Frequent Lineage Research Articles

Whole-genome comparative analysis of the genetic, virulence and antimicrobial resistance diversity of Campylobacter spp. from Spain

Whole-Genome Sequencing has the potential to be an effective method for surveillance and control of foodborne diseases. This study aims to determine the genetic relatedness and prevalence of virulence-associated genes and antimicrobial resistance determinants in 135 Campylobacter jejuni, seven Campylobacter coli and three Campylobacter lari isolates from the poultry supply chain and hospital in Spain. The isolates showed a wide genetic diversity between and within species with Clonal Complex 21 the most frequent lineage found. Among species, C. jejuni showed the highest prevalence of virulence genes (287/333) in which a high occurring variability was observed in the capsule biosynthesis and transport, O-linked flagellar glycosylation and lipooligosaccharide biosynthesis loci, with a great impact of phase-variation that led to 72 different virulence gene patterns among all isolates. High prevalence (> 90 %) of blaOXA-type β-lactamase genes and mutations in DNA gyrase gene associated with fluoroquinolones resistance were observed, and at a frequency similar to the tet(O) gene in C. jejuni (93 %) and C. coli (86 %), both of which also harboured resistance determinants to aminoglycosides with a higher occurrence rate in C. coli (43 %), that was the only species in which mutations in the 23S ribosomal subunit conferring resistance to erythromycin were identified (43 %). The present study constitutes the largest genomic survey of Campylobacter isolates in Spain providing insight into the prevalence and diversity of the pathogen along the poultry supply chain in the country.

Genetic Diversity of Mycobacterium tuberculosis Strains Isolated from HIV-Infected Patients in Mexico.

There has been very limited investigation regarding the genetic diversity of Mycobacterium tuberculosis (MTb) strains isolated from human immunodeficiency virus (HIV)-infected patients in Mexico. In this study, we isolated 93 MTb strains from pulmonary and extrapulmonary samples of HIV-infected patients treated in a public hospital in Mexico City to evaluate the genetic diversity using spoligotyping and mycobacterial interspersed repetitive unit-variable-number tandem-repeat (MIRU-VNTR) typing (based on 24 loci). The cohort comprised 80 male and 13 female individuals. There was a positive correlation between a high HIV viral load (>100,000 copies) and extrapulmonary tuberculosis (TB) (r = 0.306, p = 0.008). Lineage 4 was the most frequent lineage (79 strains). In this lineage, we found the H clade (n = 24), including the Haarlem, H3, and H1 families; the T clade (n = 22), including T1 and T2; the X clade (n = 15), including X1 and X3; the LAM clade (n = 14), including LAM1, LAM2, LAM3, LAM6, and LAM9; the S clade (n = 2); Uganda (n = 1); and Ghana (n = 1). We also found 12 strains in the EAI clade belonging to lineage 1, including the EAI2-Manila and EAI5 families. Interestingly, we identified one strain belonging to the Beijing family, which is part of lineage 2. One strain could not be identified. This study reports high genetic diversity among MTb strains, highlighting the need for a molecular epidemiological surveillance system that can help to monitor the spread of these strains, leading to more appropriate measures for TB control in HIV-infected patients.

Whole Genome Sequence Dataset of Mycobacterium tuberculosis Strains from Patients of Campania Region

Tuberculosis (TB) is one of the deadliest infectious disorders in the world. To effectively TB manage, an essential step is to gain insight into the lineage of Mycobacterium tuberculosis (MTB) and the distribution of drug resistance. Although the Campania region is declared a cluster area for the infection, to contribute to the effort to understand TB evolution and transmission, still poorly known, we have generated a dataset of 159 genomes of MTB strains, from Campania region collected during 2018–2021, obtained from the analysis of whole genome sequence. The results show that the most frequent MTB lineage is the 4 according for 129 strains (81.11%). Regarding drug resistance, 139 strains (87.4%) were classified as multi susceptible, while the remaining 20 (12.58%) showed drug resistance. Among the drug-resistance strains, 8 were isoniazid-resistant MTB, 4 multidrug-resistant MTB, while only one was classified as pre-extensively drug-resistant MTB. This dataset expands the existing available knowledge on drug resistance and evolution of MTB, contributing to further TB-related genomics studies to improve the management of this disease.

Dynamics of the MRSA Population in a Chilean Hospital: a Phylogenomic Analysis (2000-2016).

