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Molecular-epidemiology

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https://www.readbyqxmd.com/read/28634353/coronavirus-hku15-in-respiratory-tract-of-pigs-and-first-discovery-of-coronavirus-quasispecies-in-5-untranslated-region
#1
Patrick Cy Woo, Susanna Kp Lau, Chi-Ching Tsang, Candy Cy Lau, Po-Chun Wong, Franklin Wn Chow, Jordan Yh Fong, Kwok-Yung Yuen
Coronavirus HKU15 is a deltacoronavirus that was discovered in fecal samples of pigs in Hong Kong in 2012. Over the past three years, Coronavirus HKU15 has been widely detected in pigs in East/Southeast Asia and North America and has been associated with fatal outbreaks. In all such epidemiological studies, the virus was generally only detected in fecal/intestinal samples. In this molecular epidemiology study, we detected Coronavirus HKU15 in 9.6% of the nasopharyngeal samples obtained from 249 pigs in Hong Kong...
June 21, 2017: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/28630462/identification-and-molecular-characterization-of-non-polio-enteroviruses-from-children-with-acute-flaccid-paralysis-in-west-africa-2013-2014
#2
Maria D Fernandez-Garcia, Ousmane Kebe, Aichatou D Fall, Kader Ndiaye
Besides polioviruses, non-polio enteroviruses (NPEVs) may also be associated with acute flaccid paralysis (AFP). Because poliomyelitis is on the verge of eradication, more attention should be paid to study NPEVs from non-polio AFP cases and their epidemic patterns. In West African countries the epidemiology of NPEVs remains largely unexplored. We investigated the genetic diversity, frequency, circulation patterns, and molecular epidemiology of NPEVs in seven West African countries by analyzing retrospectively a panel of 3195 stool samples from children with AFP collected through routine poliomyelitis surveillance activities between 2013 and 2014...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28628461/measles-outbreak-with-unique-virus-genotyping-ontario-canada-2015
#3
Shari Thomas, Joanne Hiebert, Jonathan B Gubbay, Effie Gournis, Jennifer Sharron, Alberto Severini, Manisa Jiaravuthisan, Amanda Shane, Valerie Jaeger, Natasha S Crowcroft, Jill Fediurek, Beate Sander, Tony Mazzulli, Helene Schulz, Shelley L Deeks
The province of Ontario continues to experience measles virus transmissions despite the elimination of measles in Canada. We describe an unusual outbreak of measles in Ontario, Canada, in early 2015 that involved cases with a unique strain of virus and no known association among primary case-patients. A total of 18 cases of measles were reported from 4 public health units during the outbreak period (January 25-March 23, 2015); none of these cases occurred in persons who had recently traveled. Despite enhancements to case-patient interview methods and epidemiologic analyses, a source patient was not identified...
July 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28627832/molecular-epidemiological-traits-of-group-a-rotaviruses-in-japanese-children-during-transitional-period-of-rotavirus-vaccine-implementation-2011-2014
#4
Sayaka Takanashi, Aksara Thongprachum, Shoko Okitsu, Shuichi Nishimura, Masaaki Kobayashi, Hideaki Kikuta, Atsuko Yamamoto, Kumiko Sugita, Tsuneyoshi Baba, Satoshi Hayakawa, Masashi Mizuguchi, Hiroshi Ushijima
BACKGROUND: Group A rotavirus (RVA) vaccines have been introduced in Japan since 2011. To investigate the molecular epidemiological traits of RVA during the transitional period of rotavirus vaccine implementation in Japan, this study was undertaken by following up three-decade long surveillance conducted in the same regions. METHODS: RVA were screened and genotyped by RT-PCR from diarrheal samples collected from non-hospitalized patients in six localities (Hokkaido, Tokyo, Shizuoka, Osaka, Kyoto, and Saga) during 2011 - 2014...
May 1, 2017: Clinical Laboratory
https://www.readbyqxmd.com/read/28624549/evaluation-of-a-new-trilocus-sequence-based-multiplex-pcr-to-detect-major-acinetobacter-baumannii-clonal-complexes-circulating-in-brazil
#5
Francielli Mahnic de Vasconcellos, Monique Ribeiro Tiba Casas, Laís Calissi Brisolla Tavares, William Vaz de Sousa, Doroti de Oliveira Garcia, Carlos Henrique Camargo
Dissemination of carbapenem-resistant Acinetobacter baumannii (CRAB) is mainly due to the spread of clonal lineages, particularly those included into the clonal complexes (CC) CC1, CC2, CC15, CC25, and CC79. We evaluated the usefulness of a recently modified PCR-based trilocus sequence-based typing (m3LST) in comparison with the standard multilocus sequence typing (MSLT) of 7 housekeeping genes as per the Institute Pasteur Scheme to assign the clonal complexes in CRAB. A collection of 78 CRAB isolated from 67 different Brazilian health institutions was submitted to both methodologies, and concordance rate was calculated...
