Summary: Using MOLECULAR BIOLOGY techniques, such as DNA SEQUENCE ANALYSIS; PULSED-FIELD GEL ELECTROPHORESIS; and DNA FINGERPRINTING, to identify, classify, and compare organisms and their subtypes.
- Stefani M, Avanzi C, Bührer Sékula S, Benjak A, Loiseau C, Singh P, et al. Whole genome sequencing distinguishes between relapse and reinfection in recurrent leprosy cases. PLoS Negl Trop Dis. 2017;11:e0005598 pubmed publisher..leprae DNA extracted from biopsies to discriminate between cases of relapse and reinfection, thereby providing a powerful tool for evaluating different outcomes of therapeutic regimens and for following disease transmission. ..
- Bartels M, Larner Svensson H, Meiniche H, Kristoffersen K, Schonning K, Nielsen J, et al. Monitoring meticillin resistant Staphylococcus aureus and its spread in Copenhagen, Denmark, 2013, through routine whole genome sequencing. Euro Surveill. 2015;20: pubmed..Creation of a MRSA database allows clustering of isolates based on single nucleotide polymorphism (SNP) calling and has improved our understanding of MRSA transmission. ..
- Sookan L, Coovadia Y. A laboratory-based study to identify and speciate non-tuberculous mycobacteria isolated from specimens submitted to a central tuberculosis laboratory from throughout KwaZulu-Natal Province, South Africa. S Afr Med J. 2014;104:766-8 pubmed..Although molecular tests for identifying NTM are relatively expensive, they have the advantage of providing rapid and accurate identification of the various NTM species. ..
- . Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014;511:543-50 pubmed publisher..These data establish a foundation for classification and further investigations of lung adenocarcinoma molecular pathogenesis. ..
- Tau N, Smith A, Wain J, Tarupiwa A, Coulibaly K, Keddy K, et al. Development and evaluation of a multiple-locus variable-number tandem-repeats analysis assay for subtyping Salmonella Typhi strains from sub-Saharan Africa. J Med Microbiol. 2017;66:937-945 pubmed publisher..984 (95?% CI 0.974-0.994)]. The MLVA assay presented in this study is a simple, rapid and more accessible tool that serves as a good alternative to other molecular subtyping methods for S. Typhi. ..
- Ciszewski M, Szewczyk E. Potential Factors Enabling Human Body Colonization by Animal Streptococcus dysgalactiae subsp. equisimilis Strains. Curr Microbiol. 2017;74:650-654 pubmed publisher..Those virulence factors might be horizontally transferred from human streptococci to animal SDSE strains, enabling their ability to colonize human organism. ..
- Peters T, Bertrand S, Björkman J, Brandal L, Brown D, Erdősi T, et al. Multi-laboratory validation study of multilocus variable-number tandem repeat analysis (MLVA) for Salmonella enterica serovar Enteritidis, 2015. Euro Surveill. 2017;22: pubmed publisher..However, differences in assigned MLVA profiles remain between well-established protocols and should be taken into account when exchanging data. ..
- Zeddeman A, van Gent M, Heuvelman C, van der Heide H, Bart M, Advani A, et al. Investigations into the emergence of pertactin-deficient Bordetella pertussis isolates in six European countries, 1996 to 2012. Euro Surveill. 2014;19: pubmed..In order to substantiate this hypothesis, trends in the European B. pertussis population should be monitored continuously. ..
- Seto J, Wada T, Suzuki Y, Ikeda T, Mizuta K, Mitarai S, et al. Convenient PCR method for variable-number tandem-repeat typing of Mycobacterium tuberculosis clinical isolates. J Microbiol Methods. 2017;139:12-14 pubmed publisher..However, cumbersome PCR procedures for the typing have disturbed routine analyses. We proposed a convenient PCR method for the typing using a PCR master mix that provides rapidity and long-term stability of the frozen PCR cocktail. ..
- Lalor M, Anderson L, Hamblion E, Burkitt A, Davidson J, Maguire H, et al. Recent household transmission of tuberculosis in England, 2010-2012: retrospective national cohort study combining epidemiological and molecular strain typing data. BMC Med. 2017;15:105 pubmed publisher..Improvements in contact tracing have the potential to reduce transmission of TB in low incidence countries. ..