The global dissemination of methicillin-resistant Staphylococcus aureus (MRSA) is associated with the emergence and establishment of clones in specific geographic areas. The Chilean-Cordobes clone (ChC) (ST5-SCCmecI) has been the predominant MRSA clone in Chile since its first description in 1998, despite the report of other emerging MRSA clones in recent years. Here, we characterize the evolutionary history of MRSA from 2000 to 2016 in a Chilean tertiary health care center using phylogenomic analyses. We sequenced 469 MRSA isolates collected between 2000 and 2016. We evaluated the temporal trends of the circulating clones and performed a phylogenomic reconstruction to characterize the clonal dynamics. We found a significant increase in the diversity and richness of sequence types (STs; Spearman r = 0.8748, P < 0.0001) with a Shannon diversity index increasing from 0.221 in the year 2000 to 1.33 in 2016, and an effective diversity (Hill number; q = 2) increasing from 1.12 to 2.71. The temporal trend analysis revealed that in the period 2000 to 2003 most of the isolates (94.2%; n = 98) belonged to the ChC clone. However, since then, the frequency of the ChC clone has decreased over time, accounting for 52% of the collection in the 2013 to 2016 period. This decline was accompanied by the rise of two emerging MRSA lineages, ST105-SCCmecII and ST72-SCCmecVI. In conclusion, the ChC clone remains the most frequent MRSA lineage, but this lineage is gradually being replaced by several emerging clones, the most important of which is clone ST105-SCCmecII. To the best of our knowledge, this is the largest study of MRSA clonal dynamics performed in South America. IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is a major public health pathogen that disseminates through the emergence of successful dominant clones in specific geographic regions. Knowledge of the dissemination and molecular epidemiology of MRSA in Latin America is scarce and is largely based on small studies or more limited typing techniques that lack the resolution to represent an accurate description of the genomic landscape. We used whole-genome sequencing to study 469 MRSA isolates collected between 2000 and 2016 in Chile providing the largest and most detailed study of clonal dynamics of MRSA in South America to date. We found a significant increase in the diversity of MRSA clones circulating over the 17-year study period. Additionally, we describe the emergence of two novel clones (ST105-SCCmecII and ST72-SCCmecVI), which have been gradually increasing in frequency over time. Our results drastically improve our understanding of the dissemination and update our knowledge about MRSA in Latin America.

Methicillin-resistant and methicillin-sensitive Staphylococcus aureus in pork industry workers, Catalonia, Spain

BackgroundMethicillin-resistant S. aureus (MRSA) especially ST398, is a zoonotic agent. This study aimed to determine the prevalence of methicillin-susceptible S. aureus (MSSA) and MRSA among workers in the pork production chain. Methods659 workers associated with 123 pig farms, livestock transporters, one pig slaughterhouse, pork transporters and 23 pork butcheries were studied for S. aureus recovery, and all isolates were characterized (antibiotic resistance, MLST and spa-typing). ResultsThe prevalence of S. aureus was 35.5%, 75.6% of isolates being MRSA. The prevalence of MRSA was 68.7% (149/217) among pig farm, 33.9% (19/56) livestock transporters, 2.9% (9/306) slaughterhouse, 0% in pork transporters (0/36) and butchery workers (0/44). Of the 234 S. aureus-positive workers, 100% (149/149) of pig farm workers, 82.6% (19/23) of livestock transporters, and 16.4% (9/55) of slaughterhouse workers carried MRSA isolates (p < 0.001). Of the workers who had contact with live swine, 61.8% (178/288) were S. aureus-positive, MRSA being detected in 96.1% of cases (p < 0.001). The most frequent lineage among MRSA were: ST398 (97.7%; 173/177) and ST1 (1.7%; 3/177); and among MSSA were ST30 (19.2%; 11/57) and ST5 (10.5%; 6/57). The most frequent spa-types among MRSA were t011 (93.8%, 166/177) and t1451 (2.25%, 4/177), and among MSSA: t084 (10.5%, 6/57) and t021 (7.0%, 4/57). All MRSA isolates showed resistance to tetracycline, 92.7% to clindamycin, 81.9% to erythromycin and 40.1% to cotrimoxazole. ConclusionsPig industry workers having occupational contact with live animals present a high risk of colonization of MRSA, especially by MRSA-ST398. Prevention measures should be intensified in any employment sector involving live animals.

