Molecular Strain Typing Research Articles

Molecular typing of Acinetobacter baumannii clinical strains by enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR)

Acinetobacter baumannii is one of the most important causes of nosocomial infections. Because of the prevalence and recurrence of infections associated with A. baumannii that occur in different regions of hospitals, such as the ICU ward, is important to find the source of the infection by different techniques including molecular methods. This study aimed to determine A. baumannii isolates by ERIC-PCR.In this cross-sectional study, 80 A. baumannii isolates were retrieved from patients admitted to ICU, CCU, and post CCU wards of Ghaem hospital, Karaj, Iran. After detecting the isolates by phenotypic methods, standard biochemical tests were first used to identify the isolates and then API 20NE System kits (Biomerieux, France). The final confirmation was done by tracking the blaOXA-51 gene through PCR. Then, isolates were typed by the ERIC-PCR technique. The gel electrophoresis image was then analyzed by GEL compareII software and the relating dendrogram was depicted.The dendrogram obtained from the results of the study showed that the isolates were divided into 14 clusters using ERIC-PCR method.The present study showed that the ERIC-PCR technique is a useful tool for studying the genetic diversity of A. baumannii isolates. Also, A. baumannii isolates were rotating between ICU, CCU, and post CCU of Ghaem hospital, Karaj, Iran. And also, no specific pattern was observed in the distribution of the isolates from one ward to another.

Molecular analysis and epidemiological typing of Vancomycin-resistant Enterococcus outbreak strains

Outbreaks of multidrug resistant bacteria including vancomycin-resistant enterococci (VRE) in healthcare institutions are increasing in Norway, despite a low level of resistance compared to other European countries. In this study, we describe epidemiological relatedness of vancomycin-resistant Enterococcus faecium isolated during an outbreak at a Norwegian hospital in 2012–2013. During the outbreak, 9454 fecal samples were screened for VRE by culture and/or PCR. Isolates from 86 patients carrying the vanA resistance gene were characterized using pulsed-field gel electrophoresis (PFGE), MALDI-TOF mass spectrometry and single nucleotide polymorphism typing. PFGE revealed two main clusters, the first comprised 56 isolates related to an initial outbreak strain, and the second comprised 21 isolates originating from a later introduced strain, together causing two partly overlapping outbreaks. Nine isolates, including the index case were not related to the two outbreak clusters. In conclusion, the epidemiological analyses show that the outbreak was discovered by coincidence, and that infection control measures were successful. All typing methods identified the two outbreak clusters, and the experiment congruence between the MALDI-TOF and the PFGE clustering was 63.2%, with a strong correlation (r = 72.4%). Despite lower resolution compared to PFGE, MALDI-TOF may provide an efficient mean for real-time monitoring spread of infection.

Seroepidemiology of foot and mouth disease (FMD) virus non-structural protein (NSP) antibodies in the livestock of Oman

Foot and mouth disease (FMD) is a highly contagious acute viral disease that causes severe economic losses to the affected countries. To estimate the serological prevalence of the local livestock to the natural infection with FMD virus, a cross-sectional study was conducted from 2015 to 2017 in Oman. Sera from 5807 randomly selected animals (1792 cattle, 2119 goats and 1896 sheep) belonging to 884 herds were tested for the presence of antibodies against 3ABC non-structural protein (NSP) of the FMD virus by a Competition ELISA. Prevalence along with confidence intervals (CI) and odds ratio (OR) was calculated, and the data were further analysed through univariable and multivariable techniques. The herd-level seroprevalence of NSP (41.4%) varied significantly among 11 governorates of Oman. At herd-level seroprevalence varied significantly among cattle (55.2%), goats (38.2%) and sheep (37.7%). At animal-level, the significantly higher prevalence was recorded in cattle (26.8%) followed by sheep (17.9%) and goats (17.3%). Binary logistic regression analysis at the individual level indicated that cattle (OR: 1.88), livestock above one year of age (OR: 3.47), imported breeds (OR: 1.82) and females (OR: 1.27) were the risk factors associated with higher prevalence. Whereas, sedentary (OR: 2.63) farming system, vaccination against FMD (OR: 5.98) and previous history of FMD (OR: 5.55) were the variables found associated with higher seroprevalence at the herd-level. We conclude that natural infection of FMDV is widespread in Oman and in future molecular typing of FMD virus outbreaks strains and vaccine matching studies should be employed to develop an effective control program in Oman.