- Orquera Tornakian G, Garrido P, Kronmiller B, Hunger R, Tyler B, Garzón C, et al. Identification and characterization of simple sequence repeats (SSRs) for population studies of Puccinia novopanici. J Microbiol Methods. 2017;139:113-122 pubmed publisher..andropogonis. Thus, these markers could be useful for DNA fingerprinting and population structure analysis for population genetics, epidemiology and ecological studies of P. novopanici and potentially other related Puccinia species. ..
- Martiny D, Bart A, Vandenberg O, Verhaar N, Wentink Bonnema E, Moens C, et al. Subtype determination of Blastocystis isolates by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS). Eur J Clin Microbiol Infect Dis. 2014;33:529-36 pubmed..MALDI-TOF MS proved to be an effective technology for efficiently discriminating Blastocystis STs in axenic cultures. ..
- Adams N, Byrne L, Smith G, Elson R, Harris J, Salmon R, et al. Shiga Toxin-Producing Escherichia coli O157, England and Wales, 1983-2012. Emerg Infect Dis. 2016;22:590-7 pubmed publisher..Studies assessing interventions and consideration of policies and guidance should be undertaken to reduce Shiga toxin-producing E. coli O157 infections in England and Wales in line with the latest epidemiologic findings. ..
- Camassa S, Palucci I, Iantomasi R, Cubeddu T, Minerva M, De Maio F, et al. Impact of pe_pgrs33 Gene Polymorphisms on Mycobacterium tuberculosis Infection and Pathogenesis. Front Cell Infect Microbiol. 2017;7:137 pubmed publisher..Together, these results further support the role of PE_PGRS33 in the pathogenesis and virulence of Mtb. ..
- Zhou H, Liu W, Xu L, Deng L, Deng Q, Zhuo J, et al. Spread of Neisseria meningitidis serogroup W clone, China. Emerg Infect Dis. 2013;19:1496-9 pubmed publisher..The epidemiologic investigation suggested recent transmission of this clonal complex in southeastern China. ..
- Ferdinand S, Millet J, Accipe A, Cassadou S, Chaud P, Levy M, et al. Use of genotyping based clustering to quantify recent tuberculosis transmission in Guadeloupe during a seven years period: analysis of risk factors and access to health care. BMC Infect Dis. 2013;13:364 pubmed publisher..tuberculosis population structure and to identify transmission chains and risk factors by prospective molecular typing in conjunction with conventional epidemiological investigations in the French overseas department of ..
- Abdalhamid B, Elhadi N, Albunayan S, Alsamman K, Aljindan R. First description of methyltransferases in extensively drug-resistant Klebsiella pneumoniae isolates from Saudi Arabia. J Med Microbiol. 2017;66:859-863 pubmed publisher..At least 93.2?% clonal relatedness was detected among these strains. To our knowledge, this is the first report describing XDRKPN encoding at least seven resistance determinants and harbouring methyltransferases in Saudi Arabia. ..
- Ardanuy C, de la Campa A, Garcia E, Fenoll A, Calatayud L, Cercenado E, et al. Spread of Streptococcus pneumoniae serotype 8-ST63 multidrug-resistant recombinant Clone, Spain. Emerg Infect Dis. 2014;20:1848-56 pubmed publisher..One recombination point was upstream of pbp2x and another was within pbp1a. A serotype 8-ST63 clone was identified as a cause of invasive disease in Spain. ..
- Serrano I, Oliveira M, Santos J, Bilocq F, Leitão A, Tavares L, et al. Antimicrobial resistance and genomic rep-PCR fingerprints of Pseudomonas aeruginosa strains from animals on the background of the global population structure. BMC Vet Res. 2017;13:58 pubmed publisher..This study confirms earlier results that P. aeruginosa has a non-clonal population structure, and shows that P. aeruginosa population from animals is homogeneously scattered and indistinguishable from the global population structure. ..