Lineages and Sublineages of Human Papillomavirus Type 16 in Cervical Samples of Iranian Women

Aim: This study was designed to analyze intratypic variations of human papillomavirus type 16 (HPV16) and to assess the risk of these variants for progression to cervical cancer. Materials &amp; Methods: HPV16 variants of 58 women were determined by PCR-directed sequencing. Results: The most frequent lineage was D (67.2%) followed by A (32.8%). Lineage A was found predominantly in normal (62.5%) and cervical intraepithelial neoplasia-1 (CIN-1) (83.3%), while lineage D was the most prevalent variant in cervical cancer (100%). Conclusion: The present study revealed a distinct pattern of HPV16 variants in Iran. Based on our data, the predominant HPV16 lineage was D and there was a significant association between lineage D variants and cervical cancer.

Genotypic Characteristics and Antimicrobial Resistance of Escherichia coli ST141 Clonal Group

Escherichia coli ST141 is one of the ExPEC lineages whose incidence is rising in France, even if no epidemic situation involving multidrug resistant isolates has been reported so far. Nonetheless, in a 2015-2017 monocentric study conducted in our French University hospital, ST141 was the most frequent lineage after ST131 in our collection of phylogroup B2 ESBL-producing E. coli. The genomes of 187 isolates representing ST141 group, including 170 genomes from public databases and 17 from our local collection, of which 13 produced ESBL, were analyzed to infer the maximum likelihood phylogeny SNP-based (Single Nucleotide Polymorphism) free-recombinant tree defining the ST141 population structure. Genomes were screened for genes encoding virulence factors (VFs) and antimicrobial resistance (AMR). We also evaluated the distribution of isolates according to their origin (host, disease, country) and the distribution of VFs or AMR genes. Finally, the phylogenic tree revealed that ST141 isolates clustered into two main sublineages, with low genetic diversity. Contrasting with a highly virulent profile, as many isolates accumulated VFs, the prevalence of AMR was limited, with no evidence of multidrug resistant emerging lineage. However, our results suggest that surveillance of this clonal group, which has the potential to spread widely in the community, would be essential.

Identifying SARS-CoV-2 Lineage Mutation Hallmarks and Correlating Them With Clinical Outcomes in Egypt: A Pilot Study.

The SARS-CoV-2 pandemic has led to over 4.9 million deaths as of October 2021. One of the main challenges of creating vaccines, treatment, or diagnostic tools for the virus is its mutations and emerging variants. A couple of variants were declared as more virulent and infectious than others. Some approaches were used as nomenclature for SARS-CoV-2 variants and lineages. One of the most used is the Pangolin nomenclature. In our study, we enrolled 35 confirmed SARS-CoV-2 patients and sequenced the viral RNA in their samples. We also aimed to highlight the hallmark mutations in the most frequent lineage. We identified a seven-mutation signature for the SARS-CoV-2 C36 lineage, detected in 56 countries and an emerging lineage in Egypt. In addition, we identified one mutation which was highly negatively correlated with the lineage. On the other hand, we found no significant correlation between our clinical outcomes and the C36 lineage. In conclusion, the C36 lineage is an emerging SARS-CoV-2 variant that needs more investigation regarding its clinical outcomes compared to other strains. Our study paves the way for easier diagnosis of variants of concern using mutation signatures.

Insights from a comprehensive study of Trypanosoma cruzi: A new mitochondrial clade restricted to North and Central America and genetic structure of TcI in the region.

More than 100 years since the first description of Chagas Disease and with over 29,000 new cases annually due to vector transmission (in 2010), American Trypanosomiasis remains a Neglected Tropical Disease (NTD). This study presents the most comprehensive Trypanosoma cruzi sampling in terms of geographic locations and triatomine species analyzed to date and includes both nuclear and mitochondrial genomes. This addresses the gap of information from North and Central America. We incorporate new and previously published DNA sequence data from two mitochondrial genes, Cytochrome oxidase II (COII) and NADH dehydrogenase subunit 1 (ND1). These T. cruzi samples were collected over a broad geographic range including 111 parasite DNA samples extracted from triatomines newly collected across North and Central America, all of which were infected with T. cruzi in their natural environment. In addition, we present parasite reduced representation (Restriction site Associated DNA markers, RAD-tag) genomic nuclear data combined with the mitochondrial gene sequences for a subset of the triatomines (27 specimens) collected from Guatemala and El Salvador. Our mitochondrial phylogenetic reconstruction revealed two of the major mitochondrial lineages circulating across North and Central America, as well as the first ever mitochondrial data for TcBat from a triatomine collected in Central America. Our data also show that within mtTcIII, North and Central America represent an independent, distinct clade from South America, named here as mtTcIIINA-CA, geographically restricted to North and Central America. Lastly, the most frequent lineage detected across North and Central America, mtTcI, was also an independent, distinct clade from South America, noted as mtTcINA-CA. Furthermore, nuclear genome data based on Single Nucleotide Polymorphism (SNP) showed genetic structure of lineage TcI from specimens collected in Guatemala and El Salvador supporting the hypothesis that genetic diversity at a local scale has a geographical component. Our multiscale analysis contributes to the understanding of the independent and distinct evolution of T. cruzi lineages in North and Central America regions.

