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Phenotypic and molecular characterization of multi-drug resistant Klebsiella spp. isolates recovered from clinical settings Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-03-12 Hassan Diab, Kelven Rahy, Tamima Jisr, Mira El Chaar, Edmond Abboud, Sima Tokajian
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 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
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A novel metagenomic approach uncovers phage genes as markers for increased disinfectant tolerance in mixed Listeria monocytogenes communities Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-03-11 Agnete Kirstine Karlsmose, Mirena Ivanova, Martin Laage Kragh, Jette Sejer Kjeldgaard, Saria Otani, Christina Aaby Svendsen, Bojan Papić, Irena Zdovc, Taurai Tasara, Roger Stephan, Even Heir, Solveig Langsrud, Trond Møretrø, Paw Dalgaard, Annette Fagerlund, Lisbeth Truelstrup Hansen, Frank M. Aarestrup, Pimlapas Leekitcharoenphon
is an important human pathogen with a high mortality rate. Consumption of contaminated ready-to-eat food is the main mode of transmission to humans. Disinfectant-tolerant L. have emerged, which are believed to have increased persistence potential. Elucidating the mechanisms of L. disinfectant tolerance has been the focus of previous studies using pure cultures. A limitation of such approach is the
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The A2 haplotype of Echinococcus multilocularis is the predominant variant infecting humans and dogs in Yili Prefecture, Xinjiang Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-03-01 Baoping Guo, Cairen, Jianyong Wu, Wenli Wang, Bingjie Wang, Yuan Ren, Mayire Aizezi, Rongsheng Mi, Li Zhao, Hao Wen
Alveolar echinococcosis (AE), caused by is an important zoonotic disease. Yili Prefecture in Xinjiang is endemic for AE, however the molecular variability of in this region is poorly understood. In this study, 127 samples were used for haplotypes analysis, including 79 tissues from humans, 43 liver tissues from small rodents, and 5 fecal samples from dogs. Genetic variability in was studied using complete
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Revisiting genetic diversity in Echinococcus multilocularis, the role for EmsB microsatellite: A commentary Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-02-29 Mohammad Ali Mohammadi, Majid Fasihi Harandi
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Exploring the resistome and virulome in major sequence types of Acinetobacter baumannii genomes: Correlations with genome divergence and sequence types Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-02-27 Rachana Banerjee, Stephy Mol Robinson, Abhishake Lahiri, Prateek Verma, Ayushman Kumar Banerjee, Sohom Basak, Kausik Basak, Sandip Paul
The increasing global prevalence of antimicrobial resistance in has led to concerns regarding the effectiveness of infection treatment. Moreover, the critical role of virulence factor genes in s pathogenesis and its propensity to cause severe disease is of particular importance. Comparative genomics, including multi-locus sequence typing (MLST), enhances our understanding of epidemiology. While there
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Whole genome sequence-based characterization of Campylobacter isolated from broiler carcasses over a three-year period in a big poultry slaughterhouse reveals high genetic diversity and a recurring genomic lineage of Campylobacter jejuni Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-02-27 Marc J.A. Stevens, Roger Stephan, Jule Anna Horlbog, Nicole Cernela, Magdalena Nüesch-Inderbinen
is among the most frequent agents of bacterial gastroenteritis in Europe and is primarily linked to the consumption of contaminated food. The aim of this study was to assess genomic diversity and to identify antimicrobial resistance and virulence genes of 155 isolated from broiler carcasses (neck skin samples) in a large-scale Swiss poultry abattoir over a three-year period. Samples originated from
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Assessment of the genetic diversity of lymnaeid (Gastropoda: Pulmonata) snails and their infection status with trematode cercariae in different regions of Thailand Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-02-24 Abdulhakam Dumidae, Chanakan Subkrasae, Jiranun Ardpairin, Supawan Pansri, Chanatinat Homkaew, Chadaporn Nuchjangreed Gordon, Bandid Mangkit, Aunchalee Thanwisai, Apichat Vitta
Lymnaeid snails are some of the most widespread snails and are the first intermediate host of trematode parasites that affect human and livestock health. A full understanding of the genetic relationship of hosts and parasites is of paramount importance for effective parasite management. The present study assessed the prevalence of trematode larvae in lymnaeid snails and examined the genetic diversity
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Dissecting the genome sequence of a clinical isolated Cunninghamella bertholletiae Z2 strain with rich cytochrome P450 enzymes (Article) Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-02-23 En-Min Zhou, Xin-Ai Chen, Ming-Ming Zhou, Li-Yao Xu, Di Wang, He-Ping Shen, Wei-Qun Xu
Mucormycosis is receiving much more attention because of its high morbidity and extremely high mortality rate in immunosuppressed populations. In this study, we isolated a Cunnignhamella bertholletiae Z2 strain from a skin lesion of a 14 year, 9 months old girl with acute lymphoblastic leukemia who die of infection from the Z2 strain. Genome sequencing was performed after isolation and amplification
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Evolution of SARS-CoV-2 in the Rhine-Neckar/Heidelberg Region 01/2021 – 07/2023 Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-02-23 Christian Bundschuh, Niklas Weidner, Julian Klein, Tobias Rausch, Nayara Azevedo, Anja Telzerow, Jan-Philipp Mallm, Heeyoung Kim, Simon Steiger, Isabelle Seufert, Kathleen Börner, Katharina Bauer, Daniel Hübschmann, Katharina Laurence Jost, Sylvia Parthé, Paul Schnitzler, Michael Boutros, Karsten Rippe, Barbara Müller, Ralf Bartenschlager, Hans-Georg Kräusslich, Vladimir Benes
In January 2021, the monitoring of circulating variants of SARS-CoV-2 was initiated in Germany under the Corona Surveillance Act, which was discontinued after July 2023. This initiative aimed to enhance pandemic containment, as specific amino acid changes, particularly in the spike protein, were associated with increased transmission and reduced vaccine efficacy.