- Aslantas O, Yilmaz E. Prevalence and molecular characterization of extended-spectrum ?-lactamase (ESBL) and plasmidic AmpC ?-lactamase (pAmpC) producing Escherichia coli in dogs. J Vet Med Sci. 2017;79:1024-1030 pubmed publisher..coli clone O25b:ST131/B2. To the best of our knowledge, this is the first study to show fecal carriage of ESBL/pAmpC type ?-lactamase producing E. coli isolates among dogs in Turkey. ..
- Wen H, Zhao L, Zhai S, Chi Y, Cui F, Wang D, et al. Severe fever with thrombocytopenia syndrome, Shandong Province, China, 2011. Emerg Infect Dis. 2014;20:1-5 pubmed publisher..Clinical and laboratory manifestations included fever (100%), gastrointestinal symptoms (91%), myalgia (55%), chills (41%), thrombocytopenia (100%), and leukopenia (95%). ..
- Zhu B, Xu Z, Du P, Xu L, Sun X, Gao Y, et al. Sequence Type 4821 Clonal Complex Serogroup B Neisseria meningitidis in China, 1978-2013. Emerg Infect Dis. 2015;21:925-32 pubmed publisher..These findings suggest that CC4821 serogroup C N. meningitidis is the probable origin of highly pathogenic CC4821 serogroup B strains. ..
- Mojica M, Correa A, Vargas D, Maya J, Montealegre M, Rojas L, et al. Molecular correlates of the spread of KPC-producing Enterobacteriaceae in Colombia. Int J Antimicrob Agents. 2012;40:277-9 pubmed
- Origgi F, Frey J, Pilo P. Characterisation of a new group of Francisella tularensis subsp. holarctica in Switzerland with altered antimicrobial susceptibilities, 1996 to 2013. Euro Surveill. 2014;19: pubmed..The data show a previously undetected spread of group B.13 westwards in Europe, associated with changes in the antibiotic resistance profile relevant to treatment of tularaemia. ..
- Chen Q, Shi X, Li Y, Jiang Y, Lin Y, Qiu Y, et al. Rapid genetic typing of diarrheagenic Escherichia coli using a two-tube modified molecular beacon based multiplex real-time PCR assay and its clinical application. Ann Clin Microbiol Antimicrob. 2014;13:30 pubmed publisher..The developed multiplex rtPCR assay for the identification of DEC was high sensitive and specific and could be applied to the rapid identification of DEC in clinical and public health laboratories. ..
- Demczuk W, Martin I, Hoang L, Van Caeseele P, Lefebvre B, Horsman G, et al. Phylogenetic analysis of emergent Streptococcus pneumoniae serotype 22F causing invasive pneumococcal disease using whole genome sequencing. PLoS ONE. 2017;12:e0178040 pubmed publisher..pneumoniae serotype 22F has been observed, increasing prevalence of S. pneumoniae serotype 22F can be attributed to an evolving homogenous clone expanding nationally through local transmission events. ..
- Shao X, Wen Y, Ba H, Zhang X, Yue Z, Wang K, et al. Novel amdoparvovirus infecting farmed raccoon dogs and arctic foxes. Emerg Infect Dis. 2014;20:2085-8 pubmed publisher..Phylogenetic analyses showed that RFAV belongs to a new species within the genus Amdoparvovirus of the family Parvoviridae. An RFAV strain was isolated in Crandell feline kidney cell culture. ..
- Fink M, Schleicher C, Gonano M, Prodinger W, Pacciarini M, Glawischnig W, et al. Red deer as maintenance host for bovine tuberculosis, Alpine region. Emerg Infect Dis. 2015;21:464-7 pubmed publisher..Free-ranging red deer (Cervus elaphus) were a maintenance host in a hot-spot area, mainly located in Austria. ..
- David S, Afshar B, Mentasti M, Ginevra C, Podglajen I, Harris S, et al. Seeding and Establishment of Legionella pneumophila in Hospitals: Implications for Genomic Investigations of Nosocomial Legionnaires' Disease. Clin Infect Dis. 2017;64:1251-1259 pubmed publisher..However, deep hospital sampling is frequently required due to the potential coexistence of multiple populations, existence of substantial diversity, and similarity of hospital isolates to local populations. ..