Genetic and Molecular Typing of Canine Parvovirus Strains Circulating in Symptomatic Dogs in Egypt

Canine parvovirus (CPV) is considered one of the serious and problematic diseases in young puppies. It causes hemorrhagic enteritis and myocarditis in affected dogs. The aim of the present study was to detect CPV-2 in feces of clinically diseased puppies by polymerase chain reaction (PCR) followed by VP2 gene partial sequencing and molecular characterization of circulating strains in Egypt as well as studying some factors associated with the disease incidence. Forty fecal samples were collected from clinically suspected dogs with CPV-2. The clinical diagnosis was confirmed in 35 suspected clinical cases (87.5%) by PCR using common and specific primers sets for detection of (CPV-2, CPV-2a, CPV-2b, CPV-2c) validating that presumptive clinical diagnosis is practically dependable. Nucleotide sequencing of parvovirus (CPV-2) isolates showed that all the three antigenic types (2a, 2b, and 2c) are currently circulating in Egypt.

Decrease in vancomycin-resistant Enterococcus colonization associated with a reduction in carbapenem use as empiric therapy for febrile neutropenia in patients with acute leukemia.

To compare the effects of empiric carbapenems versus cycling cefepime and piperacillin/tazobactam on the rates of vancomycin-resistant Enterococcus (VRE) colonization, bloodstream infections, and outcomes of patients admitted with acute leukemia. Retrospective clinical study with VRE molecular strain typing and gastrointestinal microbiome comparison. A regional referral center for acute leukemia. 342 consecutive patients admitted with newly diagnosed acute leukemia. In September 2015, we changed our empiric antibiotic of choice for neutropenic fever from a carbapenem to the cycling regimen. We studied 214 consecutive patients during the carbapenem period and 128 during the cycling period. Surveillance for VRE stool colonization was conducted weekly. Representative stool samples were analyzed for VRE MLST types and changes in the composition and diversity of the fecal microbiota. The change in empiric antibiotics was associated with a significant decrease in VRE colonization (hazard ratio [HR], 0.35; 95% confidence interval [CI], 0.27-0.66), a switch in the dominant VRE MLST types on the unit, and some modifications in the gastrointestinal microbiome. There were no differences in total gram-positive or gram-negative BSIs. During the carbapenem period, we observed higher absolute numbers of Candida spp and fewer ESBL BSIs, but these did not reach statistical significance. Patients during the carbapenem period had longer lengths of stay and durations of severe neutropenia and 10% higher hospital cost. Carbapenem-sparing empiric antibiotic regimens may have advantages related to VRE ecology, gastrointestinal dysbiosis, duration of neutropenia, cost and length of stay.

Improved molecular typing of toxigenic Clostridium difficile strains affecting animal and human health

Clostridium difficile is a Gram-positive, spore forming bacterium, which remains a formidable pathogen as the etiological agent of C. difficile infection (CDI). Substantial effort goes into diagnosis of CDI and characterisation of circulating toxigenic C. difficile strains for epidemiology and infection prevention and control. Currently, molecular typing of C. difficile requires 9 days following diagnosis through PCR ribotyping and multilocus variable number tandem repeat (VNTR) analysis. There is a need for more rapid typing methods to investigate possible linkage between CDI cases in healthcare settings. This study developed a one-step, closed tube real-time PCR and high resolution melt (HRM) assay targeting the intergenic spacer region (ISR) and several VNTR loci, with results generated in 2.5 h. The discriminatory power of the PCR-HRM assay was investigated by typing previously characterised toxigenic clinical and animal C. difficile isolates (n=90). Through comparison of HRM profiles targeting the ISR of isolates belonging to 17 PCR ribotypes, 13 HRM genotypes were recognised with 11 PCR ribotypes resolved from each other. Using correlation between HRM data and known VNTR repeat numbers at the B7, C6 and G8 loci, VNTR repeat numbers for isolates could be predicted within an average absolute difference of 1.8 at the B7 locus, 2.1 at the C6 locus, and 2.5 at the G8 locus. These results suggest that a PCR-HRM assay with a multilocus panel targeting ISR and selected VNTR loci could form part of an improved molecular typing scheme for toxigenic C. difficile strains that is faster than currently available methods.

Molecular drug susceptibility testing and strain typing of tuberculosis by DNA hybridization.

