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Transmission, infection, SIngle nucleotide polymorphism

H Harvala, E Alm, T Åkerlund, K Rizzardi
An aggregation of moxifloxacin-resistant Clostridium difficile ribotype 231 (RT231) isolates was first identified in the county of Stockholm in 2008, and by the end of 2015 isolates of RT231 had spread to 13 of 21 Swedish counties. We investigated the epidemiology of C. difficile RT231 in Sweden between 2006 and 2015 using whole genome sequencing (WGS) and evaluated whether its emergence could be associated with extended moxifloxacin use. We performed WGS and phylogenetic analysis of 51 C. difficile RT231 strains isolated in Sweden over a 10-year period...
November 2016: New Microbes and New Infections
Bruce McCollister, Cassandra V Kotter, Daniel N Frank, Taylor Washburn, Michael G Jobling
We report a case of ceftriaxone (CTX) treatment failure for bacteremia caused by Salmonella enterica subsp. enterica serovar Typhimurium, due to the in vivo acquisition of a blaCTX-M-27-encoding IncFII group transmissible plasmid. The original β-lactamase-susceptible isolate ST882S was replaced by the resistant isolate ST931R during ceftriaxone treatment. After relapse, treatment was changed to ciprofloxacin and the patient recovered. Isolate ST931R could transfer resistance to E. coli at 37 °C. We used whole-genome sequencing of ST882S and ST931R, the E...
September 26, 2016: Antimicrobial Agents and Chemotherapy
Sophia David, Christophe Rusniok, Massimo Mentasti, Laura Gomez-Valero, Simon R Harris, Pierre Lechat, John Lees, Christophe Ginevra, Philippe Glaser, Laurence Ma, Christiane Bouchier, Anthony Underwood, Sophie Jarraud, Timothy G Harrison, Julian Parkhill, Carmen Buchrieser
Legionella pneumophila is an environmental bacterium and the leading cause of Legionnaires' disease. Just five sequence types (ST), from >2000 currently described, cause nearly half of disease cases in North West Europe. Here we report the sequence and analyses of 364 L. pneumophila genomes including 337 from the five disease-associated STs and 27 representative of the species diversity. Phylogenetic analyses revealed that the five STs have independent origins within a highly diverse species. The number of de novo mutations is extremely low with maximum pairwise single nucleotide polymorphisms (SNPs) ranging from 19 (ST47) to 127 (ST1), which suggests emergences within the last century...
September 23, 2016: Genome Research
Alison E Mather, Becki Lawson, Elizabeth de Pinna, Paul Wigley, Julian Parkhill, Nicholas R Thomson, Andrew J Page, Mark A Holmes, Gavin K Paterson
: Passerine salmonellosis is a well-recognised disease of birds in the order Passeriformes, including common songbirds such as finches and sparrows, caused by infection with Salmonella enterica serovar Typhimurium. Previous research has suggested that some subtypes of S. Typhimurium - definitive phage types (DT) 40, 56 variant, and 160 - are host-adapted to passerines, and that these birds may represent a reservoir of infection for humans and other animals. Here, we have used whole genome sequences of 11 isolates from British passerines, five isolates of similar DTs from humans and a domestic cat, and previously published S...
September 9, 2016: Applied and Environmental Microbiology
Kanwal Maheshwari, Renato M Silva, Leticia Guajardo-Morales, Gustavo P Garlet, Alexandre R Vieira, Ariadne Letra
INTRODUCTION: Heat shock proteins (HSPs) protect cells under adverse conditions such as infection, inflammation, and disease. The differential expression of HSPs in human periapical granulomas suggests a potential role for these proteins in periapical lesion development, which may contribute to different clinical outcomes. Therefore, we hypothesized that polymorphisms in HSP genes leading to perturbed gene expression and protein function may contribute to an individual's susceptibility to periapical lesion development...