June 14, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28622949/changed-epidemiology-during-intra-and-interhospital-spread-of-high-risk-clones-of-vana-containing-enterococcus-in-brazilian-hospitals
#6
Andrey G Sacramento, Rosemeire C Zanella, Fernanda Esposito, Emanuela A S Costa, Lara M de Almeida, Carlos Pires, Artemir C de Brito, Elsa M Mamizuka, Louise T Cerdeira, Nilton Lincopan
We report changes in the molecular epidemiology of vanA-containing Enterococcus during the intra and interhospital spread of high-risk clones, in Southeastern Brazil. While VRE faecalis predominated during 1998 to 2006, a reversal has been observed in the last years, where VRE faecium belonging to ST114, ST203, ST412, ST478 and ST858 have become endemic.
May 18, 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/28619013/mlst-genotypes-of-campylobacter-jejuni-isolated-from-broiler-products-dairy-cattle-and-human-campylobacteriosis-cases-in-lithuania
#7
Sigita Ramonaite, Egle Tamuleviciene, Thomas Alter, Neringa Kasnauskyte, Mindaugas Malakauskas
BACKGROUND: Campylobacter (C.) jejuni is the leading cause of human campylobacteriosis worldwide. We performed a molecular epidemiological study to investigate the genetic relationship among C. jejuni strains isolated from human diarrhoeal patients, broiler products and dairy cattle in Lithuania. METHODS: The C. jejuni isolates from human clinical cases, dairy cattle and broiler products were genotyped using multilocus sequence typing (MLST). Allele numbers for each housekeeping gene, sequence type (ST), and clonal complex (CC) were assigned by submitting the DNA sequences to the C...
June 15, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28617836/molecular-diversity-and-frequency-of-the-diarrheagenic-enteric-protozoan-giardia-duodenalis-and-cryptosporidium-spp-in-a-hospital-setting-in-northern-spain
#8
José Manuel Azcona-Gutiérrez, Aida de Lucio, Marta Hernández-de-Mingo, Concepción García-García, Luis Miguel Soria-Blanco, Lucía Morales, María Aguilera, Isabel Fuentes, David Carmena
BACKGROUND: Human giardiosis and cryptosporidiosis are caused by the enteric protozoan parasites Giardia duodenalis and Cryptosporidium spp. Both pathogens are major contributors to the global burden of diarrhoeal disease, affecting primarily children and immunodebilitated individuals in resource-poor settings. Giardiosis and cryptosporidiosis also represent an important, often underestimate, public health threat in developed countries. In Spain only limited information is currently available on the epidemiology of these infections...
2017: PloS One
https://www.readbyqxmd.com/read/28617524/high-prevalence-of-methicillin-resistant-coagulase-negative-staphylococci-isolated-from-a-university-environment-in-thailand
#9
Rathanin Seng, Udomluk Leungtongkam, Rapee Thummeepak, Wassana Chatdumrong, Sutthirat Sitthisak
The present study was conducted to isolate and characterize the molecular epidemiology of the methicillin-resistant staphylococci in the general university environment, where all five locations; the library, restrooms, canteens, computer rooms and outdoor surfaces, are in common use by a large population of students. We used Mannitol Salt Agar (MSA) supplemented with 4 μg/ml of oxacillin to screen the methicillin-resistant staphylococci. The species level was identified by PCR of rdr (Staphylococcus epidermidis), groESL (Staphylococcus haemolyticus) and nuc (Staphylococcus aureus and Staphylococcus warneri) genes and DNA sequencing of tuf and dnaJ genes...