In Mycobacterium tuberculosis (Mtb) the detection of single nucleotide polymorphisms (SNPs) is of high importance both for diagnostics, since drug resistance is primarily caused by the acquisition of SNPs in multiple drug targets, and for epidemiological studies in which strain typing is performed by SNP identification. To provide the necessary coverage of clinically relevant resistance profiles and strain types, nucleic acid-based measurement techniques must be able to detect a large number of potential SNPs. Since the Mtb problem is pressing in many resource-poor countries, requiring low-cost point-of-care biosensors, this is a non-trivial technological challenge. This paper presents a proof-of-concept in which we chose simple DNA-DNA hybridization as a sensing principle since this can be transferred to existing low-cost hardware platforms, and we pushed the multiplex boundaries of it. With a custom designed probe set and a physicochemical-driven data analysis it was possible to simultaneously detect the presence of SNPs associated with first- and second-line drug resistance and Mtb strain typing. We have demonstrated its use for the identification of drug resistance and strain type from a panel of phylogenetically diverse clinical strains. Furthermore, reliable detection of the presence of a minority population (<5%) of drug-resistant Mtb was possible.

Molecular typing of Streptococcus suis strains isolated from diseased and healthy pigs between 1996-2016.

Streptococcus suis is an economically important pathogen of pigs as well as a zoonotic cause of human disease. Serotyping is used for further characterization of isolates; some serotypes seem to be more virulent and more widely spread than others. This study characterizes a collection of German field isolates of Streptococcus suis from pigs dating from 1996 to 2016 with respect to capsular genes (cps) specific for individual serotypes and pathotype by multiplex PCR and relates results to the clinical background of these isolates. The most prominent finding was the reduction in prevalence of serotype-2/serotype-1/2 among invasive isolates during this sampling period, which might be attributed to widely implemented autogenous vaccination programs in swine against serotype 2 in Germany. In diseased pigs (systemically ill; respiratory disease) isolates of serotype-1/serotype-14, serotype-2/serotype-1/2, serotype 3 to 5 and 7 to 9 were most frequent while in carrier isolates a greater variety of cps types was found. Serotype-1/serotype-14 seemed to be preferentially located in joints, serotype 4 and serotype 3 in the central nervous system, respectively. The virulence associated extracellular protein factor was almost exclusively associated with invasive serotype-1/serotype-14 and serotype-2/serotype-1/2 isolates. In contrast, lung isolates of serotype-2/serotype-1/2 mainly harbored the gene for muramidase-released protein. Serotype 4 and serotype 9 isolates from clinically diseased pigs most frequently carried the muramidase-released protein gene and the suilysin gene. When examined by transmission electron microscopy all but one of the isolates which were non-typable by molecular and serological methods showed various amounts of capsular material indicating potentially new serotypes among these isolates. Given the variety of cps types/serotypes detected in pigs, not only veterinarians but also medical doctors should consider other serotypes than just serotype 2 when investigating potential human cases of Streptococcus suis infection.

Public health outcome of Tuberculosis Cluster Investigations, England 2010–2013

ObjectivesTuberculosis (TB) is a serious re-emergent public health problem in the UK. In response to rising case incidence a National TB Strain-Typing Service based on molecular strain-typing was established. This facilitates early detection and investigation of clusters, targeted public health action, and prevention of further transmission. We review the added public health value of investigating molecular TB strain-typed (ST) clusters. MethodsA structured questionnaire for each ST cluster investigated in England between 1 January 2010 and 30 June 2013 was completed. Questions related to epidemiological links and public health action and the perceived benefits of ST cluster investigation. ResultsThere were 278 ST cluster investigations (CIs) involving 1882 TB cases. Cluster size ranged from 2 to 92. CIs identified new epidemiological links in 36% of clusters; in 18% STs were discordant refuting transmission thought to have occurred. Additional public health action was taken following 23% of CI. ConclusionsWe found positive benefits of TB molecular ST and CI, in identifying new epidemiological links between cases and taking public health action and in refuting transmission and saving resources. This needs to be translated to a decrease in transmission to provide evidence of public health value in this low prevalence high resource setting.