October 2016: Journal of Endodontics
Jianmin Zhang, Guojie Cao, Xuebin Xu, Marc Allard, Peng Li, Eric Brown, Xiaowei Yang, Haijian Pan, Jianghong Meng
Listeria monocytogenes is a significant foodborne pathogen causing severe systemic infections in humans with high mortality rates. The objectives of this work were to establish a phylogenetic framework of L. monocytogenes from China and to investigate sequence diversity among different serotypes. We selected 17 L. monocytogenes strains recovered from patients and foods in China representing serotypes 1/2a, 1/2b, and 1/2c. Draft genome sequences were determined using Illumina MiSeq technique and associated protocols...
2016: Frontiers in Microbiology
Dilrini De Silva, Joanna Peters, Kevin Cole, Michelle J Cole, Fiona Cresswell, Gillian Dean, Jayshree Dave, Daniel Rh Thomas, Kirsty Foster, Alison Waldram, Daniel J Wilson, Xavier Didelot, Yonatan H Grad, Derrick W Crook, Tim E A Peto, A Sarah Walker, John Paul, David W Eyre
BACKGROUND: New approaches are urgently required to address increasing rates of gonorrhoea and the emergence and global spread of antibiotic-resistant Neisseria gonorrhoeae. We used whole-genome sequencing to study transmission and track resistance in N gonorrhoeae isolates. METHODS: We did whole-genome sequencing of isolates obtained from samples collected from patients attending sexual health services in Brighton, UK, between Jan 1, 2011, and March 9, 2015. We also included isolates from other UK locations, historical isolates from Brighton, and previous data from a US study...
July 11, 2016: Lancet Infectious Diseases
David J King, Graham L Freimanis, Richard J Orton, Ryan A Waters, Daniel T Haydon, Donald P King
Due to the poor-fidelity of the enzymes involved in RNA genome replication, foot-and-mouth disease (FMD) virus samples comprise of unique polymorphic populations. In this study, deep sequencing was utilised to characterise the diversity of FMD virus (FMDV) populations in 6 infected cattle present on a single farm during the series of outbreaks in the UK in 2007. A novel RT-PCR method was developed to amplify a 7.6kb nucleotide fragment encompassing the polyprotein coding region of the FMDV genome. Illumina sequencing of each sample identified the fine polymorphic structures at each nucleotide position, from consensus level changes to variants present at a 0...
October 2016: Infection, Genetics and Evolution
K Mhandire, K Duri, D Mhandire, C Musarurwa, B Stray-Pedersen, C Dandara
Apolipoprotein B mRNA-editing catalytic polypeptide like-3G (APOBEC3G) is an antiviral enzyme that reduces viral fitness by introducing uracil to thymidine hypermutations in viral genomes. Thus, polymorphisms in the APOBEC3G gene have been implicated in differential outcomes of HIV infection and disease progression. However, there is insufficient evidence on the role of APOBEC3G gene variants on HIV infection, especially in African populations. This study therefore describes polymorphisms in the APOBEC3G gene in a Zimbabwean paediatric population and evaluates their effects on susceptibility to HIV infection among children born to HIV-infected mothers...
June 2016: South African Medical Journal, Suid-Afrikaanse Tydskrif Vir Geneeskunde
Moataz Abd El Ghany, Xiaolu Shi, Yinghui Li, Hifzur R Ansari, Grant A Hill-Cawthorne, Y S Ho, Raeece Naeem, Derek Pickard, John D Klena, Xuebing Xu, Arnab Pain, Qinghua Hu
Human infections with Salmonella enterica subspecies enterica serovar Senftenberg are often associated with exposure to poultry flocks, farm environments, or contaminated food. The recent emergence of multidrug-resistant isolates has raised public health concerns. In this study, comparative genomics and phenotypic analysis were used to characterize 14 Salmonella Senftenberg clinical isolates recovered from multiple outbreaks in Shenzhen and Shanghai, China, between 2002 and 2011. Single-nucleotide polymorphism analyses identified two phylogenetically distinct clades of S Senftenberg, designated SC1 and SC2, harboring variations in Salmonella pathogenicity island 1 (SPI-1) and SPI-2 and exhibiting distinct biochemical and phenotypic signatures...