June 2017: International Microbiology: the Official Journal of the Spanish Society for Microbiology
https://www.readbyqxmd.com/read/28611955/uncovering-differences-in-virulence-markers-associated-with-achromobacter-species-of-cf-and-non-cf-origin
#10
Brankica Filipic, Milka Malesevic, Zorica Vasiljevic, Jovanka Lukic, Katarina Novovic, Milan Kojic, Branko Jovcic
Achromobacter spp. are recognized as emerging pathogens in hospitalized as well as in cystic fibrosis (CF) patients. From 2012 to 2015, we collected 69 clinical isolates (41 patient) of Achromobacter spp. from 13 patients with CF (CF isolates, n = 32) and 28 patients receiving care for other health conditions (non-CF isolates, n = 37). Molecular epidemiology and virulence potential of isolates were examined. Antimicrobial susceptibility, motility, ability to form biofilms and binding affinity to mucin, collagen, and fibronectin were tested to assess their virulence traits...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28610789/comparative-study-of-genotypes-of-mycobacterium-tuberculosis-from-a-northern-indian-setting-with-strains-reported-from-other-parts-of-india-and-neighboring-countries
#11
Pragya Sharma, Kiran Katoch, Shilpi Chandra, Devendra Singh Chauhan, Vishnu Dutt Sharma, David Couvin, Nalin Rastogi, Vishwa Mohan Katoch
This study was carried out to characterize Mycobacterium tuberculosis population in Ghatampur, Kanpur, North India, by spoligotyping and Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTRs) typing. A total of 335 isolates were genotyped by spoligotyping and Central Asian (CAS) sub-lineage was the most prevalent, comprising 59.1% of all isolates. Other lineages were: East-African Indian (EAI) (19.10%), T (5.07%), Beijing (3.28%), Manu (2.98%), X (2.68%), S (0.89%), H3 (0...
July 2017: Tuberculosis
https://www.readbyqxmd.com/read/28607013/pena-pona-porb1-and-mtrr-mutations-and-molecular-epidemiological-typing-of-neisseria-gonorrhoeae-with-decreased-susceptibility-to-cephalosporin
#12
Kayo Osawa, Katsumi Shigemura, Yukie Nukata, Koichi Kitagawa, Fukashi Yamamichi, Hiroyuki Yoshida, Toshiro Shirakawa, Soichi Arakawa, Masato Fujisawa
In recent years, N. gonorrhoeae strains with decreased susceptibilities (DS; MIC > 0.064 mg/L) or resistance to cefixime (CFM) or ceftriaxone (CRO), have been classed as a "superbug" and have spread worldwide, resulting in treatment failures for gonorrhea (1-3).….
June 12, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28606119/molecular-epidemiology-of-avian-rotaviruses-group-a-and-d-shed-by-different-bird-species-in-nigeria
#13
Maude Pauly, Oluwole O Oni, Aurélie Sausy, Ademola A Owoade, Christopher A O Adeyefa, Claude P Muller, Judith M Hübschen, Chantal J Snoeck
BACKGROUND: Avian rotaviruses (RVs) cause gastrointestinal diseases of birds worldwide. However, prevalence, diversity, epidemiology and phylogeny of RVs remain largely under-investigated in Africa. METHODS: Fecal samples from 349 birds (158 symptomatic, 107 asymptomatic and 84 birds without recorded health status) were screened by reverse transcription PCR to detect RV groups A and D (RVA and RVD). Partial gene sequences of VP4, VP6, VP7 and NSP4 for RVA, and of VP6 and VP7 for RVD were obtained and analyzed to infer phylogenetic relationship...
June 12, 2017: Virology Journal
https://www.readbyqxmd.com/read/28604828/genotype-diversity-and-molecular-evolution-of-noroviruses-a-30-year-1982-2011-comprehensive-study-with-children-from-northern-brazil
#14
Jones Anderson Monteiro Siqueira, Renato da Silva Bandeira, Darleise de Souza Oliveira, Liann Filiphe Pereira Dos Santos, Yvone Benchimol Gabbay
A chronologically comprehensive 30-year study was conducted that involved children living in Belém, in the Amazon region of Northern Brazil, who participated in eight different studies from October 1982 to April 2011. The children were followed either in the community or in health units and hospitals in order to identify the norovirus genotypes involved in infections during this time. A total of 2,520 fecal specimens were obtained and subjected to RT-PCR and nucleotide sequencing for regions A, B, C, D and P2 of the viral genome...
2017: PloS One
https://www.readbyqxmd.com/read/28604331/evidence-of-persistence-of-prevotella-spp-in-the-cystic-fibrosis-lung
#15
D F Gilpin, K A Nixon, M Bull, S J McGrath, L Sherrard, J M Rolain, E Mahenthiralingam, J S Elborn, M M Tunney
PURPOSE: Prevotella spp. represent a diverse genus of bacteria, frequently identified by both culture and molecular methods in the lungs of patients with chronic respiratory infection. However, their role in the pathogenesis of chronic lung infection is unclear; therefore, a more complete understanding of their molecular epidemiology is required. METHODOLOGY: Pulsed Field Gel Electrophoresis (PFGE) and Random Amplified Polymorphic DNA (RAPD) assays were developed and used to determine the degree of similarity between sequential isolates (n=42) from cystic fibrosis (CF) patients during periods of clinical stability and exacerbation...