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Metagenomic next-generation sequencing for diagnosis of fatal Balamuthia amoebic encephalitis Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-02-19 Lixia Qin, Yaqin Xiang, Ziwei Wu, Hainan Zhang, Xiaomei Wu, Qihua Chen
Balamuthia amoebic encephalitis (BAE), caused by , is a rare and life-threatening infectious disease with no specific and effective treatments available. The diagnosis of BAE at an early stage is difficult because of the non-specific clinical manifestations and neuroimaging. A 52-year-old male patient, who had no previous history of skin lesions, presented to the emergency department with an acute
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The analysis of complete genome sequence and comparative genomics of Vibrio parahaemolyticus LF1113 in Hainan Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-02-18 Linlin Hu, Aiyun Meng, Zhigang Tu, Shuwen Jia, Qingming Liu, Fuxiao Chen
is a Gram-negative, halophilic and polymorphic coccobacillus. It is world-widely distributed and has resulted in great economic losses since its first appearance. In this study, a pathogenic strain was isolated from diseased pearl gentian grouper and identified as based on the sequencing results of 16S rDNA gene. In order to gain a comprehensive understanding of this isolation, the whole genome sequencing
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Comprehensive analysis of antigenic variations and genomic properties of hepatitis B virus in clinical samples in the mid-north east region of Bangladesh Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-02-16 Md. Golzar Hossain, Mahfuz Islam, Yusha Araf, Shyamal Kumar Paul, Sharmin Akter, Mohammad Kamruzzaman Khan, Muzahed Uddin Ahmed, Sakirul Khan, Sheikh Mohammad Fazle Akbar, Chitta Ranjan Debnath
This investigation delineates an exhaustive analysis of the clinical, immunological, and genomic landscapes of hepatitis B virus (HBV) infection across a cohort of 22 verified patients. The demographic analysis unveiled a pronounced male bias (77.27%), with patient ages spanning 20 to 85 years and durations of illness ranging from 10 days to 4 years. Predominant clinical manifestations included fever
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Epidemiology and genetic diversity of Theileria equi and Babesia caballi in Mongolian horses Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-02-15 Davaajav Otgonsuren, Tovuu Amgalanbaatar, Sandagdorj Narantsatsral, Batsaikhan Enkhtaivan, Dalantai Munkhgerel, Myagmar Zoljargal, Batbold Davkharbayar, Punsantsogvoo Myagmarsuren, Banzrach Battur, Badgar Battsetseg, Thillaiampalam Sivakumar, Naoaki Yokoyama
Equine piroplasmosis is a tick-borne disease caused by and in horses. Because of its impact on horse industry, control of this disease is crucial for endemic countries. The control of equine piroplasmosis may be influenced by the genotypic diversity of and . Mongolia, a country with a thriving livestock industry, is endemic for and . However, nationwide epidemiological surveys have not been conducted
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Polymorphisms in the human angiotensin converting enzyme gene (ACE) linked to susceptibility of COVID-19 and malaria infections in the Ghanaian population Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-02-15 Nancy O. Duah-Quashie, Philip Opoku-Agyeman, Marta Lanza, Jose Miguel Rubio
Genetic variations in the human angiotensin converting enzyme gene () influence enzyme expression levels in humans and subsequently influence both communicable and non-communicable disease outcomes. More recently, polymorphisms in this gene have been linked to susceptibility and outcomes of infectious diseases such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and malaria infections
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First report of Anaplasma spp., Ehrlichia spp., and Rickettsia spp. in Amblyomma gervaisi ticks infesting monitor lizards (Varanus begalensis) of Pakistan Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-02-13 Shakir Ullah, Jing-Syuan Huang, Afshan Khan, Raquel Cossío-Bayúgar, Nasreen Nasreen, Sadaf Niaz, Adil Khan, Tsai-Ying Yen, Kun-Hsien Tsai, Mourad Ben Said
Ticks pose significant health risks to both wildlife and humans due to their role as vectors for various pathogens. In this study, we investigated tick infestation patterns, tick-associated pathogens, and genetic relationships within the tick species , focusing on its prevalence in monitor lizards () across different districts in Pakistan. We examined 85 monitor lizards and identified an overall mean
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Genotypic analysis of hepatitis E virus (HEV) from sporadic symptomatic cases in Pakistan Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-02-09 Momina Ejaz, Ali Zohaib, Muhammad Usman, Muhammad Moaaz Anwar, Hafiz Sajid Khan, Muhammad Ammar, Muhammad Saqib, Sadia Ghani Khan, Muhammad Ammar Athar, Muhammad Khalid Mansoor, Ahsaan Ullah, Mehvish Naseem, Muhammad Hammad Hussain, Aneela Javed
Pakistan is the fifth most populous nation in the world and faces several challenges, including devastating floods, sub-optimal sanitary conditions, clustered accommodations, and unregulated cross-border movements. These drastic population shifts make it vulnerable to the efficient spread of the Hepatitis E virus (HEV). The current study analyzed the genotypic characteristics and variants of the Hepatitis
