scholarly journals A comparative study of pan-genome methods for microbial organisms: Acinetobacter baumannii pan-genome reveals structural variation in antimicrobial resistance-carrying plasmids

2021 ◽  
Vol 7 (11) ◽  
Author(s):  
Aysun Urhan ◽  
Thomas Abeel
Keyword(s):  
Acinetobacter Baumannii ◽  
Type Species ◽  
Variant Calling ◽  
Reference Sequence ◽  
Beta Lactam ◽  
Final Size ◽  
Content Type ◽  
Pan Genome ◽  
Link Type ◽  
Microbial Organisms

Microbial organisms have diverse populations, where using a single linear reference sequence in comparative studies introduces reference-bias in downstream analyses, and leads to a failure to account for variability in the population. Recently, pan-genome graphs have emerged as an alternative to the traditional linear reference with many successful applications and a rapid increase in the number of methods available in the literature. Despite this enthusiasm, there has been no attempt at exploring these graph construction methods in depth, demonstrating their practical use. In this study, we aim to develop a general guide to help researchers who may want to incorporate pan-genomes in their analyses of microbial organisms. We evaluated the state-of-the art pan-genome construction tools to model a collection of 70 Acinetobacter baumannii strains. Our results suggest that all tools produced pan-genome graphs conforming to our expectations based on previous literature, and that their approach to homologue detection is likely to be the most influential in determining the final size and complexity of the pan-genome. The graphs overlapped most in the core pan-genome content while the cloud genes varied significantly among tools. We propose an alternative approach for pan-genome construction by combining two of the tools, Panaroo and Ptolemy, to further exploit them in downstream analyses, and demonstrate the effectiveness of our pipeline for structural variant calling in beta-lactam resistance genes in the same set of A. baumannii isolates, identifying various transposon structures for carbapenem resistance in chromosome, as well as plasmids. We identify a novel plasmid structure in two multidrug-resistant clinical isolates that had previously been studied, and which could be important for their resistance phenotypes.

scholarly journals Accuracy of an amplicon-sequencing nanopore approach to identify variants in tuberculosis drug-resistance-associated genes

2021 ◽  
Vol 7 (12) ◽  
Author(s):  
Carla Mariner-Llicer ◽  
Galo A. Goig ◽  
Laura Zaragoza-Infante ◽  
Manuela Torres-Puente ◽  
Luis Villamayor ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Type Species ◽  
Variant Calling ◽  
Targeted Sequencing ◽  
Clinical Samples ◽  
Drug Resistant ◽  
Content Type ◽  
Link Type ◽  
Resistant Strains ◽  
Drug Resistant Strains

A rapid and accurate diagnostic assay represents an important means to detect Mycobacterium tuberculosis , identify drug-resistant strains and ensure treatment success. Currently employed techniques to diagnose drug-resistant tuberculosis include slow phenotypic tests or more rapid molecular assays that evaluate a limited range of drugs. Whole-genome-sequencing-based approaches can detect known drug-resistance-conferring mutations and novel variations; however, the dependence on growing samples in culture, and the associated delays in achieving results, represents a significant limitation. As an alternative, targeted sequencing strategies can be directly performed on clinical samples at high throughput. This study proposes a targeted sequencing assay to rapidly detect drug-resistant strains of M. tuberculosis using the Nanopore MinION sequencing platform. We designed a single-tube assay that targets nine genes associated with drug resistance to seven drugs and two phylogenetic-determining regions to determine strain lineage and tested it in nine clinical isolates and six sputa. The study’s main aim is to calibrate MinNION variant calling to detect drug-resistance-associated mutations with different frequencies to match the accuracy of Illumina (the current gold-standard sequencing technology) from both culture and sputum samples. After calibrating Nanopore MinION variant calling, we demonstrated 100% agreement between Illumina WGS and our MinION set up to detect known drug resistance and phylogenetic variants in our dataset. Importantly, other variants in the amplicons are also detected, decreasing the recall. We identify minority variants and insertions/deletions as crucial bioinformatics challenges to fully reproduce Illumina WGS results.