- Mawer D, Eyre D, Griffiths D, Fawley W, Martin J, Quan T, et al. Contribution to Clostridium Difficile Transmission of Symptomatic Patients With Toxigenic Strains Who Are Fecal Toxin Negative. Clin Infect Dis. 2017;64:1163-1170 pubmed publisher..Although transmission from symptomatic patients with either fecal toxin status accounted for a low overall proportion of new cases, both groups should be infection control targets. ..
- Baffoni L, Gaggia F, Garofolo G, Di Serafino G, Buglione E, Di Giannatale E, et al. Evidence of Campylobacter jejuni reduction in broilers with early synbiotic administration. Int J Food Microbiol. 2017;251:41-47 pubmed publisher..Experimental results demonstrate that the synbiotic approach at farm level can be an effective strategy, combined with biosecurity measures, to improve the safety of poultry meat. ..
- Blanton L, Vohra R, Bouyer D, Walker D. Reemergence of murine typhus in Galveston, Texas, USA, 2013. Emerg Infect Dis. 2015;21:484-6 pubmed publisher..An isolate from 1 patient was confirmed to be Rickettsia typhi. Reemergence of murine typhus in Galveston emphasizes the importance of vector control and awareness of this disease by physicians and public health officials. ..
- Rufai S, Singh A, Singh J, Kumar P, Sankar M, Singh S. Diagnostic usefulness of Xpert MTB/RIF assay for detection of tuberculous meningitis using cerebrospinal fluid. J Infect. 2017;75:125-131 pubmed publisher..5%), 31 (81.6%) and 3 (7.9%) were found to be rifampicin resistant, sensitive and indeterminate respectively. Xpert MTB/RIF assay showed lower sensitivity as compared to MGIT 960 culture for the diagnosis of TBM from CSF samples. ..
- Fowler H, Brown P, Rovira A, Shade B, Klammer K, Smith K, et al. Streptococcus suis meningitis in swine worker, Minnesota, USA. Emerg Infect Dis. 2013;19:330-1 pubmed
- Khurana S, Mathur P, Kapil A, Valsan C, Behera B. Molecular epidemiology of beta-lactamase producing nosocomial Gram-negative pathogens from North and South Indian hospitals. J Med Microbiol. 2017;66:999-1004 pubmed publisher..Thus, their detection and characterization is important from a clinical-epidemiological, laboratory and infection control point of view. Knowledge of this epidemiology can predict the empiric antimicrobial treatment. ..
- Zhao X, Rødland E, Tibshirani R, Plevritis S. Molecular subtyping for clinically defined breast cancer subgroups. Breast Cancer Res. 2015;17:29 pubmed publisher..Compared with standard gene centering, our proposed subgroup-specific gene centering produced more accurate molecular subtype assignments in a study cohort with skewed clinicopathological characteristics relative to the training cohort. ..
- Perez Trallero E, Zigorraga C, Artieda J, Alkorta M, Marimón J. Two outbreaks of Listeria monocytogenes infection, Northern Spain. Emerg Infect Dis. 2014;20:2155-7 pubmed publisher..Fifteen cases in 2 epidemiologically unrelated outbreaks were caused by a rare type of Listeria monocytogenes, sequence type 87 serotype 1/2b. ..
- Soni D, Singh M, Singh D, Dubey S. Virulence and genotypic characterization of Listeria monocytogenes isolated from vegetable and soil samples. BMC Microbiol. 2014;14:241 pubmed publisher..monocytogenes in the selected agricultural farm samples. The increase in the number of strains resistant to ciprofloxacin and/or cefoxitin seems to pose serious public health consequences. ..
- Duan Y, Wu F, Wang W, He D, Gu J, Feng H, et al. The microbial community characteristics of ancient painted sculptures in Maijishan Grottoes, China. PLoS ONE. 2017;12:e0179718 pubmed publisher..Thus, proper management strategies and potential risk monitoring should be used in the Maijishan Grottoes to improve the conservation of these precious painted sculptures. ..