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Trypanosomatid diversity in a bat community of an urban area in Campo Grande, Mato Grosso do Sul, Brazil Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-01-30 Jaire Marinho Torres, Carina Elisei de Oliveira, Filipe Martins Santos, Nayara Yoshie Sano, Érica Verneque Martinez, Fernanda Moreira Alves, Luiz Eduardo Roland Tavares, André Luiz Rodrigues Roque, Ana Maria Jansen, Heitor Miraglia Herrera
Bats have a long evolutionary history with trypanosomatids, but the role of these flying mammals on parasite transmission cycles in urban areas, especially for Trypanosoma and Leishmania species, remains poorly known. The objective of this study was to evaluate the species richness of trypanosomatids parasitizing a bat community in Campo Grande (CG), a state capital within the Cerrado of the Brazilian
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Genetic diversity of G9, G3, G8 and G1 rotavirus group A strains circulating among children with acute gastroenteritis in Vietnam from 2016 to 2021 Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-02-03 Ly K.T. Le, Mai N.T. Chu, Jacqueline E. Tate, Baoming Jiang, Michael D. Bowen, Mathew D. Esona, Rashi Gautam, Jose Jaimes, Thao P.T. Pham, Nguyen T. Huong, Dang D. Anh, Nguyen V. Trang, Umesh Parashar
Rotavirus group A (RVA) is the most common cause of severe childhood diarrhea worldwide. The introduction of rotavirus vaccination programs has contributed to a reduction in hospitalizations and mortality caused by RVA. From 2016 to 21, we conducted surveillance to monitor RVA prevalence and genotype distribution in Nam Dinh and Thua Thien Hue (TT Hue) provinces where a pilot Rotavin-M1 vaccine (Vietnam)
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Detection of multiple recombinations of avian coronavirus in South Korea by whole-genome analysis Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-02-02 Da-Won Kim, Ji-Yun Kim, Dong-Wook Lee, Hyuk-Chae Lee, Chang-Seon Song, Dong-Hun Lee, Jung-Hoon Kwon
Infectious bronchitis virus (IBV), an avian coronavirus, has caused considerable damage to the poultry industry. In Korea, indigenous KM91-like and newly introduced QX-like lineages belonging to the GI-19 lineage have been prevalent despite constant vaccination. In this study, complete genome sequences of 23 IBV isolates in Korea from 2010 to 2020 were obtained using next-generation sequencing, and
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Molecular detection of Coxiella burnetii in ticks collected from Iran Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-02-01 Ahmad Enferadi, Saeedeh Sarani, Shirin Mohammadipour, Sayyed Jafar Hasani, Afshin Ajdari, Maryam Najafi Asl, Peyman Khademi
The present study was conducted with the aim of investigating the prevalence and genetic structure of in tick samples collected from domestic animals in Hormozgan province146 tick samples were randomly collected from cattle, sheep, goat, camel and dog herds in seven cities of Hormozgan. After the DNA was extracted from each tick sample; Nested-PCR method was used to identify the presence of using transposon
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Host genetics and the profile of COVID-19 in indigenous people from the Brazilian Amazon: A pilot study with variants of the ACE1, ACE2 and TMPRSS2 genes Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-02-01 Eliene Rodrigues Putira Sacuena, Carlos Neandro Cordeiro Lima, Isabella Nogueira Abreu, Lucas Matheus Cavalcante da Silva, Lilian Karen Goes Belleza, Renan Barbosa Lemes, Gilderlânio Santana de Araújo, Hilton Pereira da Silva, Antônio Carlos Rosário Vallinoto, João Farias Guerreiro
This pilot study aimed to investigate genetic factors that may have contributed to the milder clinical outcomes of COVID-19 in Brazilian indigenous populations. 263 Indigenous from the Araweté, Kararaô, Parakanã, Xikrin do Bacajá, Kayapó and Munduruku peoples were analyzed, 55.2% women, ages ranging from 10 to 95 years (average 49.5 ± 20.7). Variants in genes involved in the entry of SARS-CoV-2 into
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Genome analysis deciphered Chryseobacterium indicum is a distinct species associated with freshwater pufferfish Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-01-26 Manish Prakash Victor, Ritu Rani Archana Kujur, Lipika Das, Subrata K. Das
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Serological and molecular epidemiological investigation of Mediterranean spotted fever in Yunnan Province, China Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-01-21 Suyi Luo, Shuyue Yang, Aihua Liu, Hanxin Wu, Li Gao, Xinya Wu, Yan Dong, Bingxue Li, Weijiang Ma, Li Peng, Fukai Bao
Objectives Given the limited research and its potential hazards, the study aimed to determine the prevalence of Mediterranean spotted fever (MSF) caused by Rickettsia conorii (R. conorii), a tick-borne disease, in Yunnan Province, China. Methods Through stratified sampling across five distinct regions in Yunnan, 5358 blood samples were obtained from the general healthy population. Enzyme-linked immunosorbent