666. Molecular Epidemiology of Methicillin-Resistant Staphylococcus aureus in Chile between 1999-2018

BackgroundThe global spread of methicillin-resistant Staphylococcus aureus (MRSA) is associated with distinct genetic lineages that predominate in specific geographical regions. Available evidence suggests the Chilean-Cordobes clone (ChC), an ST5-SCCmecI lineage, has largely predominated in Chilean hospitals since its first description in the late 1990’s. Although the circulation of other MRSA lineages, including community-associated clones, has been well documented, the dynamics of clonal replacement over time has not been explored. Therefore, we aimed to study the molecular epidemiology and dynamics of clonal replacement using a large collection of clinical MRSA strains recovered from Chile during the last two decades.MethodsWe used whole-genome sequencing (WGS) and core-based phylogenomic analysis to identify genetic lineages and explore their relationship in 798 MRSA isolates obtained between 1999-2018 from two tertiary-care Chilean hospitals. ResultsOverall, the most frequently identified clones were the ST5-SCCmecI ChC (n=476, 60%), followed by ST105-SCCmecII (n=119, 15%), ST72-SCCmecIV (n=74, 9%), and ST8-SCCmecII (n=26, 3%). Phylogenomic reconstruction demonstrated 7 major clades: Clade I (CC30); Clade II (CC22); Clade III (CC97); Clade IV (CC8); Clade V (ST72); Clade VI (CC5/ST225 and ST105) and Clade VII (CC5/ST5-SCCmecI) (Fig. 1). The ChC clone remained the most frequent MRSA lineage throughout the study period (Fig. 2). However, its relative abundance decreased from >90% of isolates in 1999 to ca. 40% in 2018. This decrease began around 2005 and was associated with a progressive expansion of the ST105-SCCmecII and ST72-SCCmecIV lineages (Fig. 2). A Bayesian molecular clock analysis established the most recent common ancestor in 1964 (95% HPD interval=1961.975-1966.218) and corroborated a CC5 expansion event starting in Chile in 1999 (Fig. 3). Interestingly, our analyses revealed two branches within the ST5-SCCmecI lineage: one predominating in 1999-2006, and a more recent branch (related to the ST105-SCCmecII clone) that emerged around 2008. Figure 1. Core genome phylogenomic reconstruction of the 798 MRSA isolates. The seven major clades are represented by colored sections. The Clade I (purple section) was composed of isolates belonging to the CC30. Clade II (cyan section) includes four isolates of CC22. Clade III (red section) is composed of isolates of CC97. Clade IV (blue section) grouped isolates of different ST239 and ST8, belonging to the CC8. Clade V (orange section) includes isolates of ST72. Clade VI (yellow section) includes isolates of ST225 and ST105, both belonging to CC5. Clade VII (green section) is mostly composed of isolates of ST5-SCCmecI. The inner ring shows the ST of the isolates; the external ring shows the staphylococcal chromosomal cassette mec (SCCmec) type.Figure 2. Relative frequency of MRSA clones from 1999 to 2018. The genomes were grouped according to their isolation dates. Most frequent MRSA clones are represented by colored sections.Figure 3. Maximum clade credibility tree from the molecular clock analysis of the 798 MRSA genomes. A Bayesian molecular clock analysis was performed with BEAST using the isolation date of each genome as a calibrator. The colored strip showed the most frequent clones. The red dot shows a major event of divergence in 2008.ConclusionThe ChC clone remains the most prevalent MRSA in Chile. However, our data is consistent with the evolution of this clone and a progressive replacement of with ST105 and ST72 genetic lineages. Disclosures Lorena Diaz, PhD , Nothing to disclose Cesar A. Arias, M.D., MSc, Ph.D., FIDSA, Entasis Therapeutics (Grant/Research Support)MeMed Diagnostics (Grant/Research Support)Merk (Grant/Research Support)

Genomic surveillance of invasive Streptococcus pneumoniae isolates in the period pre-PCV10 and post-PCV10 introduction in Brazil.