scholarly journals Co-existence of multiple distinct lineages in Vibrio parahaemolyticus serotype O4:K12

2020 ◽  
Vol 6 (12) ◽  
Author(s):  
Lin Zhao ◽  
Hongyou Chen ◽  
Xavier Didelot ◽  
Zhenpeng Li ◽  
Yinghui Li ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Vibrio Parahaemolyticus ◽  
Type Species ◽  
Genomic Islands ◽  
Content Type ◽  
Pan Genome ◽  
Link Type ◽  
Gene Segregation ◽  
Strain Collection ◽  
The Usa

Vibrio parahaemolyticus is an important cause of foodborne gastroenteritis globally. Thermostable direct haemolysin (TDH) and the TDH-related haemolysin are the two key virulence factors in V. parahaemolyticus. Vibrio pathogenicity islands harbour the genes encoding these two haemolysins. The serotyping of V. parahaemolyticus is based on the combination of O and K antigens. Frequent recombination has been observed in V. parahaemolyticus , including in the genomic regions encoding the O and K antigens. V. parahaemolyticus serotype O4:K12 has caused gastroenteritis outbreaks in the USA and Spain. Recently, outbreaks caused by this serotype of V. parahaemolyticus have been reported in China. However, the relationships among this serotype of V. parahaemolyticus strains isolated in different regions have not been addressed. Here, we investigated the genome variation of the V. parahaemolyticus serotype O4:K12 using the whole-genome sequences of 29 isolates. We determined five distinct lineages in this strain collection. We observed frequent recombination among different lineages. In contrast, little recombination was observed within each individual lineage. We showed that the lineage of this serotype of V. parahaemolyticus isolated in America was different from those isolated in Asia and identified genes that exclusively existed in the strains isolated in America. Pan-genome analysis showed that strain-specific and cluster-specific genes were mostly located in the genomic islands. Pan-genome analysis also showed that the vast majority of the accessory genes in the O4:K12 serotype of V. parahaemolyticus were acquired from within the genus Vibrio . Hence, we have shown that multiple distinct lineages exist in V. parahaemolyticus serotype O4:K12 and have provided more evidence about the gene segregation found in V. parahaemolyticus isolated in different continents.

scholarly journals Prospective multi-center evaluation on risk factors, clinical characteristics and outcomes due to carbapenem resistance in Acinetobacter baumannii complex bacteraemia: experience from the Chinese Antimicrobial Resistance Surveillance of Nosocomial Infections (CARES) Network

2020 ◽  
Vol 69 (7) ◽  
pp. 949-959
Author(s):  
Yudong Liu ◽  
Qi Wang ◽  
Chunjiang Zhao ◽  
Hongbin Chen ◽  
Henan Li ◽  
...  
Keyword(s):  
Risk Factors ◽  
Acinetobacter Baumannii ◽  
Endotracheal Intubation ◽  
Type Species ◽  
Clinical Characteristics ◽  
Carbapenem Resistance ◽  
Male Gender ◽  
Content Type ◽  
Link Type ◽  
All Cause Mortality

