properties associated with the enhanced virulence favouring its clonal dissemination in this region.

New EndemicLegionella pneumophilaSerogroup I Clones, Ontario, Canada

The water-borne pathogen Legionella pneumophila serogroup 1 (Lp1) is the most commonly reported etiologic agent of legionellosis. To examine the genetic diversity, the long-term epidemiology, and the molecular evolution of Lp1 clinical isolates, we conducted sequence-based typing on a collection of clinical isolates representing 3 decades of culture-confirmed legionellosis in Ontario, Canada. Analysis showed that the population of Lp1 in Ontario is highly diverse and combines lineages identified worldwide with local strains. Identical types were identified in sporadic and outbreak-associated strains. In the past 15 years, the incidence of some lineages distributed worldwide has tended to decrease, and local endemic clones and lineages have emerged. Comparative geographic distribution analysis suggests that some lineages are specific to eastern North America. These findings have general clinical implications for the study of Lp1 molecular evolution and for the identification of Lp1 circulating strains in North America.

Characterisation of MRSA from Malta and the description of a Maltese epidemic MRSA strain

Malta has one of the highest prevalence rates of methicillin-resistant Staphylococcus aureus (MRSA) in Europe. However, only limited typing data are currently available. In order to address this situation, 45 MRSA isolates from the Mater Dei Hospital in Msida, Malta, were characterised using DNA microarrays. The most common strain was ST22-MRSA-IV (UK-EMRSA-15, 30 isolates). Sporadic strains included ST36-MRSA-II (UK-EMRSA-16, two isolates), PVL-positive ST80-MRSA-IV (European Clone, one isolate), ST228-MRSA-I (Italian Clone/South German Epidemic Strain, one isolate) and ST239-MRSA-III (Vienna/Hungarian/Brazilian Epidemic Strain, one isolate). Ten MRSA isolates belonged to a clonal complex (CC) 5/ST149, spa type t002 strain. This strain harboured an SCCmec IV element (mecA, delta mecR, ugpQ, dcs, ccrA2 and ccrB2), as well as novel alleles of ccrA/B and the fusidic acid resistance element Q6GD50 (previously described in the sequenced strain MSSA476, BX571857.1:SAS0043). It also carried the gene for enterotoxin A (sea) and the egc enterotoxin locus, as well as (in nine out of ten isolates) genes encoding the toxic shock syndrome toxin (tst1) and enterotoxins C and L (sec, sel). While the presence of the other MRSA strains suggests foreign importation due to travel between Malta and other European countries, the CC5/t002 strain appears, so far, to be restricted to Malta.

Comparative genomics of epidemic versus sporadic Staphylococcus aureus strains does not reveal molecular markers for epidemicity

Staphylococcus aureus, especially when it is methicillin resistant, has been recognised as a major cause of nosocomial and community-acquired infections. It has also been shown that certain strains were able to cause clonal epidemics whereas others showed a more incidental occurrence. On the basis of this behavioural distinction, a genetic feature underlying this difference in epidemicity can be assumed. Understanding the difference will not only contribute to the development of markers for the identification of epidemic strains but will also shed light on the evolution of clones. Genomes of strains from two independent collections ( n = 18 and n = 10 strains) were analysed. Both collections were composed of carefully selected, genetically diverse strains with clinically well-defined epidemic and sporadic behaviour. Comparative genome hybridisation (CGH) was performed using an Agilent array for one collection (up to 11 probes per open reading frame – ORF), and an Affymetrix array for the other (up to 30 probes per ORF). Presence and absence information of probe homologues and ORFs was taken for analysis of molecular variance (AMOVA) at the strain and behaviour levels. Not a single probe showed 100% concordant differences between epidemic and sporadic strains. Moreover, probe differences between groups were always smaller than those within groups. This was also true, when the analysis was focussed on presence versus absence of ORF's or when probe information was transformed into allelic profiles. These findings present strong evidence against the presence or absence of a single common specific genetic factor differentiating epidemic from sporadic S. aureus clones.

Legionella pneumophilaGoes Clonal—Paris and Lorraine Strain‐Specific Risk Factors

<i>Legionella pneumophila</i>Goes Clonal—Paris and Lorraine Strain‐Specific Risk Factors

Host‐Related Risk Factors and Clinical Features of Community‐Acquired Legionnaires Disease Due to the Paris and Lorraine Endemic Strains, 1998–2007, France