In 2010, Brazil introduced the 10-valent pneumococcal conjugate vaccine (PCV10) into the national children’s immunization programme. This study describes the genetic characteristics of invasive Streptococcus pneumoniae isolates before and after PCV10 introduction. A subset of 466 [pre-PCV10 (2008–2009): n=232, post-PCV10 (2012–2013): n=234;<5 years old: n=310, ≥5 years old: n=156] pneumococcal isolates, collected through national laboratory surveillance, were whole-genome sequenced (WGS) to determine serotype, pilus locus, antimicrobial resistance and genetic lineages. Following PCV10 introduction, in the <5 years age group, non-vaccine serotypes (NVT) serotype 3 and serotype 19A were the most frequent, and serotypes 12F, 8 and 9 N in the ≥5 years old group. The study identified 65 Global Pneumococcal Sequence Clusters (GPSCs): 49 (88 %) were GPSCs previously described and 16 (12 %) were Brazilian clusters. In total, 36 GPSCs (55 %) were NVT lineages, 18 (28 %) vaccine serotypes (VT) and 11 (17 %) were both VT and NVT lineages. In both sampling periods, the most frequent lineage was GPSC6 (CC156, serotypes 14/9V). In the <5 years old group, a decrease in penicillin (P=0.0123) and cotrimoxazole (P<0.0001) resistance and an increase in tetracycline (P=0.019) were observed. Penicillin nonsusceptibility was predicted in 40 % of the isolates; 127 PBP combinations were identified (51 predicted MIC≥0.125 mg l−1); cotrimoxazole (folA and/or folP alterations), macrolide (mef and/or ermB) and tetracycline (tetM, tetO or tetS/M) resistance were predicted in 63, 13 and 21.6 % of pneumococci studied, respectively. The main lineages associated with multidrug resistance in the post-PCV10 period were composed of NVT, GPSC1 (CC320, serotype 19A), and GPSC47 (ST386, serotype 6C). The study provides a baseline for future comparisons and identified important NVT lineages in the post-PCV10 period in Brazil.

Central Nervous System Injury in Patients With Severe Acute Respiratory Syndrome Coronavirus 2: MRI Findings

Due to the presence of a new and rapidly spreading coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the World Health Organization declared the coronavirus disease 2019 (COVID-19) outbreak a pandemic on March 11, 2020. This new disease has a multisystemic effect that predominantly targets the respiratory system; however, neurologic symptoms have been documented in approximately 36% of patients with confirmed COVID-19. During the period of March 2020 to March 2021, 481 brain MRI studies were performed by medical request. Of these, 9.7% (n = 47) were hospitalized with a diagnosis of COVID-19 pneumonia confirmed by SARS-CoV-2 reverse transcriptase-polymerase chain reaction (RT-PCR) test with the following findings: microbleeds, osmotic demyelination, arterial thrombosis, ischemic infarcts, venous thrombosis, metabolic cerebellar syndrome, posterior reversible leukoencephalopathy, abnormal signal intensity in the frontal lobes and olfactory bulbs, microangiopathy, gliosis, and findings consistent with hypoxic-ischemic encephalopathy. In patients with histories of malignant central nervous system (CNS) tumors, the most frequent histological lineage being high-grade glioma, 100% progression was identified with respect to previous imaging studies, without other significant findings. In two patients, a brain MRI was performed due to altered alertness, identifying only involutive changes in the brain parenchyma; MRI was repeated 72 hours later, after a lack of improvement in higher functions, without identifying imaging findings. To date, limited studies have documented CNS abnormalities related to COVID-19 using MRI. Therefore, the purpose of this study is to present abnormal imaging findings in patients with SARS-CoV-2 infection and their clinical correlations.

Reconstruction of ancestral karyotype illuminates chromosome evolution in the genus Cucumis.

Karyotype dynamics driven by complex chromosome rearrangements constitute a fundamental issue in evolutionary genetics. The evolutionary events underlying karyotype diversity within plant genera, however, have rarely been reconstructed from a computed ancestral progenitor. Here, we developed a method to rapidly and accurately represent extant karyotypes with the genus, Cucumis, using highly customizable comparative oligo-painting (COP) allowing visualization of fine-scale genome structures of eight Cucumis species from both African-origin and Asian-origin clades. Based on COP data, an evolutionary framework containing a genus-level ancestral karyotype was reconstructed, allowing elucidation of the evolutionary events that account for the origin of these diverse genomes within Cucumis. Our results characterize the cryptic rearrangement hotspots on ancestral chromosomes, and demonstrate that the ancestral Cucumis karyotype (n=12) evolved to extant Cucumis genomes by hybridizations and frequent lineage- and species-specific genome reshuffling. Relative to the African species, the Asian species, including melon (Cucumis melo, n=12), Cucumis hystrix (n=12) and cucumber (Cucumis sativus, n=7), had highly shuffled genomes caused by large-scale inversions, centromere repositioning and chromothripsis-like rearrangement. The deduced reconstructed ancestral karyotype for the genus allowed us to propose evolutionary trajectories and specific events underlying the origin of these Cucumis species. Our findings highlight that the partitioned evolutionary plasticity of Cucumis karyotype is primarily located in the centromere-proximal regions marked by rearrangement hotspots, which can potentially serve as a reservoir for chromosome evolution due to their fragility.