Introduction. Increasing evidence demonstrates unfavourable outcomes in bloodstream infections (BSI) due to the carbapenem-resistant Acinetobacter baumannii complex (CRAB). Aim. To investigate the differences in risk factors, clinical characteristics and outcomes in patients with A. baumannii complex BSI stratified by carbapenem resistance, a prospective multi-center study was conducted. Methodology. Information was collected in a predefined form. A total of 317 cases was included for comparison between CRAB BSI vs. carbapenem-susceptible A. baumannii complex (CSAB) BSI. Among these cases, 229 cases were defined as CRAB BSI and 88 cases as CSAB BSI. Results. Univariable analysis showed that male gender, underlying neurologic disease, prior carbapenems exposure, intensive care unit (ICU) stay, presence of central venous catheter, endotracheal intubation, tracheotomy, Foley catheter, nasogastric intubation, lower respiratory tract infections and catheter-related infections were more prevalent in CRAB BSI. Only male gender, prior carbapenems exposure and presence of endotracheal intubation persisted as independent risk factors for acquiring CRAB BSI. Patients with CRAB BSI displayed unfavourable outcomes characterized by failure of pathogen clearance, continuous fever, disease aggravation and higher incidence of 30-day all-cause mortality. Multivariate analysis demonstrated carbapenem resistance as an independent risk factor for 30-day all-cause mortality. Conclusion. Our findings reveal the epidemiological differences between CRAB BSI and CSAB BSI in a Chinese cohort. Our data suggest that carbapenem resistance has a significant impact on mortality for patients with A. baumannii complex BSI, further strengthening the importance of active prevention and control strategies for the spread of CRAB in Chinese hospitals.

scholarly journals Molecular docking, dynamics and free energy analyses of Acinetobacter baumannii OXA class enzymes with carbapenems investigating their hydrolytic mechanisms

2020 ◽  
Vol 69 (8) ◽  
pp. 1062-1078
Author(s):  
Balajee Ramachandran ◽  
Jeyaraman Jeyakanthan ◽  
Bruno S. Lopes
Keyword(s):  
Free Energy ◽  
Acinetobacter Baumannii ◽  
Type Species ◽  
Three Dimensional ◽  
World Health ◽  
Phenotypic Data ◽  
Content Type ◽  
Beta Lactamases ◽  
Link Type ◽  
Class D

Introduction. Acinetobacter baumannii is a critical priority pathogen listed by the World Health Organization due to increasing levels of resistance to carbapenem classes of antibiotics. It causes wound and other nosocomial infections, which can be life-threatening. Hence, there is an urgent need for the development of new classes of antibiotics. Aim. To study the interaction of carabapenems with class D beta-lactamases (oxacillinases) and analyse drug resistance by studying enzyme–substrate complexes using modelling approaches as a means of establishing correlations with the phenotypic data. Methodology. The three-dimensional structures of carbapenems (doripenem, ertapenem, imipenem and meropenem) were obtained from DrugBank and screened against class D beta-lactamases. Further, the study was extended with their variants. The variants’ structure was homology-modelled using the Schrödinger Prime module (Schrödinger LLC, NY, USA). Results. The first discovered intrinsic beta-lactamase of Acinetobacter baumannii , OXA-51, had a binding energy value of −40.984 kcal mol−1, whereas other OXA-51 variants, such as OXA-64, OXA-110 and OXA-111, have values of −60.638, –66.756 and −67.751 kcal mol−1, respectively. The free energy values of OXA-51 variants produced better results than those of other groups. Conclusions. Imipenem and meropenem showed MIC values of 2 and 8 µg ml−1, respectively against OXA-51 in earlier studies, indicating that these are the most effective drugs for treatment of A. baumannii infection. According to our results, OXA-51 is an active enzyme that shows better interactions and is capable of hydrolyzing carbapenems. When correlating the hydrogen-bonding interaction with MIC values, the predicted results are in good agreement and might provide initial insights into performing similar studies related to OXA variants or other antibiotic–enzyme-based studies.

scholarly journals High frequency of colonization by diverse clones of beta-lactam-resistant Gram-negative bacilli in haemodialysis: different sources of transmission outside the renal unit?

2020 ◽  
Vol 69 (9) ◽  
pp. 1132-1144
Author(s):  
Johanna M. Vanegas ◽  
Lorena Salazar-Ospina ◽  
Daniela Montoya-Urrego ◽  
Julián Builes ◽  
Gustavo E. Roncancio ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Type Species ◽  
Molecular Characteristics ◽  
Renal Unit ◽  
Beta Lactam ◽  
High Genetic Diversity ◽  
Gram Negative ◽  
Content Type ◽  
Link Type ◽  
Stool Samples