August 2016: Journal of Clinical Microbiology
Mingbo Yin, Xiao Liu, Bin Xu, Jian Huang, Qi Zheng, Zhong Yang, Zheng Feng, Ze-Guang Han, Wei Hu
Schistosoma infection is a major cause of morbidity and mortality worldwide. Schistosomiasis japonica is endemic in mainland China along the Yangtze River, typically distributed in two geographical categories of lake and mountainous regions. Study on schistosome genetic diversity is of interest in respect of understanding parasite biology and transmission, and formulating control strategy. Certain genetic variations may be associated with adaptations to different ecological habitats. The aim of this study is to gain insight into Schistosoma japonicum genetic variation, evolutionary origin and associated causes of different geographic lineages through examining homozygous Single Nucleotide Polymorphisms (SNPs) based on resequenced genome data...
September 2016: Acta Tropica
Andrea Gloria-Soria, W Augustine Dunn, Erich L Telleria, Benjamin R Evans, Loyce Okedi, Richard Echodu, Wesley C Warren, Michael J Montague, Serap Aksoy, Adalgisa Caccone
The tsetse fly Glossina fuscipes fuscipes (Gff) is the insect vector of the two forms of Human African Trypanosomiasis (HAT) that exist in Uganda. Understanding Gff population dynamics, and the underlying genetics of epidemiologically relevant phenotypes is key to reducing disease transmission. Using ddRAD sequence technology, complemented with whole-genome sequencing, we developed a panel of ∼73,000 single-nucleotide polymorphisms (SNPs) distributed across the Gff genome that can be used for population genomics and to perform genome-wide-association studies...
2016: G3: Genes—Genomes—Genetics
D S Blanc, B Gomes Magalhaes, M Abdelbary, G Prod'hom, G Greub, J B Wasserfallen, P Genoud, G Zanetti, L Senn
BACKGROUND: During an environmental investigation of Pseudomonas aeruginosa in intensive care units, the liquid hand soap was found to be highly contaminated (up to 8 × 10(5)cfu/g) with this pathogen. It had been used over the previous five months and was probably contaminated during manufacturing. AIM: To evaluate the burden of this contamination on patients by conducting an epidemiological investigation using molecular typing combined with whole genome sequencing (WGS)...
May 2016: Journal of Hospital Infection
Emilie Søndberg, Lotte Jelsbak
BACKGROUND: Typhoid fever caused by Salmonella enterica serovar Typhi (S. Typhi) is a severe systemic human disease and endemic in regions of the world with poor drinking water quality and sewage treatment facilities. A significant number of patients become asymptomatic life-long carriers of S. Typhi and serve as the reservoir for the disease. The specific mechanisms and adaptive strategies enabling S. Typhi to survive inside the host for extended periods are incompletely understood. Yet, elucidation of these processes is of major importance for improvement of therapeutic strategies...
2016: BMC Microbiology
Zhenzhen Kong, Peipei Zhao, Haibing Liu, Xiang Yu, Yanyan Qin, Zhaoliang Su, Shengjun Wang, Huaxi Xu, Jianguo Chen
Staphylococcus aureus is a globally disseminated drug-resistant bacterial species. It remains a leading cause of hospital-acquired infection, primarily among immunocompromised patients. In 2012, the Affiliated People's Hospital of Jiangsu University experienced a putative outbreak of methicillin-resistant S. aureus (MRSA) that affected 12 patients in the Neurosurgery Department. In this study, whole-genome sequencing (WGS) was used to gain insight into the epidemiology of the outbreak caused by MRSA, and traditional bacterial genotyping approaches were also applied to provide supportive evidence for WGS...