Genetic variability of human papillomavirus type 39 based on E6, E7 and L1 genes in Southwest China

BackgroundHuman papillomavirus type 39 associated with genital intraepithelial neoplasia and invasive cancers, has a high prevalence in Southwest China. HPV E6, E7 are two main papillomavirus oncoproteins, closely relate to the function of HPV immortalization, cell transformation, and carcinogenesis. L1 is the major capsid protein, can reflect the replication status of the virus in cells and the progression of cervical lesions. The purpose of this study is to reveal the prevalence of HPV 39 and the genetic polymorphisms of HPV39 based on E6, E7 and L1 gene in southwest China.MethodsCell samples were collected by cervical scraped for HPV detecting and typing, and HPV39 positive samples were selected out. Important E6, E7 and L1 genes of HPV39 were sequenced and analyzed for the study of HPV39 genetic polymorphisms. Phylogenetic trees were constructed by Maximum-likelihood and Kimura 2-parameters methods in Molecular Evolutionary Genetics Analysis version 6.0. The selection pressures of E6, E7 and L1 genes were estimated by Datamonkey web server. The secondary and three-dimensional structure of HPV39 E6, E7 proteins were created by sopma server and SWISS-MODEL software.Results344 HPV39 positive samples were selected from 5718 HPV positive cell samples. Among HPV39 E6-E7 sequences, 20 single nucleotide mutations were detected, including 10 non-synonymous and 10 synonymous mutations; 26 single nucleotide mutations were detected in HPV39 L1 sequences, including 7 non-synonymous and 19 synonymous mutations respectively. 11 novel variants of HPV39 E6-E7 (5 in E6 and 6 in E7) and 14 novel variants of HPV39 L1 were identified in this study. A-branch was the most frequent HPV39 lineage in southwest China during our investigation. Selective pressure analysis showed that codon sites 26, 87, 151 in E6 and 75, 180, 222, 272, 284, 346, 356 in L1 were positively selected sites, as well as codon sites 45, 138, 309, 381 were negative selection sites in L1 gene, E7 has neither positive selection sites nor negative selection sites. A certain degree of secondary and three-dimensional structure dislocation was existed due to the non-synonymous mutations.ConclusionsAmino acid substitution affected the secondary and three-dimensional structure of HPV39, and resulting in the differences of carcinogenic potential and biological functions as well as the immune response due to the antigen epitopes difference, the antigen epitopes with stronger adaptability in Southwest will be screened out based on the above research results for the later vaccine development. And gene polymorphism of HPV39 in Southwest China may improve the effectiveness of clinical test and vaccine design, specifically for women in Southwest China.

Tumores malignos de las glándulas salivales: estudio retrospectivo de los pacientes tratados en el Hospital La Paz, entre 2008 y 2018

ABSTRACT Introduction: Salivary gland tumors are rare malignant neoplasms, with a higher incidence in the parotid gland. Despite their low incidence, the possible complications derived from them can lead to high comorbidity in patients. Methods: We conducted a retrospective, observational and descriptive study of 105 patients diagnosed with malignant neoplasms of the salivary glands at the Hospital Universitario La Paz. 102 correspond to primary tumors and 3 of them are metastases of pulmonary origin. Results: In our series the parotid gland is the most frequent site. Histologically, adenoid cystic carcinoma is the most common tumor. The 75.23 % of the patients were diagnosed with cytology by fine needle aspiration and puncture (FNA), and the remaining cases with biopsy. The most indicated treatment was surgery, especially for tumors of epithelial lineage. Some 33.5 % received adjuvant treatment. Some 18 % of the patients who suffered post-surgical complications presented facial paralysis. During the course of the disease, 23.80 % of the total developed distant metastases, the lung being the most affected organ. Of the patients, 26.66 % suffered at least one recurrence. Survival at 2 years was 87.6 % and at 5 years 75.3 %. Discussion: Unlike other studies, in our case the most frequent lineage of salivary glands tumors is adenoid cystic carcinoma. This could be explained because our hospital is a reference in facial paralysis. One of the most important points in the management of these patients is not only the local and distant control of the tumor, but also the treatment of possible sequelae.

