F Baquero, A E Pérez-Cobas, S Aracil-Gisbert, T M Coque, J Zamora
We aimed to determine the importance of selection (mostly dependent on the anthropogenic use of antimicrobials) and transmission (mostly dependent on hygiene and sanitation) as drivers of the spread of antibiotic-resistant bacterial populations. The first obstacle to estimating the relative weight of both independent variables is the lack of detailed quantitative data concerning the number of bacterial cells, potentially either pathogenic or harmless, and bacterial species exposed to antimicrobial action in the microbiotas of specific environments...
May 18, 2024: Infection, Genetics and Evolution
Man Zhang, Yue Wang, Hai-Mo Shen, Shen-Bo Chen, Tian-Yu Wang, Kokouvi Kassegne, Jun-Hu Chen
Plasmodium vivax Merozoite Surface Protein 8 (PvMSP8) is a promising candidate target for the development of multi-component vaccines. Therefore, determining the genetic variation pattern of msp8 is essential in providing a reference for the rational design of the P. vivax malaria vaccines. This study delves into the genetic characteristics of the Pvmsp8 gene, specifically focusing on samples from the China-Myanmar border (CMB) region, and contrasts these findings with broader global patterns. The study uncovers that Pvmsp8 exhibits a notable level of conservation across different populations, with limited polymorphisms and relatively low nucleotide diversity (0...
May 15, 2024: Infection, Genetics and Evolution
Andrea Fořtová, Petra Straková, Jan Haviernik, Pavel Svoboda, Tomáš Bartonička, Jana Kvičerová, Daniel Růžek, Jiří Salát
Bats are known reservoirs of various emerging pathogens, and have recently been found to host a novel hantavirus, named Brno loanvirus (BRNV), from the Mammantavirinae subfamily (family Hantaviridae, order Bunyavirales). Here we report BRNV detection in bats from the urban area of Brno, Czech Republic in March 2022. Specifically, we uncovered a high prevalence of BRNV (8.8%, 5/57) among hibernating bats (Nyctalus noctula) in urban area, which poses a risk of human exposure. The positive bats included adult females (3/9 positive), a juvenile female (1/32 positive), and an adult male (1/6 positive)...
May 14, 2024: Infection, Genetics and Evolution
Qingwen Ding, Bing Hu, Xuan Yao, Min Gan, Dan Chen, Nailou Zhang, Jinbo Wei, Kun Cai, Zhenhua Zheng
Hepatitis E, caused by the hepatitis E virus (HEV), is a global public health issue. Low similarity between the gene sequences of mouse and human HEV led to the belief that the risk of human infection was low. Recent reports of chronic and acute hepatitis E caused by murine HEV infection in humans in Hong Kong have raised global concerns. Therefore, it is crucial to investigate the epidemiology and prevalence of HEV in China. We comprehensively analyzed different rodent HEV strains to understand rocahepevirus occurrence in Hubei Province, China...
May 10, 2024: Infection, Genetics and Evolution
Zhengwei Liu, Xiangchen Li, Haiyan Xiong, Qingrong Zhou, Huaiming Yi, Kunyang Wu, Zonglei Zhou, Yewei Lu, Yelei Zhu, Lin Zhou, Mingwu Zhang, Junshun Gao, Junli Gao, Songhua Chen, Xiaomeng Wang, Weibing Wang
In the mountainous, rural regions of eastern China, tuberculosis (TB) remains a formidable challenge; however, the long-term molecular epidemiological surveillance in these regions is limited. This study aimed to investigate molecular and spatial epidemiology of TB in two mountainous, rural counties of Zhejiang Province, China, from 2015 to 2021, to elucidate the recent transmission and drug-resistance profiles. The predominant Lineage 2 (L2) Beijing family accounted for 80.1% of total 532 sequenced Mycobacterium tuberculosis (Mtb) strains, showing consistent prevalence over seven years...