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Molecular epidemiology and phylogeny of the emerging zoonotic virus Rocahepevirus: A global genetic analysis Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-01-19 Han Wu, Lu Zhou, Fengge Wang, Zixiang Chen, Yihan Lu
Human infections with Rocahepevirus ratti genotype C1 (HEV-C1) in Hong Kong of China, Canada, Spain, and France have drawn worldwide concern towards Rocahepevirus. This study conducted a global genetic analysis of Rocahepevirus, aiming to furnish comprehensive molecular insights and promote further research. We retrieved 817 Rocahepevirus sequences from the GenBank database through October 31, 2023
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Consanguineous marriages increase the incidence of recurrent tuberculosis: Evidence from whole exome sequencing Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-01-23 Noor ul Akbar, Sajjad Ahmad, Taj Ali Khan, Muhammad Tayyeb, Naheed Akhter, Laraib Shafiq, Shahid Niaz Khan, Mohammad Mahtab Alam, Alduwish Manal Abdullah, Muhammad Fayyaz ur Rehman, Majed A. Bajaber, Muhammad Safwan Akram
Background In this study, we have identified multiple mutations in the IL-12R1 gene among Pakistani patients who have inherited them through consanguineous marriages. These patients have experienced severe Bacille-Calmette-Guérin (BCG) infection as well as recurrent tuberculosis. We will demonstrate the pivotal role of interleukin (IL)-12/interferon (IFN)-γ axis in the regulation of mycobacterial diseases
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Understanding SARS-CoV-2 spike glycoprotein clusters and their impact on immunity of the population from Rio Grande do Norte, Brazil Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-01-17 Diego Gomes Teixeira, João Firmino Rodrigues-Neto, Dayse Caroline Severiano da Cunha, Selma Maria Bezerra Jeronimo
SARS-CoV-2 genome underwent mutations since it started circulating within the human population. The aim of this study was to understand the fluctuation of the spike clusters concomitant to the population immunity either due to natural infection and/or vaccination in a state of Brazil that had both high rate of natural infection and vaccination coverage. A total of 1725 SARS-CoV-2 sequences from the
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Phylogenetic congruence of Plasmodium spp. and wild ungulate hosts in the Peruvian Amazon Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-01-19 Gabriela M. Ulloa, Alex D. Greenwood, Omar E. Cornejo, Frederico Ozanan Barros Monteiro, Alessandra Scofield, Meddly L. Santolalla Robles, Andres G. Lescano, Pedro Mayor
Malaria parasites are known to infect a variety of vertebrate hosts, including ungulates. However, ungulates of Amazonia have not been investigated. We report for the first time, the presence of parasite lineages closely related to Plasmodium odocoilei clade 1 and clade 2 in free-ranging South American red-brocket deer (Mazama americana; 44.4%, 4/9) and gray-brocket deer (Mazama nemorivaga; 50.0%,
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Genetic polymorphisms of Plasmodium vivax ookinete (sexual stage) surface proteins (Pvs25 and Pvs28) from Thailand Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-01-18 Jiraporn Kuesap, Nutnicha Suphakhonchuwong, Kanchana Rungsihirunrat
Plasmodium vivax is the most geographically widespread malaria parasite in human presently. The ookinete surface proteins of sexual stage of malaria parasites, Pvs25 and Pvs28, are candidates for the transmission blocking vaccine. The antigenic variation in population might be barrier for vaccine development. The objective of this study was to investigate the genetic diversity of Pvs25 and Pvs28 in
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Genetic characteristics of a novel HIV-1 circulating recombinant form (CRF128_07B) identified among MSM in Guangdong Province, China Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-01-17 Yun Lan, Ruolei Xin, Xizi Deng, Feng Li, Xuemei Ling, Kun Zeng, Chuyu Zhang, Linghua Li, Fengyu Hu
Objective To obtain and investigate the genetic characteristics of four HIV-1 near full-length genome sequences (NFLGs), aiming at a description of a novel circulating recombinant form (CRF) in Guangdong China. Methods Plasma samples were collected from HIV-1 infected MSM patients in Guangdong Province who had no epidemiological association with each other. The NFLGs were amplified with two overlapping
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Metagenomic analysis of the ocular toxoplasmosis in children uveitis from Fayoum governorate, Egypt Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-01-11 Marwa A. Elmallawany, Amany A. Abdel-Aal, Khaled G. Abu Eleinen, Ahmed H. Nadar, Azza I. El-Adawy, Marwa A. EL-Dardiry, Yosra N. Abddel-Hafez, Ahmed A. Kotb, Ahmed T.S. Saif, Hoda A.A. Shaheen, Ahmed Sayed, Omar Samir, Adham A. Alatyar, Mostafa A. Sheble, Mostafa Elnakib, Mohamed S. Badr, Reham K. Nahnoush
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Direct detection of canine picornavirus complete coding sequence in wastewater using long-range reverse-transcriptase polymerase chain reaction and long-read sequencing Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-01-08 Temitope O.C. Faleye, Erin M. Driver, Jillian M. Wright, Rolf U. Halden, Arvind Varsani, Matthew Scotch
