scholarly journals Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter

2021 ◽  
Author(s):  
Evangelos Mourkas ◽  
Koji Yahara ◽  
Sion C. Bayliss ◽  
Jessica K. Calland ◽  
Håkan Johansson ◽  
...  

AbstractHorizontal gene transfer (HGT) can allow traits that have evolved in one bacterial species to transfer to another. This has potential to rapidly promote new adaptive trajectories such as zoonotic transfer or antimicrobial resistance. However, for this to occur requires gaps to align in barriers to recombination within a given time frame. Chief among these barriers is the physical separation of species with distinct ecologies in separate niches. Within the genus Campylobacter there are species with divergent ecologies, from rarely isolated single host specialists to multi-host generalist species that are among the most common global causes of human bacterial gastroenteritis. Here, by characterising these contrasting ecologies, we can quantify HGT among sympatric and allopatric species in natural populations. Analysing recipient and donor population ancestry among genomes from 30 Campylobacter species we show that cohabitation in the same host can lead to a 6-fold increase in HGT between species. This accounts for up to 30% of all SNPs within a given species and identifies highly recombinogenic genes with functions including host adaptation and antimicrobial resistance. As described in some animal and plant species, ecological factors are a major evolutionary force for speciation in bacteria and changes to the host landscape can promote partial convergence of distinct species through HGT.

mBio ◽  
2018 ◽  
Vol 9 (5) ◽  
Author(s):  
Orchid M. Allicock ◽  
Cheng Guo ◽  
Anne-Catrin Uhlemann ◽  
Susan Whittier ◽  
Lokendra V. Chauhan ◽  
...  

ABSTRACT We report a platform that increases the sensitivity of high-throughput sequencing for detection and characterization of bacteria, virulence determinants, and antimicrobial resistance (AMR) genes. The system uses a probe set comprised of 4.2 million oligonucleotides based on the Pathosystems Resource Integration Center (PATRIC) database, the Comprehensive Antibiotic Resistance Database (CARD), and the Virulence Factor Database (VFDB), representing 307 bacterial species that include all known human-pathogenic species, known antimicrobial resistance genes, and known virulence factors, respectively. The use of bacterial capture sequencing (BacCapSeq) resulted in an up to 1,000-fold increase in bacterial reads from blood samples and lowered the limit of detection by 1 to 2 orders of magnitude compared to conventional unbiased high-throughput sequencing, down to a level comparable to that of agent-specific real-time PCR with as few as 5 million total reads generated per sample. It detected not only the presence of AMR genes but also biomarkers for AMR that included both constitutive and differentially expressed transcripts. IMPORTANCE BacCapSeq is a method for differential diagnosis of bacterial infections and defining antimicrobial sensitivity profiles that has the potential to reduce morbidity and mortality, health care costs, and the inappropriate use of antibiotics that contributes to the development of antimicrobial resistance.


2020 ◽  
Vol 15 ◽  
Author(s):  
Akshatha Prasanna ◽  
Vidya Niranjan

Background: Since bacteria are the earliest known organisms, there has been significant interest in their variety and biology, most certainly concerning human health. Recent advances in Metagenomics sequencing (mNGS), a culture-independent sequencing technology have facilitated an accelerated development in clinical microbiology and our understanding of pathogens. Objective: For the implementation of mNGS in routine clinical practice to become feasible, a practical and scalable strategy for the study of mNGS data is essential. This study presents a robust automated pipeline to analyze clinical metagenomic data for pathogen identification and classification. Method: The proposed Clin-mNGS pipeline is an integrated, open-source, scalable, reproducible, and user-friendly framework scripted using the Snakemake workflow management software. The implementation avoids the hassle of manual installation and configuration of the multiple command-line tools and dependencies. The approach directly screens pathogens from clinical raw reads and generates consolidated reports for each sample. Results: The pipeline is demonstrated using publicly available data and is tested on a desktop Linux system and a High-performance cluster. The study compares variability in results from different tools and versions. The versions of the tools are made user modifiable. The pipeline results in quality check, filtered reads, host subtraction, assembled contigs, assembly metrics, relative abundances of bacterial species, antimicrobial resistance genes, plasmid finding, and virulence factors identification. The results obtained from the pipeline are evaluated based on sensitivity and positive predictive value. Conclusion: Clin-mNGS is an automated Snakemake pipeline validated for the analysis of microbial clinical metagenomics reads to perform taxonomic classification and antimicrobial resistance prediction.