May 7, 2024: Infection, Genetics and Evolution
Shane Whelan, Francesca Bottacini, Colin Buttimer, Karen Finn, Brigid Lucey
Urinary tract infections (UTI) caused by uropathogenic Escherichia coli (UPEC) pose a global health concern. Resistance mechanisms, including genetic mutations in antimicrobial target genes, efflux pumps, and drug deactivating enzymes, hinder clinical treatment. These resistance factors often spread through mobile genetic elements. Molecular techniques like whole genome sequencing (WGS), multilocus sequence typing (MLST), and phylotyping help decode bacterial genomes and categorise resistance genes. In this study, we analysed 57 UPEC isolates from different UTI patients following EUCAST guidelines...
April 29, 2024: Infection, Genetics and Evolution
Victor Gomes de Paula, Rayane Sarafim de Sousa, Rafaella Christina Moreira Rocha da Silva, Everton Giovani Alves, Alexandre Rodrigues Caetano, Patrícia Ianella, Tatiana Amabile de Campos
Whopping cough (or Pertussis) is an acute infectious respiratory disease caused by Bordetella pertussis bacteria. The disease is highly transmissible and can be fatal in children under two years old. Since the introduction of vaccine immunization in 1940, Pertussis incidence decreased worldwide. In Brazil, the immunization was introduced in 1977 using the whole cell (wP) vaccine. Despite the high vaccination coverage, an unexpected increase in the number of observed Pertussis cases was observed in 2012. In this year, 2257 cases were reported exceeding the average incidence rate of <1000 cases per year until 2010...
April 26, 2024: Infection, Genetics and Evolution
Evangelia Georgia Kostaki, Sotirios Roussos, Anastasia Maria Kefala, Stefanos Limnaios, Mina Psichogiou, Eleni Papachristou, Georgios Nikolopoulos, Eleni Flountzi, Samuel R Friedman, Pagona Lagiou, Angelos Hatzakis, Vana Sypsa, Gkikas Magiorkinis, Apostolos Beloukas, Dimitrios Paraskevis
BACKGROUND: New diagnoses of HIV-1 infection among people who inject drugs (PWID) in Athens, Greece, saw a significant increase in 2011 and a subsequent decline after 2013. Despite this, ongoing HIV-1 transmission persisted from 2014 to 2020 within this population. Our objective was to estimate the time of infection for PWID in Athens following the HIV-1 outbreak, explore the patterns of HIV-1 dispersal over time, and determine the duration from infection to diagnosis. METHODS: Time from HIV-1 infection to diagnosis was estimated for 844 individuals infected within 4 PWID-specific clusters and for 8 PWID infected with sub-subtype A6 diagnosed during 2010-2019...
April 23, 2024: Infection, Genetics and Evolution
Luana Boff, Humberlânia de Sousa Duarte, Gabriela Bergiante Kraychete, Gabriel Taddeucci-Rocha, Bianca Diniz Oliveira, Rodolpho Mattos Albano, Ana Paula D'Alincourt Carvalho-Assef, Silvana Vargas Superti, Ianick Souto Martins, Renata Cristina Picão
Klebsiella pneumoniae is an opportunistic pathogen that can colonize the gastrointestinal tract (GIT) of humans. The mechanisms underlying the successful translocation of this pathogen to cause extra-intestinal infections remain unknown, although virulence and antimicrobial resistance traits likely play significant roles in the establishment of infections. We investigated K. pneumoniae strains isolated from GIT colonization (strains Kp_FZcol-1, Kp_FZcol-2 and Kp_FZcro-1) and from a fatal bloodstream infection (strain Kp_HM-1) in a leukemia patient...