Lung emphysema and lung cancer: what do we know about it?

Emphysema and lung cancer (LC) are two diseases which share common risk factors, e.g., smoking. In recent years, many studies have sought to analyse this association. By way of illustration, we conducted a review of the scientific literature of the studies published to date, whose main designated aim was to demonstrate the relationship between emphysema and LC, and this association’s influence on the histology, prognosis and molecular mechanisms responsible. We included over 40 studies (ranging from case-control and cohort studies to systematic reviews and meta-analyses), which highlight the association between emphysema and LC, independently of smoking habit. These studies also report a possible influence on histology, with adenocarcinoma being the most frequent lineage, and an association with poor prognosis, which affects both survival and post-operative complications. Oxidative stress, which generates chronic inflammatory status as well as the presence of certain polymorphisms in various genes (CYP1A1, TERT, CLPTM1L, ERK), gives rise—in the case of patients with emphysema—to alteration of cellular repair mechanisms, which in turn favours the proliferation of neoplastic epithelial cells responsible for the origin of LC.

Pleistocene extinctions as drivers of biogeographical patterns on the easternmost Canary Islands

AbstractSubtropical islands are often viewed as refuges where Quaternary climatic shifts driving global episodes of extinction were buffered. Island biodiversity, however, may have been impacted by climatic fluctuations at local scales, particularly in spatially heterogeneous island systems. In this study, we generated a conceptual framework for predicting the potential impact of Pleistocene extinctions on the biogeographical pattern of the Canarian spermatophyte flora, with a focus on the easternmost Canarian islands (ECI). Then, we performed an exhaustive bibliographic revision (270 studies) to examine whether taxonomic, phylogenetic and phylogeographical data support our predictions. Although molecular information is limited for many lineages, the available data suggest that the majority of extant ECI plant taxa may be the result of relatively recent (&lt;1 Ma) dispersal from surrounding insular and mainland areas. Different lines of evidence are compatible with the idea of a Pleistocene period of frequent lineage extirpation on ECI. Extinction may thus have provided new ecological opportunities for recent (re)colonization, with some cases of recent establishment mediated by facilitation. Considering background extinction on ECI, we describe five general patterns of colonization for Canarian plant lineages. In addition to factors related to island ontogeny and long‐distance dispersal, we suggest that Pleistocene extinctions may have significantly contributed to extant biogeographical patterns in the Canarian archipelago, such as the biased distribution ranges of island plants and the low endemic richness on ECI. This new scenario provides testable hypotheses for future studies dealing with the phylogeography, taxonomy and conservation of terrestrial biodiversity on the Canarian islands, and possibly, on other near‐shore islands.

Genetic variability of human papillomavirus type 51 E6, E7, L1 and L2 genes in Southwest China

Genetic variations among HR-HPV types lead to altered biological functions with possible clinical significance in different geographical locations. To explore intratype genetic variations of HPV51 E6, E7, L1 and L2 genes originating from Southwest China, a total of 5204 cervical scraped cell samples were collected for DNA extraction and HPV typing. And then the E6, E7, L1 and L2 genes of HPV51 (n = 79) were sequenced and compared to the reference sequence (M62877). The ConSurf server was used for identification of conserved structural and functional amino acids of the E6 and E7 oncogenes, and the changes of the secondary structure were analyzed by PSIPred software. Phylogenetic trees were constructed by the maximum likelihood method implemented in IQ-TREE. The selection pressure acting on the E6, E7, L1 and L2 genes was estimated by Datamonkey web server. 13 nucleotide polymorphism sites were observed in E6-E7 gene and the most common mutation sites were C395T (S100L), C756T (S66L), C796T, A832G. 36 nucleotide polymorphism sites were identified in full length L1 gene and the non-synonymous mutations T6311G, A6312T (V264G), G6313A (G265S) A5674C (I52L), A6335C (N272T), A6586C (T354P) and synonymous mutations A5649T, C6147T, A6435G, G6570A, A6651G, T6774C, A6784C, A6882G, C6918A, and G6984A were the most common mutations. 53 nucleotide variation sites were identified in full-length L2 gene including four insertion sites (4418A, 4670G, 4693A, 4694C) and one deletion site (A4430). Besides, the non-synonymous mutations G4227A (V32I), A4407G (I92V), G4945A (D271N), C4985A (T284K), T5260G (L376V), A5335C (T401P) and the synonymous mutations A4166G, G4229A, G4283A, T4453C, C4566A, T4596C, C4695T, C4830T, G4839A, A5160C, and T5286G were the most common mutations. Specially, a triallelic mutation site (G4461C/A) in L2 was identified, with 26% G4461C (E109D) being non-synonymous mutation. Selective pressure analysis showed that only codon site 66 in E7 and 52 in L1 were the positively selected sites and codon sites 72, 107, 342, 412, 427 were negatively selected sites in L2 gene. Our investigation also suggests that A2 and A4 were the most frequent HPV51 lineage in Southwest China.