2020 ◽  
Vol 41 (S1) ◽  
pp. s521-s522
Author(s):  
Debarka Sengupta ◽  
Vaibhav Singh ◽  
Seema Singh ◽  
Dinesh Tewari ◽  
Mudit Kapoor ◽  
...  

Background: The rising trend of antibiotic resistance imposes a heavy burden on healthcare both clinically and economically (US$55 billion), with 23,000 estimated annual deaths in the United States as well as increased length of stay and morbidity. Machine-learning–based methods have, of late, been used for leveraging patient’s clinical history and demographic information to predict antimicrobial resistance. We developed a machine-learning model ensemble that maximizes the accuracy of such a drug-sensitivity versus resistivity classification system compared to the existing best-practice methods. Methods: We first performed a comprehensive analysis of the association between infecting bacterial species and patient factors, including patient demographics, comorbidities, and certain healthcare-specific features. We leveraged the predictable nature of these complex associations to infer patient-specific antibiotic sensitivities. Various base-learners, including k-NN (k-nearest neighbors) and gradient boosting machine (GBM), were used to train an ensemble model for confident prediction of antimicrobial susceptibilities. Base learner selection and model performance evaluation was performed carefully using a variety of standard metrics, namely accuracy, precision, recall, F1 score, and Cohen κ. Results: For validating the performance on MIMIC-III database harboring deidentified clinical data of 53,423 distinct patient admissions between 2001 and 2012, in the intensive care units (ICUs) of the Beth Israel Deaconess Medical Center in Boston, Massachusetts. From ~11,000 positive cultures, we used 4 major specimen types namely urine, sputum, blood, and pus swab for evaluation of the model performance. Figure 1 shows the receiver operating characteristic (ROC) curves obtained for bloodstream infection cases upon model building and prediction on 70:30 split of the data. We received area under the curve (AUC) values of 0.88, 0.92, 0.92, and 0.94 for urine, sputum, blood, and pus swab samples, respectively. Figure 2 shows the comparative performance of our proposed method as well as some off-the-shelf classification algorithms. Conclusions: Highly accurate, patient-specific predictive antibiogram (PSPA) data can aid clinicians significantly in antibiotic recommendation in ICU, thereby accelerating patient recovery and curbing antimicrobial resistance.Funding: This study was supported by Circle of Life Healthcare Pvt. Ltd.Disclosures: None


Author(s):  
Anna Lavecchia ◽  
Matteo Chiara ◽  
Caterina De Virgilio ◽  
Caterina Manzari ◽  
Carlo Pazzani ◽  
...  

Abstract Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.


2008 ◽  
Vol 9 (2) ◽  
pp. 177-186 ◽  
Author(s):  
Trudy M. Wassenaar ◽  
Peter Silley

AbstractThe relative contribution of veterinary and human clinical treatments to the selection of antimicrobial resistance in zoonotic pathogens remains controversial. In this review, we consider bacterial pathogens that differ in host specificity and address their resistance profiles: pathogens that only occur in the human host, pathogens that are specific to particular food-producing animals and pathogens that occur in both host types. Compared with those pathogens restricted to a single animal host, pathogens found in both human and animal hosts appear to have higher incidences of resistance. However, the most urgent and severe resistance problems occur with pathogens exclusively infecting humans. Differences exist in the available genetic repertoire of a bacterial species and these are reflected in the observed resistance patterns; it is important to note that different bacterial species do not automatically result in similarly resistant populations when they undergo comparable selection in different host species. Thus, within a bacterial species, prevalence of resistance can differ between populations isolated from different hosts. For some species, fluctuations in dominant subpopulations, for instance particular serotypes, can be the most important factor determining resistance. The frequently expressed opinion that veterinary use of antimicrobials is at the heart of many resistance problems may be an oversimplification of the complex forces at play.