Introduction. While colonization by Staphylococcus aureus in haemodialysis patients has been assessed, knowledge about colonization by beta-lactam-resistant Gram-negative bacilli is still limited. Aim. To describe clinical and molecular characteristics in haemodialysis patients colonized by S. aureus (MSSA-MRSA) and beta-lactam-resistant Gram-negative bacilli in an ambulatory renal unit. Methodology. The study included patients with central venous catheters in an outpatient haemodialysis facility in Medellín, Colombia (October 2017–October 2018). Swab specimens were collected from the nostrils and skin around vascular access to assess colonization by S. aureus (MSSA-MRSA). Stool samples were collected from each patient to evaluate beta-lactam-resistant Gram-negative bacilli colonization. Molecular typing included PFGE, multilocus sequence typing (MLST), spa typing and enterobacterial repetitive intergenic consensus-PCR (ERIC). Clinical information was obtained from medical records and personal interview. Results. A total of 210 patients were included in the study. S. aureus colonization was observed in 33.8 % (n=71) of the patients, 4.8 % (n=10) of which were colonized by methicillin-resistant S. aureus . Stool samples were collected from 165 patients and of these 41.2 % (n=68) and 11.5 % (n=19) were colonized by extended-spectrum-beta-lactamase-producing (ESBL) and carbapenem-resistant bacilli, respectively. Typing methods revealed high genetic diversity among S. aureus and ESBL-producing Gram-negative bacilli (ESBL-GNB). Antibiotic use and hospitalization in the previous 6 months were observed in more than half of the studied population. Conclusion. The high colonization by ESBL-GNB in haemodialysis patients shows evidence for the need for stronger surveillance, not only for S. aureus but also for multidrug-resistant bacilli in order to avoid their spread. Additionally, the high genetic diversity suggests other sources of transmission outside the renal unit instead of horizontal transmission between patients.

scholarly journals Insights into the complete genomes of carbapenem-resistant Acinetobacter baumannii harbouring bla OXA-23, bla OXA-420 and bla NDM-1 genes using a hybrid-assembly approach

2020 ◽  
Vol 2 (8) ◽  
Author(s):  
Saranya Vijayakumar ◽  
Chand Wattal ◽  
Oberoi J.K. ◽  
Sanjay Bhattacharya ◽  
Karthick Vasudevan ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Type Species ◽  
Carbapenem Resistance ◽  
Complete Characterization ◽  
Hybrid Assembly ◽  
Content Type ◽  
Link Type ◽  
Type Iv ◽  
Carbapenem Resistant ◽  
Complete Genomes

Carbapenem resistance in Acinetobacter baumannii is due to bla OXA-23, which is endemic in India. Recently, the sporadic presence of bla OXA-58 as well as the occurrence of dual carbapenemases were observed. The mobility as well as the dissemination of these resistance genes were mainly mediated by various mobile genetic elements. The present study was aimed at characterizing the genetic arrangement of bla OXA-23, bla NDM-1 and bla OXA-58 identified in two complete genomes of carbapenem-resistant A. baumannii (CRAB). Complete genomes obtained using a hybrid-assembly approach revealed the accurate arrangement of Tn2006 with bla OXA-23, ISAba125 with bla NDM and ISAba3 with bla OXA-58. In addition, the association of IntI1 integrase with the bla CARB-2 gene and several virulence factors required for type-IV pili assembly, motility and biofilm formation have been identified. The current study provided deeper insight into the complete characterization of insertion sequences and transposons associated with the carbapenem-resistant genes using short reads of IonTorrent PGM and long reads of MinIon in A. baumannii .

scholarly journals The open pan-genome architecture and virulence landscape of Mycobacterium bovis

2021 ◽  
Vol 7 (10) ◽  
Author(s):  
Ana C. Reis ◽  
Mónica V. Cunha
Keyword(s):  
Mycobacterium Bovis ◽  
Type Species ◽  
Genome Structure ◽  
Genome Architecture ◽  
Evolutionary Potential ◽  
Content Type ◽  
Accessory Genome ◽  
Pan Genome ◽  
Link Type ◽  
Clusters Of Orthologous Groups