1214. High Frequency of Genes Encoding Resistance to Heavy Metals in Methicillin-Resistant Staphylococcus aureus (MRSA) Endemic Lineages From South America

BackgroundMRSA-USA300 is a community-associated clone that has spread worldwide, becoming the most successful clone in the USA. Since 2005, the MRSA-USA300 Latin-American Variant (USA300-LV) has disseminated in community and hospitals in Northern South America. Phylogenetic analysis revealed that USA300-LV is not derived from the USA300 (NA-USA300) but rather, the two clones diverged from a common ancestor. During their evolution, NA-USA300 strains incorporated the ACME element and USA300-LV acquired a copper and mercury resistance mobile element designated COMER. Interestingly, contamination by heavy metals in South American has been recently highlighted and could be driving the selection of resistant genetic lineages. We investigated the frequency of merA, merB, and copB in genomes of clinical isolates of S. aureus from Latin America (LA).MethodsThe presence of merA/merB and copB encoding mercury and copper resistance, respectively, were investigated in 515 S. aureus sequenced genomes recovered from bacteremic patients in hospitals from nine Latin American hospitals trough BLAST searches.ResultsThe prevalence of merAB in S. aureus was 35% (181 out of 515 genomes). Interestingly, among 181 merAB-positive S. aureus, 174 were MRSA (96%). Moreover, 71%, 60%, 59%, and 51% of MRSA genomes from Peru, Ecuador, Colombia, and Venezuela, respectively, harbored mercury resistance genes. Similarly, 65%, 60%, and 22% of MRSA genomes from Ecuador, Colombia, and Venezuela, contained the copB gene. Among 174 MRSA harboring merAB, ST8 and ST5 were the most predominant lineages in (43% and 45% of genomes, respectively). In contrast, among 95 MRSA carrying copB, ST8 was the most frequent lineage (96% of isolates). MRSA from countries with high prevalence of mercury genes showed association with ST5 and ST8. 88% of Colombian and 87% of Ecuadorian MRSA harboring merAB belonged to ST8 lineage, whereas ST5 was predominant in 88% of Peruvian MRSA. In Venezuela, ST5 and ST8 were found in 44% and 33%, respectively, of MRSA positive for merAB.ConclusionHigh levels of mercury in rivers of Colombia, Ecuador and Peru has been reported. Thus, the prevalence of heavy metal resistance genes in MRSA clinical isolates suggest an adaptation of endemic genotypes to heavy metal contamination caused by activities like metal mining.Disclosures J. M. Munita, Pfizer: Grant Investigator, Research grant. C. Arias, Merck & Co., Inc.: Grant Investigator, Research support. MeMed: Grant Investigator, Research support. Allergan: Grant Investigator, Research support.

Whole Y-chromosome sequences reveal an extremely recent origin of the most common North African paternal lineage E-M183 (M81)

E-M183 (E-M81) is the most frequent paternal lineage in North Africa and thus it must be considered to explore past historical and demographical processes. Here, by using whole Y chromosome sequences from 32 North African individuals, we have identified five new branches within E-M183. The validation of these variants in more than 200 North African samples, from which we also have information of 13 Y-STRs, has revealed a strong resemblance among E-M183 Y-STR haplotypes that pointed to a rapid expansion of this haplogroup. Moreover, for the first time, by using both SNP and STR data, we have provided updated estimates of the times-to-the-most-recent-common-ancestor (TMRCA) for E-M183, which evidenced an extremely recent origin of this haplogroup (2,000–3,000 ya). Our results also showed a lack of population structure within the E-M183 branch, which could be explained by the recent and rapid expansion of this haplogroup. In spite of a reduction in STR heterozygosity towards the West, which would point to an origin in the Near East, ancient DNA evidence together with our TMRCA estimates point to a local origin of E-M183 in NW Africa.