We describe four complete coding sequence (cCDS) of canine picornavirus from wastewater in Arizona, USA detected by coupling cCDS single-contig (∼7.5 kb) reverse-transcriptase polymerase chain reaction (RT-PCR) and low-cost long-read high-throughput sequencing. For viruses of medical/veterinary importance, this workflow expands possibilities of wastewater based genomic epidemiology for exploring virus
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In vivo biological validation of in silico analysis: A novel approach for predicting the effects of TLR4 exon 3 polymorphisms on brucellosis Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-01-11 Antonio Gentile, Andrea Fulgione, Barbara Auzino, Valentina Iovane, Daniela Gallo, Raffaele Garramone, Nunzia Iaccarino, Antonio Randazzo, Giuseppe Iovane, Paola Cuomo, Rosanna Capparelli, Domenico Iannelli
The role of the Toll-like receptor 4 (TLR4) is of recognising intracellular and extracellular pathogens and of activating the immune response. This process can be compromised by single nucleotide polymorphisms (SNPs) which might affect the activity of several TLRs. The aim of this study is of ascertaining whether SNPs in the TLR4 of Bubalus bubalis infected by Brucella abortus, compromise the protein
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Evolutionary analysis of major histocompatibility complex variants in chytrid-resistant and susceptible amphibians Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-01-11 Minjie Fu
An amphibian emerging infectious disease (EID), chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd), originated in Asia but primarily led to declines and extinctions in amphibian populations outside of Asia. Host major histocompatibility complex (MHC) molecules exhibit high polymorphism, and the evolution of MHC can be influenced by recombination and pathogens. Previous studies have indicated
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Characteristics of Cervical Cancer Caused by the Human Papillomavirus 18 and Its Genetic Variations in Vietnamese Women Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-01-03 Than Manh Hung, Hoang Xuan Son, Le Van Nguyen Bang, Le Van Duyet
Background The involvement of HPV18 in cervical cancer pathogenesis, as well as its high oncogenic potential and influence on the variation of cervical cancer distribution in different geographical regions, makes assessing the characteristics of cervical cancer and its variants the basis for considering potential carcinogenic HPV18 sequence variations and vaccine strategies. Methods A prospective study
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Comparative genomics and characterization of a multidrug-resistant Acinetobacter baumannii VRL-M19 isolated from a crowded setting in India Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-01-03 Neha Verma, Tina Sharma, Anshu Bhardwaj, Venkata Ramana Vemuluri
A crowded vegetable market serves as a mass gathering, posing a potential risk for infection transmission. In this study, we isolated a multidrug-resistant Acinetobacter baumannii strain, VRL-M19, from the air of such a market and conducted comparative genomics and phenotypic characterization. Antimicrobial susceptibility testing, genome sequencing using Illumina HiSeq X10, and pan-genome analysis
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Detection of circovirus in free-ranging brown rats (Rattus norvegicus) Infect. Genet. Evol. (IF 3.2) Pub Date : 2024-01-02 Z.L. Tarján, S. Szekeres, M.Z. Vidovszky, L. Egyed
Accidentally found, two poisoned brown rats from Hungary were surveyed for presence of circoviral DNA, using specific nested primers, designed against the rep gene of the virus. Both specimens were positive. The whole genomes were amplified using inverse PCR based on the Rep sequence parts and sequenced by the primer walking method. Genomic analyses revealed that these novel rat viruses, together with
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Biofilms: A developmental niche for vancomycin-intermediate Staphylococcus aureus Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-12-29 Jenelle E. Chapman, Shilpa E. George, Christiane Wolz, Michael E. Olson
Staphylococcus aureus are gram-positive bacteria responsible for a wide array of diseases, ranging from skin and soft tissue infections to more chronic illnesses such as toxic shock syndrome, osteomyelitis, and endocarditis. Vancomycin is currently one of the most effective antibiotics available in treating patients infected with methicillin-resistant S. aureus (MRSA), however the emergence of vancomycin-resistant
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Microsatellite markers for genotyping of Kodamaea ohmeri: Demonstrating outbreaks based on a multicenter surveillance study in China Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-12-29 Yanbing Li, Yuyan Huang, Mei Kang, Xiangyang Chen, Liwen Liu, Hongmei Zhao, Zhongju Chen, Meng Xiao, Yingchun Xu, Qiaolian Yi, Menglan Zhou
Kodamaea ohmeri, an emerging human pathogen, caused both sporadic and nosocomial infections among immunocompromised people with high mortality. However, there is limited research on the molecular epidemiology of K. ohmeri. A total of fifty microsatellite loci were designed based on K. ohmeri type strain NRRL Y-1932 and three loci were finally selected for microsatellite analysis. Non-duplicated K.