Animal tuberculosis (TB) is an emergent disease caused by Mycobacterium bovis , one of the animal-adapted ecotypes of the Mycobacterium tuberculosis complex (MTC). In this work, whole-genome comparative analyses of 70 M . bovis were performed to gain insights into the pan-genome architecture. The comparison across M. bovis predicted genome composition enabled clustering into the core- and accessory-genome components, with 2736 CDS for the former, while the accessory moiety included 3897 CDS, of which 2656 are restricted to one/two genomes only. These analyses predicted an open pan-genome architecture, with an average of 32 CDS added by each genome and show the diversification of discrete M. bovis subpopulations supported by both core- and accessory-genome components. The functional annotation of the pan-genome classified each CDS into one or several COG (Clusters of Orthologous Groups) categories, revealing ‘transcription’ (total average CDSs, n=258), ‘lipid metabolism and transport’ (n=242), ‘energy production and conversion’ (n=214) and ‘unknown function’ (n=876) as the most represented. The closer analysis of polymorphisms in virulence-related genes in a restrict group of M. bovis from a multi-host system enabled the identification of clade-monomorphic non-synonymous SNPs, illustrating clade-specific virulence landscapes and correlating with disease severity. This first comparative pan-genome study of a diverse collection of M. bovis encompassing all clonal complexes indicates a high percentage of accessory genes and denotes an open, dynamic non-conservative pan-genome structure, with high evolutionary potential, defying the canons of MTC biology. Furthermore, it shows that M. bovis can shape its virulence repertoire, either by acquisition and loss of genes or by SNP-based diversification, likely towards host immune evasion, adaptation and persistence.

scholarly journals Streptococcus pneumoniae serotypes that frequently colonise the human nasopharynx are common recipients of penicillin-binding protein gene fragments from Streptococcus mitis

2021 ◽  
Vol 7 (9) ◽  
Author(s):  
Akuzike Kalizang'oma ◽  
Chrispin Chaguza ◽  
Andrea Gori ◽  
Charlotte Davison ◽  
Sandra Beleza ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Type Species ◽  
Binding Protein ◽  
Pneumococcal Serotypes ◽  
Penicillin Binding Protein ◽  
Beta Lactam ◽  
Streptococcus Mitis ◽  
Content Type ◽  
Link Type ◽  
Close Relatives

Streptococcus pneumoniae is an important global pathogen that causes bacterial pneumonia, sepsis and meningitis. Beta-lactam antibiotics are the first-line treatment for pneumococcal disease, however, their effectiveness is hampered by beta-lactam resistance facilitated by horizontal genetic transfer (HGT) with closely related species. Although interspecies HGT is known to occur among the species of the genus Streptococcus , the rates and effects of HGT between Streptococcus pneumoniae and its close relatives involving the penicillin binding protein (pbp) genes remain poorly understood. Here we applied the fastGEAR tool to investigate interspecies HGT in pbp genes using a global collection of whole-genome sequences of Streptococcus mitis , Streptococcus oralis and S. pneumoniae . With these data, we established that pneumococcal serotypes 6A, 13, 14, 16F, 19A, 19F, 23F and 35B were the highest-ranking serotypes with acquired pbp fragments. S. mitis was a more frequent pneumococcal donor of pbp fragments and a source of higher pbp nucleotide diversity when compared with S. oralis . Pneumococci that acquired pbp fragments were associated with a higher minimum inhibitory concentration (MIC) for penicillin compared with pneumococci without acquired fragments. Together these data indicate that S. mitis contributes to reduced β-lactam susceptibility among commonly carried pneumococcal serotypes that are associated with long carriage duration and high recombination frequencies. As pneumococcal vaccine programmes mature, placing increasing pressure on the pneumococcal population structure, it will be important to monitor the influence of antimicrobial resistance HGT from commensal streptococci such as S. mitis .