April 21, 2024: Infection, Genetics and Evolution
Bianca Lara Venâncio de Godoy, Marlon do Valle Barroso, Yasmin Fontoura de Azeredo Lourenção, Letícia Kellen de Andrade, Vitória Gabriela Tosta Rodrigues, Caroline Atuí, Ana Caroline do Valle, Taís Paulino Ferreira, Mara Corrêa Lelles Nogueira, Tiago Casella
Foodstuffs are a well-documented source of multidrug-resistant bacteria, and hospitalized patients are usually susceptible to hospital infections owing to their immune status. Therefore, this study aimed to investigate the presence of beta-lactamase-producing Enterobacterales in ready-to-eat foods consumed by hospitalized patients. For this purpose, 51 vegetable and meat samples were collected over 2 months and analyzed. Enterobacterales isolates were identified and subjected to antimicrobial susceptibility testing, followed by beta-lactamase gene screening, pH tolerance assays, and whole-genome sequencing (WGS)...
April 19, 2024: Infection, Genetics and Evolution
Zewen Sun, Lin Pan, Aowen Tian, Peng Chen
The prevalence of COVID-19 critical illness varies across ethnicities, with recent studies suggesting that genetic factors may contribute to this variation. The aim of this study was to investigate natural selection signals of genes associated with critically-ill COVID-19 in sub-Saharan Africans. Severe COVID-19 SNPs were obtained from the HGI website. Selection signals were assessed in 661 sub-Sahara Africans from 1000 Genomes Project using integrated haplotype score (iHS), cross-population extended haplotype homozygosity (XP-EHH), and fixation index (Fst)...
April 16, 2024: Infection, Genetics and Evolution
Koray Ergunay, Brian P Bourke, Drew D Reinbold-Wasson, Laura Caicedo-Quiroga, Nataliya Vaydayko, Giorgi Kirkitadze, Tamar Chunashvili, Cynthia L Tucker, Yvonne-Marie Linton
Members of the Orthonairovirus genus (family Nairoviridae) include many tick-borne viruses of significant human and animal health impact, with several recently-documented pathogenic viruses lacking sufficient epidemiological information. We screened 215 adult ticks of seven species collected in Bulgaria, Georgia, Latvia and Poland for orthonairoviruses, followed by nanopore sequencing (NS) for genome characterization. Initial generic amplification revealed Sulina virus (SULV, Orthonairovirus sulinaense), for which an updated amplification assay was used, revealing an overall prevalence of 2...
April 16, 2024: Infection, Genetics and Evolution
Asad Ali, Saba Riaz
OBJECTIVES: This multicenter study, conducted from a One Health perspective, aimed to comprehensively examine the prevalence of Methicillin-resistant Staphylococcus aureus (MRSA) infections and their biofilm-forming capabilities in Pakistan. Phylogenetic analysis of the study isolates was also performed. METHODS: A total of 150 MRSA isolates were screened from various clinical samples using Cefoxitin antibiotic discs. Genotypic confirmation was conducted through mecA, S...
April 11, 2024: Infection, Genetics and Evolution
Reuben S Maghembe, Maximilian A K Magulye, Emmanuel Eilu, Simon Sekyanzi, Abdalah Makaranga, Savannah Mwesigwa, Eric Katagirya
Sepsis and multidrug resistance comprise a complex of factors attributable to mortality among intensive care unit (ICU) patients globally. Pathogens implicated in sepsis are diverse, and their virulence and drug resistance remain elusive. From a tertiary care hospital ICU in Uganda, we isolated a Citrobacter freundii strain RSM030 from a patient with sepsis and phenotypically tested it against a panel of 16 antibiotics including imipenem levofloxacin, cotrimoxazole and colistin, among others. We sequenced the organism's genome and integrated multilocus sequencing (MLST), PathogenFinder with Virulence Factor analyzer (VFanalyzer) to establish its pathogenic relevance...
April 9, 2024: Infection, Genetics and Evolution
Micheli Filippi, Meriane Demoliner, Juliana Schons Gularte, Vyctoria Malayhka de Abreu Goes Pereira, Mariana Soares da Silva, Viviane Girardi, Alana Witt Hansen, Fernando Rosado Spilki
The presence of different mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome can be related to changes in coronavirus disease (COVID-19) infection. Besides, these viral alterations associated with factors such as massive number of positive cases, vaccination and reinfections can be important in the viral evolution process. As well as, mutations found at low frequencies may have a more neutral action and consequently be less inclined to negative selection, facilitating their spread through the population...