Surveillance and molecular characterization of human adenovirus in patients with acute gastroenteritis in the era of rotavirus vaccine, Brazil, 2012–2017

BackgroundIn Brazil, limited data are available regarding the incidence and molecular epidemiology of Human Adenovirus (HAdV) in diarrheic disease, especially in the post rotavirus (RVA) vaccine era. ObjectiveThe aims of the study were to investigate the frequency of HAdV infections in patients with gastroenteritis during a 6-year period (2012–2017); conduct molecular typing of positive strains, and obtain further information on the HAdV seasonality. Study designA total of 3003 fecal samples negative for both, RVA and Norovirus, were selected and tested for HAdV by PCR. Positive HAdV samples were sequenced to obtain genotype identification. ResultsHAdV was detected in 3.9% (117/3003); 76 belong to species F (70 HAdV-F41; 6 HAdVF40), 31 to species C (15 HAdV-C1; 13 HAdV-C2; 3 HAdV-C5), 5 belong to species D (3 HAdVD56 and 2 untyped), 4 belong to species A (2 HAdV-A12; 2 HAdV-A31), and 1 belong to HAdVB3. Detection rate significantly varied according to the year, suggesting that HAdV infections show a tendency to occur in natural oscillatory fluctuation. No consistent seasonal pattern was identified. Children ≤5 years exhibited higher positivity rate, reinforcing that HAdV is an important pathogen in childhood diarrhea. Genetic analysis indicated that HAdV strains circulating in Brazil were closely related to worldwide strains, and there is no evidence for the introduction of a particular HAdV variant in the country. ConclusionsThe present investigation does not suggest that HAdV has assumed an epidemiological importance in Brazil after the RVA vaccine introduction and contributed to the definition of the clinical and public health significance of HAdV infections.

Non-toxigenic Clostridioides (Formerly Clostridium) difficile for Prevention of C. difficile Infection: From Bench to Bedside Back to Bench and Back to Bedside.

The beneficial effect of colonization of the gastrointestinal tract by non-toxigenic Clostridioides difficile (NTCD) strains as a preventive of toxigenic C. difficile infection (CDI) has been known since the early 1980s. Investigators in both the USA and United Kingdom demonstrated that prior colonization by randomly selected NTCD strains provided prevention against infection by toxigenic C. difficile in hamsters, albeit with limited durability. In the 1980s two patients with multiply recurrent CDI in the UK were treated with vancomycin followed by NTCD to prevent further recurrences, with one success and one failure. Epidemiologic studies of hospitalized patients using weekly rectal swab cultures demonstrated that asymptomatic colonization of patients by toxigenic C. difficile was much more common than CDI, but also that the rate of asymptomatic NTCD colonization of patients was unexpectedly high. Development of molecular strain typing of C. difficile was instrumental in characterizing different strains of both toxigenic C. difficile and NTCD leading to identification of NTCD strains that were effective human colonizers. These strains were reintroduced in hamsters in the 1990s and shown to prevent CDI efficiently and durably when challenged with epidemic toxigenic C. difficile strains. One strain of NTCD, NTCD-M3, was manufactured under cGMP standards and was demonstrated to be safe in a phase 1 volunteer trial. NTCD-M3 was then tested in a phase 2 double-blind placebo controlled trial for the prevention of recurrent CDI in patients experiencing their first CDI episode or first CDI recurrence. NTCD-M3 was given at doses of 104 or 107 spores per day orally for 7 or 14 days following successful treatment of CDI with vancomycin and/or metronidazole. CDI recurred in 30% of placebo patients and 11% of all NTCD-M3 patients (p = 0.006); recurrence rate for the best dose, 107 spores/d × 7 days, was 5% (p = 0.01 vs. placebo). Detection of colonization predicted prevention success; among the 86 patients who were colonized with NTCD-M3 the recurrence rate was 2% vs. 31% in patients who received NTCD-M3 but were not colonized (p < 0.001). Additional trials of NTCD-M3 for primary prevention of CDI and prevention of CDI recurrence seem warranted by these promising results.

Screening of natural Wolbachia infection in Aedes aegypti, Aedes taeniorhynchus and Culex quinquefasciatus from Guadeloupe (French West Indies)