scholarly journals Microevolution in the major outer membrane protein OmpA of Acinetobacter baumannii

2020 ◽  
Vol 6 (6) ◽  
Author(s):  
Alejandro M. Viale ◽  
Benjamin A. Evans
Keyword(s):  
Acinetobacter Baumannii ◽  
Outer Membrane ◽  
Biofilm Formation ◽  
Type Species ◽  
Acinetobacter Calcoaceticus ◽  
Content Type ◽  
Link Type ◽  
Periplasmic Domain ◽  
Host Cell Recognition ◽  
Combined Data

Acinetobacter baumannii is nowadays a relevant nosocomial pathogen characterized by multidrug resistance (MDR) and concomitant difficulties to treat infections. OmpA is the most abundant A. baumannii outer membrane (OM) protein, and is involved in virulence, host-cell recognition, biofilm formation, regulation of OM stability, permeability and antibiotic resistance. OmpA members are two‐domain proteins with an N‐terminal eight‐stranded β‐barrel domain with four external loops (ELs) interacting with the environment, and a C‐terminal periplasmic domain binding non‐covalently to the peptidoglycan. Here, we combined data from genome sequencing, phylogenetic and multilocus sequence analyses from 975 strains/isolates of the Acinetobacter calcoaceticus / Acinetobacter baumannii complex (ACB), 946 from A. baumannii , to explore ompA microevolutionary divergence. Five major ompA variant groups were identified (V1 to V5) in A. baumannii , encompassing 52 different alleles coding for 23 different proteins. Polymorphisms were concentrated in five regions corresponding to the four ELs and the C‐terminal end, and provided evidence for intra‐genic recombination. ompA variants were not randomly distributed across the A . baumannii phylogeny, with the most frequent V1(lct)a1 allele found in most clonal complex 2 (CC2) strains and the second most frequent V2(lct)a1 allele in the majority of CC1 strains. Evidence was found for assortative exchanges of ompA alleles not only between separate A . baumannii lineages, but also different ACB species. The overall results have implications for A. baumannii evolution, epidemiology, virulence and vaccine design.

scholarly journals Anti-biofilm and anti-virulence effects of zerumbone against Acinetobacter baumannii

Microbiology ◽  
2020 ◽  
Vol 166 (8) ◽  
pp. 717-726
Author(s):  
Hye-Rim Kim ◽  
Da-Seul Shin ◽  
Hye-In Jang ◽  
Yong-Bin Eom
Keyword(s):  
Acinetobacter Baumannii ◽  
Biofilm Formation ◽  
Type Species ◽  
Laser Scanning ◽  
Multidrug Resistant ◽  
Laser Scanning Microscopy ◽  
Transcriptional Analysis ◽  
Confocal Laser ◽  
Content Type ◽  
Link Type

Acinetobacter baumannii is a multidrug-resistant opportunistic pathogen that affects patients with a compromised immune system and is becoming increasingly important as a hospital-derived infection. This pathogen is difficult to treat owing to its intrinsic multidrug resistance and ability to form antimicrobial-tolerant biofilms. In the present study, we aimed to assess the potential use of zerumbone as a novel anti-biofilm and/or anti-virulence agent against A. baumannii . The results showed that zerumbone at sub-inhibitory doses decreased biofilm formation and disrupted established A. baumannii biofilms. The zerumbone-induced decrease in biofilm formation was dose-dependent based on the results of microtitre plate biofilm assays and confocal laser scanning microscopy. In addition, our data validated the anti-virulence efficacy of zerumbone, wherein it significantly interfered with the motility of A. baumannii . To support these phenotypic results, transcriptional analysis revealed that zerumbone downregulated the expression of biofilm- and virulence-associated genes (adeA, adeB, adeC and bap) in A. baumannii . Overall, our findings suggested that zerumbone might be a promising bioactive agent for the treatment of biofilm- and virulence-related infections caused by multidrug-resistant A. baumannii .

Sign in / Sign up

Export Citation Format

Share Document