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Evolutionary trends of carbapenem-resistant and susceptible Acinetobacter baumannii isolates in a major tertiary care setting from North India Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-12-18 Kanika Bansal, Tanu Saroha, Prashant P. Patil, Sanjeet Kumar, Sunil Kumar, Lipika Singhal, Vikas Gautam, Prabhu B. Patil
Emergence of carbapenem-resistant A. baumannii (CRAB) is a global, ongoing healthcare concern. CRAB is among the topmost priority pathogens, with various studies focusing on its global population structure and resistant allelic profiles. However, carbapenem-susceptible A. baumannii (CSAB) isolates are often overlooked due to their sensitivity to beta-lactams, which can provide important insights into
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High prevalence of Enterovirus E, Bovine Kobuvirus, and Astrovirus revealed by viral metagenomics in fecal samples from cattle in Central Colombia Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-12-20 Julián Esteban Medina, Sergio Castañeda, Luisa Páez-Triana, Milena Camargo, Diego J. Garcia-Corredor, Marcela Gómez, Nicolas Luna, Angie L. Ramírez, Martín Pulido-Medellín, Marina Muñoz, Juan David Ramírez
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Whole-genome sequencing and transcriptome-characterized mechanism of streptomycin resistance in Vibrio parahaemolyticus O10: K4 Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-12-17 Peng Zhang, Lei Ji, Wei Yan, Liping Chen, Xiaohua Zhu, Zhonghao Lu, Fenfen Dong
Streptomycin resistance in V. parahaemolyticus has been widespread in both clinical and environmental isolates. Therefore, it is of great significance to characterize the mechanism of streptomycin resistance in V. parahaemolyticus. O10:K4 has emerged and becoming the new dominant serotype since 2020. In this study, we isolated a total of 36 strains of V. parahaemolyticus O10:K4 from 2020 to 2022 and
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Population genetics of Aedes albopictus in the port cities of Hainan Island and Leizhou Peninsula, China Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-12-16 Minghui Zhao, Xin Ran, Dan Xing, Wei Liu, Zu Ma, Yun Liao, Qiang Zhang, Yu Bai, Lan Liu, Kan Chen, Mingyu Wu, Jian Gao, Hengduan Zhang, Tongyan Zhao
Background Aedes albopictus is an important vector of arboviral diseases, transmitting yellow fever, dengue fever, chikungunya and Zika. Monitoring its population genetic diversity and genetic differentiation has become essential for the control of infectious disease epidemics, especially in the functional areas of ports of entry. Population genetic monitoring of Ae. albopictus in the port area can
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Phyllocoptes parviflori is a distinct species and a vector of the pervasive blackberry leaf mottle associated virus Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-12-09 Tobiasz Druciarek, Andrea Sierra-Mejia, Stanislaw K. Zagrodzki, Shivani Singh, Thien Ho, Mariusz Lewandowski, Ioannis E. Tzanetakis
Several viruses are transmitted by eriophyid mites (Acariformes: Eriophyoidea) including blackberry leaf mottle-associated emaravirus (BLMaV) (Emaravirus rubi). BLMaV is transmitted by an unidentified eriophyid species and is involved in blackberry yellow vein, a devastating disease in the southeastern United States. In this study, we assessed the eriophyid mite Phylocoptes parviflori as a vector of
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Genomic characterization of Mycobacterium lepromatosis from ENL patients from India Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-12-04 Itu Singh, Vinay Kumar Pathak, Mallika Lavania, Madhvi Ahuja, Rahul Sharma, Tarun Narang, Sejal Jain, Ravindra P. Turankar, Sunil Dogra, U. Sengupta
Background Leprosy is caused by Mycobacterium leprae and Mycobacterium lepromatosis. Both organisms cannot be cultured in vitro. M. lepromatosis was found to be associated mainly with diffuse lepromatous leprosy and with Lucio's phenomena initially. Later, M. lepromatosis was observed in borderline leprosy cases (BL), lepromatous leprosy cases (LL) and leprosy reactional cases (T1R and ENL). Although
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The E6 gene polymorphism of Human papillomavirus 16 in relation to the risk of cervical cancer in Tunisian women Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-12-02 Rahima Bel Haj Rhouma, Monia Ardhaoui, Houcemeddine Othman, Zeineb Ben Jemia, Amira Zine El Abidine, Emna Fehri, Kaouther Ouerheni, Thalja Laassili, Haifa Tounsi, Ikram Guizani, Med Samir Boubaker, Emna Ennaifer
Human papillomavirus type 16 (HPV-16) is the most prevalent HPV type worldwide and in Tunisia and the major carcinogenic HPV type found in cervical precancers and cancers. Previous studies have reported that genetic diversity of HPV16-E6 oncoprotein might be associated with cervical intraepithelial neoplasia progression. In this study we aimed to investigate the prevalence of HPV-16 E6 variants in