Guadeloupe islands are threatened by several mosquito-borne viruses such as Dengue, Chikungunya, Zika and West Nile virus. It appears essential to look for alternative mosquito control methods such as the incompatible insect technique (ITT) aiming at sterilizing wild females by inundative releases of incompatible males. Before considering the implementation of such a strategy, the characterization of genetic diversity of the endocellular bacterium Wolbachia regarding the local mosquito populations is a critical issue. Here, for the first time, we describe the prevalence and diversity of Wolbachia in natural populations of three mosquito species from Guadeloupe: Aedes aegypti, Aedes taeniorhynchus and Culex quinquefasciatus. The detection of Wolbachia in natural Ae. aegypti, Ae. taeniorhynchus and Cx. quinquefasciatus populations was conducted by studying Wolbachia 16S ribosomal RNA gene using a TaqMan quantitative real-time PCR and results were confirmed by conventional PCR and sequencing. In addition, molecular typing of wPip strains in Cx. quinquefasciatus was done by PCR-RFLP. We did not find Wolbachia infection in any of Ae. aegypti and Ae. taeniorhynchus studied populations. Natural Wolbachia infection was detected in Cx. quinquefasciatus with prevalence varying from 79.2% to 95.8%. In addition, no polymorphism was found between the Wolbachia strains infecting Cx. quinquefasciatus specimens, all carrying an infection from the same Wolbachia genetic wPip-I group. These results pave the way for the evaluation of the feasibility of IIT programs to fight against these medically-important mosquito species in Guadeloupe.

New York City House Mice (Mus musculus) as Potential Reservoirs for Pathogenic Bacteria and Antimicrobial Resistance Determinants.

ABSTRACTHouse mice (Mus musculus) thrive in large urban centers worldwide. Nonetheless, little is known about the role that they may play in contributing to environmental contamination with potentially pathogenic bacteria. Here, we describe the fecal microbiome of house mice with emphasis on detection of pathogenic bacteria and antimicrobial resistance genes by molecular methods. Four hundred sixteen mice were collected from predominantly residential buildings in seven sites across New York City over a period of 13 months. 16S rRNA sequencing identified Bacteroidetes as dominant and revealed high levels of Proteobacteria. A targeted PCR screen of 11 bacteria, as indicated by 16S rRNA analyses, found that mice are carriers of several gastrointestinal disease-causing agents, including Shigella, Salmonella, Clostridium difficile, and diarrheagenic Escherichia coli. Furthermore, genes mediating antimicrobial resistance to fluoroquinolones (qnrB) and β-lactam drugs (blaSHV and blaACT/MIR) were widely distributed. Culture and molecular strain typing of C. difficile revealed that mice harbor ribotypes associated with human disease, and screening of kidney samples demonstrated genetic evidence of pathogenic Leptospira species. In concert, these findings support the need for further research into the role of house mice as potential reservoirs for human pathogens and antimicrobial resistance in the built environment.

Molecular Typing and Macrolide Resistance of Syphilis Cases in Manitoba, Canada, From 2012 to 2016.

The province of Manitoba, Canada, with a population of approximately 1.3 million, has been experiencing increased incidence of syphilis cases since 2015. In this study, we examined the detection of Treponema pallidum DNA in 354 clinical samples from 2012 to 2016, and determined molecular types and mutations conferring resistance to azithromycin in the polymerase chain reaction (PCR)-positive samples. T. pallidum DNA detection was done by PCR amplification of tpp47, bmp, and polA genes. Syphilis serology results were reviewed for the PCR-positive cases. Molecular typing of syphilis strains was done by analysis of the T, pallidum arp, tpr, and tp0548 gene targets as well as partial sequencing of the 23S rRNA gene for azithromycin resistance. Of the 354 samples tested, 74 individual cases were PCR positive. A result from the treponemal antibody chemiluminescent microparticle immunoassay test was positive in 72 of these cases and that from the Venereal Disease Research Laboratory testing was positive in 66. Mutations conferring resistance to azithromycin were found in all 74 PCR-positive samples. Molecular typing was completed on 57 PCR-positive samples, and 12 molecular types were identified with 14d/g found in 63.2%. Increased strain diversity was observed with 8 molecular types detected in 2016, whereas only 2 to 3 types were found in 2012 to 2014. A patient with 2 episodes of infection 9 months apart caused by different molecular strain types was also identified. The finding of an increase in genetic diversity in the strains in this study and an increase in macrolide resistance compared with previous Canadian reports highlighted the need for continued surveillance including strain characterization.