1948 ◽  
Vol 88 (1) ◽  
pp. 99-131 ◽  
Author(s):  
Harry Eagle ◽  
A. D. Musselman

1. The concentrations of penicillin G which (a) reduced the net rate of multiplication, (b) exerted a net bactericidal effect, and (c) killed the organisms at a maximal rate, have been defined for a total of 41 strains of α- and ß-hemolytic streptococci, Staphylococcus aureus and Staphylococcus albus, Diplococcus pneumoniae, and the Reiter treponoma. 2. The concentration which killed the organisms at a maximal rate was 2 to 20 times the minimal effective level ("sensitivity" as ordinarily defined). With some organisms, even a 32,000-fold increase beyond this maximally effective level did not further increase the rate of its bactericidal effect. However, with approximately half the strains here studied (all 4 strains of group B ß-hemolytic streptococci, 4 of 5 group C strains, 5 of 7 strains of Streptococcus fecalis, 2 of 4 other α-hemolytic streptococci, and 4 of 9 strains of staphylococci), when the concentration of penicillin was increased beyond that optimal level, the rate at which the organisms died was paradoxically reduced rather than increased, so that the maximal effect was obtained only within a relatively narrow optimal zone. 3. There were marked differences between bacterial species, and occasionally between different strains of the same species, not only with respect to the effective concentrations of penicillin, but also with respect to the maximal rate at which they could be killed by the drug in any concentration. Although there was a rough correlation between these two factors, there were many exceptions; individual strains affected only by high concentrations of penicillin might nevertheless be killed rapidly, while strains sensitive to minute concentrations might be killed only slowly. 4. Within the same bacterial suspension, individual organisms varied only to a minor degree with respect to the effective concentrations of penicillin. They varied strikingly, however, in their resistance to penicillin as measured by the times required to kill varying proportions of the cells.


Author(s):  
П.Е. Гарлов

С целью повышения эффективности искусственного воспроизводства популяций ценных видов рыб разработаны новые методы управления их размножением, выживаемостью и ростом, которые представлены в виде изобретений. Для управления размножением производителей разработаны методы стимуляции и задержки полового созревания производителей осетровых и костистых рыб. Для стимуляции полового созревания были разработаны препараты изолированной передней и изолированной задней долей гипофиза. Их внедрение в осетроводстве позволило повысить степень их рыбоводного использования в среднем на 15% и достичь экономии гипофиза до 40%. Для задержки полового созревания производителей разработан метод их промышленного резервирования в среде критической солёности 4–8‰, причём как в морской воде, так и в растворах поваренной соли. Производственными испытаниями доказана возможность сохранения рыбоводного качества производителей и получения доброкачественного потомства в этой среде при верхних нерестовых температурах в течение производственно необходимых сроков. С целью заводского воспроизводства природных популяций промысловых рыб разработан метод управления их размножением триадой адекватных экологических факторов ‒ «критической» солёностью, температурой и освещённостью при видоспецифических пороговых воздействиях. На этой основе разработан полносистемный метод воспроизводства популяций ценных видов промысловых рыб (севрюги и Балтийского лосося), охватывающий все этапы заводской биотехники. Новый метод осуществляется путём массовой морской заготовки производителей, получения потомства в морских садках и, после заводского речного выращивания молоди до готовности к миграции, конечного доращивания в морских садках крупной жизнестойкой молоди. Для промышленного внедрения всей предложенной биотехники и круглогодичной аквакультуры разработаны системы водоснабжения рыбоводных заводов и рыбоводных хозяйств на основе внесезонного подземного гидрокондиционирования среды выращивания и на природно-промышленных принципах инженерной экологии. In order to increase the efficiency of artificial reproduction of populations of valuable fish species new methods for managing their reproduction, survival and growth have been developed, which are presented in the form of inventions. To control the reproduction of producers methods have been developed to stimulate and delay puberty of sturgeon and bony fish producers. To stimulate puberty preparations for the isolated anterior and isolated posterior lobes of the pituitary gland have been developed. Their introduction in sturgeon breeding made it possible to increase the degree of their fish farming use by an average of 15% and to achieve a pituitary gland economy of up to 40%. To delay the puberty of producers, a method for their industrial reservation in an environment of critical salinity of 4–8‰ has been developed both in sea water and in solutions of sodium chloride. Production tests have proven the possibility of preserving the fish-breeding quality of producers and obtaining benign offspring in this environment at the upper spawning temperatures during the production required periods of time. With the aim of factory reproduction of natural populations of commercial fish a method has been developed to control their reproduction by a triad of adequate ecological factors – “critical” salinity, temperature and illumination under species-specific threshold effects. On this basis a full-system method of reproducing populations of valuable species of commercial fish (stellate sturgeon and Baltic salmon) has been developed covering all stages of factory biotechnology. The new method is carried out by mass marine harvesting of producers obtaining offspring in sea pens and after the factory river rearing of hatchling until ready for migration the final rearing of large viable juveniles in sea pens. For the industrial introduction of all the proposed biotechnics and year-round aquaculture, water supply systems for fish breeding plants and fish farms were developed on the basis of off-season underground hydroconditioning of the growing environment and on the natural and industrial principles of engineering ecology.