In France, Legionnaires disease is mainly caused by Legionella pneumophila. Here, we investigated possible host factors associated with susceptibility to community-acquired Legionnaires disease caused by the endemic Paris and Lorraine strains. We conducted a double-nested exploratory case-control study with use of data from the French national surveillance network of incident Legionnaires disease cases notified from 1998 through 2007. Patients with community-acquired Legionnaires disease and an L. pneumophila serogroup 1 isolate were eligible. Case patients were patients infected by the Paris or Lorraine strain, and control patients were those infected by sporadic strains. Epidemiological and clinical factors associated with infection with the Paris and Lorraine strains were assessed by calculating adjusted odds ratios (aOR) in multivariate logistic regression models. We studied 1090 patients infected by sporadic strains (n = 920), the Paris strain (n = 80), or the Lorraine strain (n = 90). Infection with the Paris strain was significantly associated with female sex (aOR, 1.98; 95% confidence interval [CI], 1.19-3.28), steroid therapy (aOR, 3.16; 95% CI, 1.76-5.68), and a history of cancer or hematologic malignancies (aOR, 2.08; 95% CI, 1.15-3.76). In addition, the mortality rate was higher among patients infected with the Paris strain than in the control group (38% vs. 25.5%). The Lorraine strain was associated with smoking (aOR, 1.82; 95% CI, 1.14-2.91) and reduced mortality (9.9%). . Several host characteristics were associated with the risk of infection by endemic strains of L. pneumophila serogroup 1. These findings may help to guide preventive measures. Factors predisposing patients to infection by specific strains need to be explored further.

Distribution of meticillin-resistant Staphylococcus aureus spa types isolated from health-care workers and patients in a Scottish university teaching hospital

Our study was aimed at comparing the meticillin-resistant Staphylococcus aureus (MRSA) strains isolated from an anonymous group of health-care workers (HCWs) with those obtained from patient samples during a 3-month time interval. We employed spa typing and virulence gene profiling to characterize the MRSA strains. Our data revealed that a total of 14 discrete spa types were circulating in both patients and HCWs. The t032 spa type, characteristic of EMRSA15 and the Barnim EMRSA ST 22 clones, accounted for over 70 % of isolates, and was equally distributed between patients and HCW groups. In addition, a number of epidemic and sporadic strains were identified, which highlighted the diversity of spa types that can be found within a health-care setting. Virulence profiling for the carriage of 7 genes by the 14 different spa types demonstrated that 10 types carried the fnbA, cna, sdrE, hlg and ica virulence factors. We concluded that there was no significant difference between the MRSA strains found circulating in the patients and the HCWs, and noted that the dominant spa types carried an identical set of virulence genes that included the key adhesins fnbA, cna and sdrE.

Community-Associated Methicillin-Resistant Staphylococcus aureus Isolated in Finland in 2004 to 2006

A nationwide population-based study on community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) in Finland during 2004 to 2006 showed that both incidence (1.9/100,000 population) and strain variation increased in comparison to years 1997 to 1999. There were 7 community-associated epidemic and 25 sporadic MRSA strain types. Half of these had Panton-Valentine leukocidin genes.

Emergence of SCCmec Type IV as the Most Common Type of Methicillin-Resistant Staphylococcus aureus in a University Hospital

The epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) has dramatically changed over the last decade by the emergence of community-associated MRSA (CA-MRSA). Recent studies indicate that these strains have already spread to hospitals. To evaluate if SCCmec type IV and Panton-Valentine leukocidin (PVL) are unambiguous markers of CA-MRSA, we analyzed 77 sporadic MRSA strains isolated, in our low MRSA incidence university hospital, from inpatients between 2000 and 2004. MRSA strains were analyzed by staphylococcal cassette chromosome mmecec (SCCmec) typing, PCR for PVL genes and pulsed-field gel electrophoresis (PFGE). MRSA was classified in HA-MRSA or CA-MRSA according to Centers for Disease Control and Prevention (CDC) criteria. Antimicrobial susceptibility testing was performed using microbroth dilution method following CLSI recommendations. Among 77 sporadic single-patient strains, SCCmec types I-IV and four subtypes were identified. Type IV/IVA was most common (42.9%).The distribution of SCCmec types changed over the years. Type IV/IVA strains increased from 33.3% in 2000 to 57.9% in 2004. Type IV strains were resistant to ciprofloxacin in 81.8%, and in 9.1% to tobramycin while type IVA strains were 100% resistant to both antimicrobials. In contrast, non-type IV/IVA strains were resistant to ciprofloxacin in 86.4%, and in 75.0% to tobramycin. Only one strain was PVL positive and harbored SCCmec type III variant. By PFGE analysis, the 33 SCCmec type IV/IVA strains comprised 12 distinct genotypes. 36.4% of 11 CA-MRSA and 43.9% of 66 HA-MRSA harbored SCCmec type IV/IVA. Type IV/IVA has become the most common SCCmec type in inpatients of our university hospital. The SCCmec type IV/IVA is present in both CA-MRSA and HA-MRSA limiting its use as a marker for CA-MRSA.