Resistance to Aminoglycosides of Methicillin-Resistant Strains of Staphylococcus aureus, Originating in the Surgical and Transplantation Wards of the Warsaw Clinical Center—A Retrospective Analysis

IntroductionAminoglycoside resistance (AR) is common in health care-associated methicillin-resistant Staphylococcus aureus (HA-MRSA). AR is most often associated with the production of antibiotic modifying enzymes: bidomain AAC(6′)-Ie/APH(2″)-Ia acetyltransferase and phosphotransferase, ANT(4′)-Ia nucleotidyltransferase, and APH(3″)-IIIa phosphotransferase. AimDetermination of aminoglycoside sensitivity, presence of genes encoding enzymes, and molecular typing of HA-MRSA strains derived from patients hospitalized in surgical and transplantation wards. Materials and methodsFifty-four HA-MRSA strains, isolated from various materials from patients in the surgical and transplantation wards of Warsaw's clinical hospital, hospitalized between 1991 and 2007. The MIC values of gentamicin-GEN/tobramycin-TOB/amikacin-AK/netilmicin-NET were determined by the E-test (CLSI/EUCAST). Genes mecA/aacA-aphD/aadD/aph(3″)-IIIa were detected using PCR. SCCmec types were determined according to the Oliveira method and the sequence type (ST)/clonal complex (CC) by the MLST method. ResultsOf the isolates tested, 36 (66.7%) showed resistance to at least one aminoglycoside: TOB (57.4%), GEN (53.7%), AK (55.6%), NET (24.1%). The aacA-aphD gene was present in 29 MRSA-GEN-R (most often in combination with aadD, 15/29 or aph(3″)-IIIa, 10/29); the aacA-aphD gene was the only determinant of resistance in 1 isolate. The AR variants mainly belonged to the CC8 clonal complex (ST239/247/241/254/8) and most frequently contained SCCmec type III (3A) cassettes. ConclusionsResistance to at least one aminoglycoside was present in 66.7% of HA-MRSA and in more than 22% to all of them. The presence of the aacA-aphD gene was sufficient to express the resistance phenotype to GEN/TOB/AK/NET. Resistant isolates were closely related to each other.

Molecular typing of Polish strains of Babesia canis protozoa isolated from dogs in the years 2013-2016

The aim of the study was the molecular analysis of B. canis strains isolated from dogs from Poland based on 18S RNA and Bc28 genes. The study involved 140 protozoan strains derived from clinical disease cases. All DNA samples of parasites were analyzed in two ways (amplification and restriction digestion) which made it possible to demonstrate the polymorphism of the Bc28 gene, and to show 18S RNA gene polymorphism (amplification and restriction digestion). Amplification of the Bc28 gene fragment and digestion of the resulting PCR products allowed for the classification of 104 isolates of B. canis to the Bc28-A group, and 36 strains of protozoa to the Bc28-B group. Amplification of the Bc28 gene fragment and digestion of the resulting PCR products allowed for the classification of 33 isolates to 18S RNA-A group, while to 18S RNA-B – 107 parasite isolates. Comparison of both groups of protozoa among themselves allowed partial but not complete correlation of polymorphisms in Bc28 and 18S RNA genes..

Development of a Multilocus Sequence Typing (MLST) scheme for Treponema pallidum subsp. pertenue: Application to yaws in Lihir Island, Papua New Guinea.

BackgroundYaws is a neglected tropical disease, caused by Treponema pallidum subsp. pertenue. The disease causes chronic lesions, primarily in young children living in remote villages in tropical climates. As part of a global yaws eradication campaign initiated by the World Health Organization, we sought to develop and evaluate a molecular typing method to distinguish different strains of T. pallidum subsp. pertenue for disease control and epidemiological purposes.Methods and principal findingsPublished genome sequences of strains of T. pallidum subsp. pertenue and pallidum were compared to identify polymorphic genetic loci among the strains. DNA from a number of existing historical Treponema isolates, as well as a subset of samples from yaws patients collected in Lihir Island, Papua New Guinea, were analyzed using these targets. From these data, three genes (tp0548, tp0136 and tp0326) were ultimately selected to give a high discriminating capability among the T. pallidum subsp. pertenue samples tested. Intragenic regions of these three target genes were then selected to enhance the discriminating capability of the typing scheme using short readily amplifiable loci. This 3-gene multilocus sequence typing (MLST) method was applied to existing historical human yaws strains, the Fribourg-Blanc simian isolate, and DNA from 194 lesion swabs from yaws patients on Lihir Island, Papua New Guinea. Among all samples tested, fourteen molecular types were identified, seven of which were found in patient samples and seven among historical isolates or DNA. Three types (JG8, TD6, and SE7) were predominant on Lihir Island.ConclusionsThis MLST approach allows molecular typing and differentiation of yaws strains. This method could be a useful tool to complement epidemiological studies in regions where T. pallidum subsp. pertenue is prevalent with the overall goals of improving our understanding of yaws transmission dynamics and helping the yaws eradication campaign to succeed.