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Genomic transmission clusters and circulating lineages of Mycobacterium tuberculosis among refugees residing in refugee camps in Ethiopia Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-11-25 Abyot Meaza, Emmanuel Riviere, Zegeye Bonsa, Vincent Rennie, Gebremedhin Gebremicael, Miguel de Diego-Fuertes, Conor J. Meehan, Girmay Medhin, Gemeda Abebe, Gobena Ameni, Annelies Van Rie, Balako Gumi
Background Understanding the transmission dynamics of Mycobacterium tuberculosis (Mtb) could benefit the design of tuberculosis (TB) prevention and control strategies for refugee populations. Whole Genome Sequencing (WGS) has not yet been used to document the Mtb transmission dynamics among refugees in Ethiopia. We applied WGS to accurately identify transmission clusters and Mtb lineages among TB cases
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Plasmodium falciparum population structure and genetic diversity of cell traversal protein for ookinetes and sporozoites (CelTOS) during malaria resurgences in Dielmo, Senegal Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-11-28 Amélé Nyedzie Wotodjo, Mary Aigbiremo Oboh, Cheikh Sokhna, Nafissatou Diagne, Fatoumata Diène-Sarr, Jean-François Trape, Souleymane Doucouré, Alfred Amambua-Ngwa, Umberto D'Alessandro
The ability to accurately measure the intensity of malaria transmission in areas with low transmission is extremely important to guide elimination efforts. Plasmodium falciparum Cell-traversal protein for ookinetes and sporozoites (PfCelTOS) is an important conserved sporozoite antigen reported as one of the promising malaria vaccine candidates, and could be used to estimate malaria transmission intensity
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Quantitative trait loci mapping for survival of virus infection and virus levels in honey bees Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-11-28 Robert X. Lu, Shilpi Bhatia, Michael Simone-Finstrom, Olav Rueppell
Israeli acute paralysis virus (IAPV) is a highly virulent, Varroa-vectored virus that is of global concern for honey bee health. Little is known about the genetic basis of honey bees to withstand infection with IAPV or other viruses. We set up and analyzed a backcross between preselected honey bee colonies of low and high IAPV susceptibility to identify quantitative trait loci (QTL) associated with
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Nasal staphylococci microbiota and resistome in healthy adults in La Rioja, northern Spain: High frequency of toxigenic S. aureus and MSSA-CC398 subclade Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-11-25 Idris Nasir Abdullahi, Carmen Lozano, Myriam Zarazaga, Islem Trabelsi, Rine Christopher Reuben, Marc Stegger, Carmen Torres
This study determined the nasal staphylococci diversity and characterized their resistome, with a focus on the mobilome of methicillin-susceptible Staphylococcus aureus (MSSA)-CC398 subclade from healthy adults in La Rioja (northern Spain). Nasal staphylococci recovered from 57 healthy individuals (HI) were identified (MALDI-TOF-MS) and their antimicrobial resistance, virulence determinants and genetic
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MALDI-TOF MS analysis of Burkholderia pseudomallei and closely related species isolated from soils and water in Khon Kaen, Thailand Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-11-22 Nut Nithimongkolchai, Yothin Hinwan, Benjawan Kaewseekhao, Pisit Chareonsudjai, Pipat Reungsang, Ratthaphol Kraiklang, Sorujsiri Chareonsudjai, Lumyai Wonglakorn, Ploenchan Chetchotisakd, Auttawit Sirichoat, Arnone Nithichanon, Kiatichai Faksri
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High throughput sequencing technology reveals alteration of lower respiratory tract microbiome in severe aspiration pneumonia and its association with inflammation Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-11-22 Pengfei Wang, Junming Wang, Lina Wang, Jiang Lv, Yiru Shao, Daikun He
Background Aspiration pneumonia is a common and severe clinical condition. The microbiome present in the lower respiratory tract plays a crucial role in regulating human inflammatory response. However, the relationship between the altered lower respiratory tract microbiome and inflammation in aspiration pneumonia remains inadequately explored. Purpose To investigate the alteration of the lower respiratory
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Genomic characterization of extended spectrum beta lactamases producing multidrug-resistant Escherichia coli clinically isolated harboring chromosomally mediated CTX-M-15 from Alkharj, KSA Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-11-15 Ehssan Moglad, Hisham N. Altayb
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Disentangling archaic introgression and genomic signatures of selection at human immunity genes Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-11-15 Alina Urnikyte, Abigaile Masiulyte, Laura Pranckeniene, Vaidutis Kučinskas
Pathogens and infectious diseases have imposed exceptionally strong selective pressure on ancient and modern human genomes and contributed to the current variation in many genes. There is evidence that modern humans acquired immune variants through interbreeding with ancient hominins, but the impact of such variants on human traits is not fully understood. The main objectives of this research were