- Sobhanipoor M, Ahmadrajabi R, Karmostaji A, Saffari F. Molecular characterization of nasal methicillin resistant Staphylococcus aureus isolates from workers of an automaker company in southeast Iran. APMIS. 2017;125:921-926 pubmed publisher..Low genetic diversity with the dominance of CC22, SCCmecIV was found. Distribution of previously found hospital-associated MRSA was demonstrated among our isolates. ..
- Parsons S, Drewe J, Gey van Pittius N, Warren R, van Helden P. Novel cause of tuberculosis in meerkats, South Africa. Emerg Infect Dis. 2013;19:2004-7 pubmed publisher..Our genetic analysis showed it to be a novel member of the Mycobacterium tuberculosis complex and closely related to the dassie bacillus. We have named this epidemiologically and genetically unique strain M. suricattae. ..
- Gehre F, Antonio M, Otu J, Sallah N, Secka O, Faal T, et al. Immunogenic Mycobacterium africanum strains associated with ongoing transmission in The Gambia. Emerg Infect Dis. 2013;19:1598-1604 pubmed publisher..africanum sublineage, characterized by spoligotype shared international type 181, which is responsible for 20% of all tuberculosis cases in the region and therefore poses a major public health threat in The Gambia. ..
- Badotti F, de Oliveira F, Garcia C, Vaz A, Fonseca P, Nahum L, et al. Effectiveness of ITS and sub-regions as DNA barcode markers for the identification of Basidiomycota (Fungi). BMC Microbiol. 2017;17:42 pubmed publisher..Our study provides information that may guide researchers in choosing the most suitable genomic markers for identifying Basidiomycota species. ..
- Vaux S, Criscuolo A, Desnos Ollivier M, Diancourt L, Tarnaud C, Vandenbogaert M, et al. Multicenter outbreak of infections by Saprochaete clavata, an unrecognized opportunistic fungal pathogen. MBio. 2014;5: pubmed publisher..clavata may transmit through contaminated medical devices or can be associated with dairy products as seen in previous European outbreaks is highly relevant for the management of future outbreaks due to this newly recognized pathogen. ..
- Piarroux R, Abedi A, Shako J, Kebela B, Karhemere S, Diatta G, et al. Plague epidemics and lice, Democratic Republic of the Congo. Emerg Infect Dis. 2013;19:505-6 pubmed
- Ugarte Torres A, Chu A, Read R, MacDonald J, Gregson D, Louie T, et al. The epidemiology of Staphylococcus aureus carriage in patients attending inner city sexually transmitted infections and community clinics in Calgary, Canada. PLoS ONE. 2017;12:e0178557 pubmed publisher..Close strain relatedness of MSSA and USA300-MRSA isolates suggests either gain or loss of the SCCmec element, respectively. ..
- Samutela M, Kalonda A, Mwansa J, Lukwesa Musyani C, Mwaba J, Mumbula E, et al. Molecular characterisation of methicillin-resistant Staphylococcus aureus (MRSA) isolated at a large referral hospital in Zambia. Pan Afr Med J. 2017;26:108 pubmed publisher..Whereas comprehensive molecular typing data of MRSA strains is available, particularly in Europe, North America and Australia, similar information ..
- Wang M, Zheng Y, Mediavilla J, Chen L, Kreiswirth B, Song Y, et al. Hospital Dissemination of tst-1-Positive Clonal Complex 5 (CC5) Methicillin-Resistant Staphylococcus aureus. Front Cell Infect Microbiol. 2017;7:101 pubmed publisher..Antibiotic susceptibility testing was performed using BD Phoenix™ Automated Microbiology System. Molecular typing identified 11 clonal complex (CC) and 28 spa types, with the CC5-spa t002 (29...
- Mustafa A, Habibi N, Osman A, Shaheed F, Khan M. Species identification and molecular typing of human Brucella isolates from Kuwait. PLoS ONE. 2017;12:e0182111 pubmed publisher..Furthermore, the combined minimum spanning tree analysis demonstrated that, compared to MLVA types discovered all over the world, the Kuwaiti isolates were a distinct group of MLVA-11 and MLVA-16 types in the East Mediterranean Region. ..