June 13, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28604100/molecular-epidemiology-of-carbapenem-resistant-acinetobacter-baumannii-in-greece-an-extended-review-2000-2015
#16
Theodoros Karampatakis, Charalampos Antachopoulos, Athanassios Tsakris, Emmanuel Roilides
Carbapenem-resistant Acinetobacter baumannii (CRAB) is endemic in Greece. CRAB initially emerged in 2000 and since then, carbapenemases still have a crucial role in CRAB appearance, except for a few cases resulting from efflux pump or outer-membrane protein mechanisms. OXA-type carbapenemases present the highest prevalence worldwide and bla OXA-23-like and bla OXA-58-like are the most important genes found; VIM-yielding CRAB have also been detected, while a single CRAB isolate producing NDM has quite recently emerged in Greece...
June 12, 2017: Future Microbiology
https://www.readbyqxmd.com/read/28603640/prevalence-and-molecular-epidemiology-of-clostridium-difficile-infection-in-indonesia
#17
D A Collins, M H Gasem, T H Habibie, I G Arinton, P Hendriyanto, A P Hartana, T V Riley
Clostridium difficile has not been studied in detail in Asia, particularly Southeast Asia. We thus performed a prevalence study across four hospitals in Central Java province, Indonesia. Stool samples were collected from patients with diarrhoea and tested by enzyme immunoassay for glutamate dehydrogenase (GDH) and toxin A/B (C DIFF QUIK CHEK COMPLETE, TechLab). Specimens were cultured and molecular typing was performed. In total, 340 samples were tested, of which 70 (20.6%) were GDH positive, with toxin detected in 19 (5...
July 2017: New Microbes and New Infections
https://www.readbyqxmd.com/read/28602726/the-changing-molecular-epidemiology-of-hiv-in-the-philippines
#18
Edsel Maurice T Salvaña, Brian E Schwem, Patrick Ching, Simon D W Frost, Sharie Keanne G Ganchua, Jill Itable
BACKGROUND: The Philippines has one of the fastest-growing HIV epidemics in the world. Possible reasons for this include increased testing, increased local transmission, and possibly more aggressive strains of HIV. This study sought to determine whether local molecular subtypes of HIV have changed. METHODS: Viruses from 81 newly diagnosed, treatment-naive HIV patients were genotyped using protease and reverse transcriptase genes. Demographic characteristics and CD4 count data were collected...
June 10, 2017: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/28600216/molecular-epidemiology-and-antibiotic-resistance-of-methicillin-resistant-staphylococcus-aureus-circulating-in-the-russian-federation
#19
Vladimir Gostev, Alexander Kruglov, Olga Kalinogorskaya, Olga Dmitrenko, Olga Khokhlova, Tatsuo Yamamoto, Yuri Lobzin, Irina Ryabchenko, Sergey Sidorenko
The aim of this study was to investigate the patterns of antimicrobial resistance and molecular features of methicillin-resistant Staphylococcus aureus (MRSA) isolates in Russia. Isolates recovered from hospital patients (n=480), healthy medical personnel (n=25), and healthy carriers (n=13) were included in the study. Hospital-acquired MRSA (HA-MRSA) demonstrated high resistance to ciprofloxacin, gentamicin, and chloramphenicol (76%-92%), moderate - to tetracycline, erythromycin, clindamycin, and rifampicin (38%-54%), and low - to fusidic acid, co-trimoxazole, mupirocin, and daptomycin (2%-7%)...
June 7, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28598251/molecular-characterization-of-methicillin-resistant-staphylococcus-aureus-isolated-from-australian-animals-and-veterinarians
#20
Kate A Worthing, Sam Abraham, Stanley Pang, Geoffrey W Coombs, Sugiyono Saputra, David Jordan, Hui S Wong, Rebecca J Abraham, Darren J Trott, Jacqueline M Norris
This study aimed to determine the frequency and molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) from Australian animals and whether animal-derived MRSA was similar to that from Australian veterinarians. A total of 1,080 clinical coagulase positive Staphylococcus isolates from Australian animals were collected during 2013. Sixteen (4%) of 360 S. aureus isolates were MRSA. Most MRSA came from companion animals, while none came from livestock. MRSA isolates were characterized using whole genome sequencing...
June 9, 2017: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
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