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Genetic diversity of Echinococcus multilocularis specimens isolated from Belgian patients with alveolar echinococcosis using EmsB microsatellites analysis Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-11-20 Rosalie Sacheli, Jenny Knapp, Caroline Pholien, Sabrina Egrek, Philippe Léonard, Jean-Baptiste Giot, Bénédicte Delaere, Noella Blétard, Stéphanie Gofflot, Marie-Cécile Nollevaux, Paul Meunier, Pierre Lovinfosse, Benoit Pirotte, Carine Truyens, Laurence Millon, Olivier Detry, Marie-Pierre Hayette
The genetic diversity of Echinococcus multilocularis (E. multilocularis) specimens isolated from patients with alveolar echinococcosis (AE), is a major field of investigation to correlate with sources of infection, clinical manifestations and prognosis of the disease. Molecular markers able to distinguish samples are commonly used worldwide, including the EmsB microsatellite. Here, we report the use
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Genetic markers of Chlamydia pecorum virulence in ruminants support short term host-pathogen evolutionary relationships in the koala, Phascolarctos cinereus Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-11-15 Cristina M. Fernandez, Mark B. Krockenberger, Mathew S. Crowther, Valentina S.A. Mella, Lachlan Wilmott, Damien P. Higgins
In ruminants infected with Chlamydia pecorum, shorter lengths of coding tandem repeats (CTR) within two genes, the inclusion membrane protein (incA) and Type III secretor protein (ORF663), have been previously associated with pathogenic outcomes. In other chlamydial species, the presence of a chlamydial plasmid has been linked to heightened virulence, and the plasmid is not ubiquitous in C. pecorum
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Assessing the association between the circulating levels of inflammatory cytokines and the risk of tuberculosis: A bidirectional two-sample mendelian randomization study Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-11-11 Shun-Xian Zhang, Zhen-Hui Lu, Mei-Ti Wang, Yu-Ping Shen, Lei Duan, Shi-Yang Guan, Mu-Xin Chen, Yan Lu, Ming Yang, Lei Wang, Guo-Bing Yang, Wen-Wen Lv, Ji-Chun Wang, Jin-Xin Zheng
Background Numerous observational studies have previously reported an association between inflammatory cytokines and tuberculosis (TB). However, the causal relationship between these factors remains unclear. Consequently, we conducted two-sample Mendelian randomization (MR) analyses to ascertain the causal link between levels of inflammatory cytokines and the risk of TB. Methods Single nucleotide polymorphisms
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Genetic variants associated with hantavirus infection in a reservoir host are related to regulation of inflammation and immune surveillance Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-11-11 Anna A. Pérez-Umphrey, Amie E. Settlecowski, Jean P. Elbers, S. Tyler Williams, Colleen B. Jonsson, Andrea Bonisoli-Alquati, Allison M. Snider, Sabrina S. Taylor
The immunogenetics of wildlife populations influence the epidemiology and evolutionary dynamic of the host-pathogen system. Profiling immune gene diversity present in wildlife may be especially important for those species that, while not at risk of disease or extinction themselves, are host to diseases that are a threat to humans, other wildlife, or livestock. Hantaviruses (genus: Orthohantavirus)
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Expanding the knowledge frontier of mitoviruses in Cannabis sativa Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-11-07 Juliana Lopez-Jimenez, Jorge Herrera, Juan F. Alzate
Mitoviruses were initially known for their presence in the mitochondria of fungi and were considered exclusive to these organisms. However, recent studies have shown that they are also present in a large number of plant species. Despite the potential impact that mitoviruses might have on the mitochondria of plant cells, there is a lack of information about these ancient RNA viruses, especially within
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In silico prediction of interaction between Nipah virus attachment glycoprotein and host cell receptors Ephrin-B2 and Ephrin-B3 in domestic and peridomestic mammals Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-11-02 Ananya Ferdous Hoque, Md. Mahfuzur Rahman, Ayeasha Siddika Lamia, Ariful Islam, John D. Klena, Syed Moinuddin Satter, Jonathan H. Epstein, Joel M. Montgomery, Mohammad Enayet Hossain, Tahmina Shirin, Iqbal Kabir Jahid, Mohammed Ziaur Rahman
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Increased prevalence of pretreatment drug resistance mutations in treatment-naïve people living with HIV-1 in Henan Province, China (2022/23) Infect. Genet. Evol. (IF 3.2) Pub Date : 2023-10-26 Jinjin Liu, Chunli Liu, Yanli Wang, Shuguang Wei, Jie Ma, Yuanyuan Li, Xuhui Chen, Qingxia Zhao, Yuqi Huo
Human deficiency virus type 1 (HIV-1) harboring drug resistance mutations (DRMs) before the initiation of antiretroviral therapy (ART) poses a serious threat to the efficacy of current ART regimens. Currently, the prevalence of pre-treatment drug resistance mutations (PDRMs) including transmitted DRMs (TDRMs) is not completely clear. Understanding this prevalence better should offer valuable data for