- Vu L, Long N, Brito B, Stenfeldt C, Phuong N, Hoang B, et al. First detection of foot-and-mouth disease virus O/Ind-2001d in Vietnam. PLoS ONE. 2017;12:e0177361 pubmed publisher..This incursion has substantial implications for epidemiology and control of FMD in Southeast Asia. ..
- Bergmann M, Llewellyn J, Hartmann K. [Diagnosis of leptospirosis in dogs]. Tierarztl Prax Ausg K Kleintiere Heimtiere. 2017;45:170-177 pubmed publisher..However, only few data on sensitivity and specificity of these tests exist so far. A reliable diagnosis can only be established in case of a positive PCR result or a fourfold titre increase in MAT. ..
- Pritsch M, Zeynudin A, Messerer M, Baumer S, Liegl G, Schubert S, et al. First report on bla NDM-1-producing Acinetobacter baumannii in three clinical isolates from Ethiopia. BMC Infect Dis. 2017;17:180 pubmed publisher..These multi-drug resistant organisms pose a serious threat to antimicrobial treatments in Jimma, Ethiopia. ..
- He Q, Xu X, Lan F, Zhao Z, Wu Z, Cao Y, et al. Molecular characteristic of mcr-1 producing Escherichia coli in a Chinese university hospital. Ann Clin Microbiol Antimicrob. 2017;16:32 pubmed publisher..Increasing the surveillance of these infections, as well as taking effective infection control measures are urgently needed to take to control the transmission of mcr-1 gene. ..
- Einsiedel L, Cassar O, Bardy P, Kearney D, Gessain A. Variant human T-cell lymphotropic virus type 1c and adult T-cell leukemia, Australia. Emerg Infect Dis. 2013;19:1639-41 pubmed publisher..No attempt has been made to control transmission to indigenous children. We report 3 fatal cases of adult T-cell leukemia/lymphoma caused by human T-cell lymphotropic virus type 1 Australo-Melanesian subtype c. ..
- Poulsen A, de Jonge N, Sugiharto S, Nielsen J, Lauridsen C, Canibe N. The microbial community of the gut differs between piglets fed sow milk, milk replacer or bovine colostrum. Br J Nutr. 2017;117:964-978 pubmed publisher..The results indicate that BC may be a useful substitute for regular milk replacers, and as a feeding supplement in the immediate post-weaning period...
- Conlan S, Mijares L, Becker J, Blakesley R, Bouffard G, Brooks S, et al. Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates. Genome Biol. 2012;13:R64 pubmed publisher..Finally, phylogenetic analyses revealed a previously unrecognized group of S. epidermidis strains characterized by reduced virulence and formate dehydrogenase, which we propose as a clinical molecular marker. ..
- Sergelidis D, Angelidis A. Methicillin-resistant Staphylococcus aureus: a controversial food-borne pathogen. Lett Appl Microbiol. 2017;64:409-418 pubmed publisher..b>Molecular typing studies have revealed genetic relatedness of these enterotoxigenic isolates with isolates incriminated in ..
- Chen B, Xie X, Ni L, Dai X, Lu Y, Wu X, et al. Factors associated with Staphylococcus aureus nasal carriage and molecular characteristics among the general population at a Medical College Campus in Guangzhou, South China. Ann Clin Microbiol Antimicrob. 2017;16:28 pubmed publisher..The S. aureus isolates selected were revealed into various sequence types and pulsotypes, indicating molecular heterogeneity among S. aureus isolates from the populations in the medical college in Guangzhou. ..
- Whatmore A, Dawson C, Muchowski J, Perrett L, Stubberfield E, Koylass M, et al. Characterisation of North American Brucella isolates from marine mammals. PLoS ONE. 2017;12:e0184758 pubmed publisher..ceti and B. pinnipedialis, was critically assessed based on improved knowledge of the global population structure of Brucella associated with marine mammals...