Molecular strain typing of Trichophyton mentagrophytes (T. mentagrophytes var. interdigitale) using non-transcribed spacer region as a molecular marker.

Background & objectives:Dermatophytes are keratinophilic fungi that infect keratinized tissues of human and animal origin. Trichophyton mentagrophytes is considered to be a species complex composed of several strains, which include both anthropophiles and zoophiles. Accurate discrimination is critical for comprehensive understanding of the clinical and epidemiological implications of the genetic heterogeneity of this complex. Molecular strain typing renders an effective way to discriminate each strain. The objective of the study was to characterize T. mentagrophytes clinical isolates to sub-species level using molecular techniques and non-transcribed spacer (NTS) region as marker.Methods:Sixty four T. mentagrophytes clinical isolates were identified by phenotypic methods. These were subjected to polymerase chain reaction targeting three sub-repeat elements (SREs), TmiS0, TmiS1 and TmiS2 of the NTS region. Sequence analysis of internal transcribed spacer (ITS) region of different types was also done.Results:Strain-specific polymorphism was observed in all three loci. Totally, 13 different PCR types were obtained on combining all the three SREs loci. No variation was observed in the ITS region.Interpretation & conclusions:The study described the usefulness of molecular strain typing technique for the discrimination of the T. mentagrophytes isolates. This will help for the future explorations into the epidemiology of T. mentagrophytes and its complex.

Decrease in Vancomycin-Resistant Enterococcus Colonization After Extensive Renovation of a Unit Dedicated to the Treatment of Hematologic Malignancies and Hematopoietic Stem-Cell Transplantation.

OBJECTIVE While a direct relation between hospital construction and concomitant infection rates has been clearly established, few data are available regarding the environmental decontamination effects of renovation in which surfaces are replaced and regarding subsequent infection incidence. DESIGN Retrospective clinical study with vancomycin-resistant Enterococcus (VRE) molecular strain typing and environmental cultures. SETTING A regional referral center for acute leukemia and hematopoietic stem-cell transplantation. PATIENTS Overall, 536 consecutive hospital admissions for newly diagnosed acute leukemia or a first autologous or allogeneic stem-cell transplantation were reviewed. INTERVENTION During 2009-2010, our unit underwent complete remodeling including replacement of all surfaces. We assessed the effects of this construction on the incidence of hospital-acquired VRE colonization before, during, and after the renovation. RESULTS We observed a sharp decrease in VRE colonization rates (hazard ratio, <0.23; 95% confidence interval, 0.18-0.44; P<.0001) during the first year after the renovation, with a return to near baseline rates thereafter. The known risk factors for VRE colonization appeared to be stable over the study interval. Environmental cultures outside of patient rooms revealed several contaminated areas that are commonly touched by unit personnel. Multilocus sequence typing of VRE isolates that were cryopreserved over the study interval showed that dominant strains prior to construction disappeared and were replaced by other strains after the renovation. CONCLUSIONS Unit reconstruction interrupted endemic transmission of VRE, which resumed with novel strains upon reopening. Contamination of environmental surfaces and shared equipment may play an important role in endemic transmission of VRE. Infect Control Hosp Epidemiol 2017;38:1055-1061.

Molecular Typing of Leuconostoc citreum Strains Isolated from Korean Fermented Foods Using a Random Amplified Polymorphic DNA Marker

For preliminary molecular typing, PCR-based fingerprinting using random amplified polymorphic DNA (RAPD) is the method of choice. In this study, 14 bacterial strains were isolated from different Korean food sources, identified using 16S rRNA gene sequencing, and characterized through RAPD-PCR. Two PCR primers (239 and KAY3) generated a total of 130 RAPD bands, 14 distinct PCR profiles, 10 polymorphic bands, one monomorphic band, and four unique bands. Dendrogram-based analysis with primer 239 showed that all 14 strains could be divided into seven clades out of which clade VII had the maximum of seven. In contrast, dendrogram analysis with the primer KAY3 divided the 14 L. citreum strains into four clades out of which clade IV consisted of a maximum of 10 strains out of 14. This research identified and characterized bacterial populations associated with different Korean foods. The proposed RAPD-PCR method, based on sequence amplification, could easily identify and discriminate the lactic acid bacteria species at the strain-specific level and could be used as a highly reliable genomic fingerprinting tool.