April 2, 2024: Infection, Genetics and Evolution
Elinambinina Rajaonarifara, Benjamin Roche, Cedric B Chesnais, Holivololona Rabenantoandro, Michelle Evans, Andres Garchitorena
BACKGROUND: Progress in lymphatic filariasis (LF) elimination is spatially heterogeneous in many endemic countries, which may lead to resurgence in areas that have achieved elimination. Understanding the drivers and consequences of such heterogeneity could help inform strategies to reach global LF elimination goals by 2030. This study assesses whether differences in age-specific compliance with mass drug administration (MDA) could explain LF prevalence patterns in southeastern Madagascar and explores how spatial heterogeneity in prevalence and age-specific MDA compliance may affect the risk of LF resurgence after transmission interruption...
March 26, 2024: Infection, Genetics and Evolution
L Boulanger, C Planchon, A Taudière, K D McCoy, S T G Burgess, A J Nisbet, K Bartley, P Galliot, P Creach, N Sleeckx, L Roy
Management of Dermanyssus gallinae, a cosmopolitan hematophagous mite responsible for damage in layer poultry farming, is hampered by a lack of knowledge of its spatio-temporal population dynamics. Previous studies have shown that the circulation of this pest between farms is of strictly anthropogenic origin, that a mitochondrial haplogroup has been expanding on European farms since the beginning of the 21st century and that its local population growth may be particularly rapid. To refine our understanding of how D...
March 21, 2024: Infection, Genetics and Evolution
Quantao Zhang, Thomas Alter, Eckhard Strauch, Inga Eichhorn, Maria Borowiak, Carlus Deneke, Susanne Fleischmann
Non-O1/non-O139 Vibrio cholerae (NOVC) are ubiquitous in aquatic ecosystems. In rare cases, they can cause intestinal and extra-intestinal infections in human. This ability is associated with various virulence factors. The presence of NOVC in German North Sea and Baltic Sea was observed in previous studies. However, data on virulence characteristics are still scarce. Therefore, this work aimed to investigating the virulence potential of NOVC isolated in these two regions. In total, 31 NOVC strains were collected and subjected to whole genome sequencing...
March 20, 2024: Infection, Genetics and Evolution
Fruzsina Tóth, Gábor Gáspár, Péter Pankovics, Péter Urbán, Róbert Herczeg, Mihály Albert, Gábor Reuter, Ákos Boros
In this study, a picornavirus and a nidovirus were identified from a single available nasopharyngeal swab (NPS) sample of a freshly deceased sheep, as the only vertebrate viruses found with viral metagenomics and next-generation sequencing methods. The sample was originated from a mixed feedlot farm in Hungary where sheep and cattle were held together but in separate stalls. Most of the sheep had respiratory signs (coughing and increased respiratory effort) at the time of sampling. Other NPS were not, but additional enteric samples were collected from sheep (n = 27) and cattle (n = 11) of the same farm at that time...
March 18, 2024: Infection, Genetics and Evolution
Hassan Diab, Kelven Rahy, Tamima Jisr, Mira El Chaar, Edmond Abboud, Sima Tokajian
Klebsiella pneumoniae is a Gram-negative bacterium that colonizes the gastrointestinal tract and nasopharynx with many being linked to nosocomial infections. Extended-spectrum β-lactamases (ESBL)-producing and carbapenem-resistant K. pneumoniae is recognized by the World Health Organization (WHO) as a critical public health concern. In this study, whole-genome sequencing (WGS) - based analysis was performed to understand the molecular epidemiology of multi-drug resistant Klebsiella spp. clinical isolates...
March 12, 2024: Infection, Genetics and Evolution
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