2016: PloS One
Anselmo J Kamada, Anna M Bianco, Luisa Zupin, Martina Girardelli, Maria C C Matte, Rúbia Marília de Medeiros, Sabrina Esteves de Matos Almeida, Marineide M Rocha, Ludovica Segat, José A B Chies, Louise Kuhn, Sergio Crovella
Bone marrow stromal cell antigen-2 (BST-2)/Tetherin is a restriction factor that prevents Human immunodeficiency virus type 1 (HIV-1) release from infected cells and mediates pro-inflammatory cytokine production. This study investigated the risk conferred by single nucleotide polymorphisms (rs919266, rs9192677, and rs9576) at BST-2 coding gene (BST2) in HIV-1 mother-to-child transmission and in disease progression. Initially, 101 HIV-1+ pregnant women and 331 neonates exposed to HIV-1 from Zambia were enrolled...
July 1, 2016: Journal of Acquired Immune Deficiency Syndromes: JAIDS
Hannes Schuler, Kirsten Köppler, Sabine Daxböck-Horvath, Bilal Rasool, Susanne Krumböck, Dietmar Schwarz, Thomas S Hoffmeister, Birgit C Schlick-Steiner, Florian M Steiner, Arndt Telschow, Christian Stauffer, Wolfgang Arthofer, Markus Riegler
Wolbachia is a maternally inherited and ubiquitous endosymbiont of insects. It can hijack host reproduction by manipulations such as cytoplasmic incompatibility (CI) to enhance vertical transmission. Horizontal transmission of Wolbachia can also result in the colonization of new mitochondrial lineages. In this study, we present a 15-year-long survey of Wolbachia in the cherry fruit fly Rhagoletis cerasi across Europe and the spatiotemporal distribution of two prevalent strains, wCer1 and wCer2, and associated mitochondrial haplotypes in Germany...
April 2016: Molecular Ecology
A C Bowen, T Harris, D C Holt, P M Giffard, J R Carapetis, P T Campbell, J McVERNON, S Y C Tong
Impetigo is common in remote Indigenous children of northern Australia, with the primary driver in this context being Streptococcus pyogenes [or group A Streptococcus (GAS)]. To reduce the high burden of impetigo, the transmission dynamics of GAS must be more clearly elucidated. We performed whole genome sequencing on 31 GAS isolates collected in a single community from children in 11 households with ⩾2 GAS-infected children. We aimed to determine whether transmission was occurring principally within households or across the community...
July 2016: Epidemiology and Infection
Kang Xiao, Bao-Yun Zhang, Xiao-Mei Zhang, Jing Wang, Cao Chen, Li-Na Chen, Yan Lv, Qi Shi, Xiao-Ping Dong
It is well known that the SMB-S15 cell line was originally established by cultures from the brains of mice affected by the Chandler scrapie strain, and this cell line may express PrPSc permanently. However, the infectivity of the S15-derived prions on experimental animals has not yet been well documented. In the present study, the cell lysates of SMB-S15 were intracerebrally inoculated into three different strains of mice, namely C57BL/6, Balb/c and CD1. Prion protein (PRNP) gene sequencing revealed the same encoded PrP proteins in the sequences of amino acids in the three strains of mice, in addition to a synonymous single nucleotide polymorphism (SNP) in CD1 mice...
March 2016: International Journal of Molecular Medicine
Margaret A Fitzpatrick, Egon A Ozer, Alan R Hauser
Acinetobacter baumannii frequently causes nosocomial infections and outbreaks. Whole-genome sequencing (WGS) is a promising technique for strain typing and outbreak investigations. We compared the performance of conventional methods with WGS for strain typing clinical Acinetobacter isolates and analyzing a carbapenem-resistant A. baumannii (CRAB) outbreak. We performed two band-based typing techniques (pulsed-field gel electrophoresis and repetitive extragenic palindromic-PCR), multilocus sequence type (MLST) analysis, and WGS on 148 Acinetobacter calcoaceticus-A...
March 2016: Journal of Clinical Microbiology
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