2021 ◽  
Vol 5 (1) ◽  
pp. 001-007
Author(s):  
Ostojic Maja ◽  
Hubana Mahir ◽  
Cvetnić Marija ◽  
Benić Miroslav ◽  
Cvetnić Zeljko

Background: Klebsiella pneumoniae is a bacterial species that often causes infections in humans. Infections occur most frequently in hospitalised or immunocompromised patients and are treated with antimicrobials. In recent decades, K. pneumoniae has developed significant resistance to many antimicrobials. Objective: The main goal of this study was to determine the frequency of resistance of isolated K. pneumoniae strains from urine samples of hospital patients and outpatients, and to find evidence of ESBL strains and their resistance to certain antibiotics. Methods: During the study period, Klebsiella pneumonia was isolated from the urine samples of 430 patients. The procedure for processing of urine samples, identification, susceptibility toward antimicrobials and evidence of ESBL strains were carried out according to the recommended standards. Results: Of the total K. pneumoniae isolates, 153 (35.6%) were isolated from hospital patients and 277 (64.4%) from outpatients. Strains isolated from hospital patients were resistant to each tested antibiotic. ESBL strains were detected in 169 (39.30%) samples, 92 (60.13%) from hospital patients and 77 (27.8%) from outpatients. Conclusion: Strains of K. pneumoniae isolated from the urine of hospital patients and outpatients have developed significant resistance against all tested antibiotic substances. A higher occurrence of ESBL strains was observed in hospital patients than in outpatients. ESBL strains were resistant to all penicillins and almost all cephalosporins. Highly effective antimicrobials were amikacin, colistine, carbapenem and fosfomycin. The best therapeutic results were achieved when patients were treated with fosfomycin and imipenem.


2018 ◽  
Vol 84 (19) ◽  
Author(s):  
Yvonne Agersø ◽  
Birgitte Stuer-Lauridsen ◽  
Karin Bjerre ◽  
Michelle Geervliet Jensen ◽  
Eric Johansen ◽  
...  

ABSTRACTBacillus megaterium(n= 29),Bacillus velezensis(n= 26),Bacillus amyloliquefaciens(n= 6),Bacillus paralicheniformis(n= 28), andBacillus licheniformis(n= 35) strains from different sources, origins, and time periods were tested for the MICs for nine antimicrobial agents by the CLSI-recommended method (Mueller-Hinton broth, 35°C, for 18 to 20 h), as well as with a modified CLSI method (Iso-Sensitest [IST] broth, 37°C [35°C forB. megaterium], 24 h). This allows a proposal of species-specific epidemiological cutoff values (ECOFFs) for the interpretation of antimicrobial resistance in these species. MICs determined by the modified CLSI method were 2- to 16-fold higher than with the CLSI-recommended method for several antimicrobials. The MIC distributions differed between species for five of the nine antimicrobials. Consequently, use of the modified CLSI method and interpretation of resistance by use of species-specific ECOFFs is recommended. The genome sequences of all strains were determined and used for screening for resistance genes against the ResFinder database and for multilocus sequence typing. A putative chloramphenicol acetyltransferase (cat) gene was found in oneB. megateriumstrain with an elevated chloramphenicol MIC compared to the otherB. megateriumstrains. InB. velezensisandB. amyloliquefaciens, a putative tetracycline efflux gene,tet(L), was found in all strains (n= 27) with reduced tetracycline susceptibility but was absent in susceptible strains. AllB. paralicheniformisand 23% ofB. licheniformisstrains had elevated MICs for erythromycin and harboredermD. The presence of these resistance genes follows taxonomy suggesting they may be intrinsic rather than horizontally acquired. Reduced susceptibility to chloramphenicol, streptomycin, and clindamycin could not be explained in all species.IMPORTANCEWhen commercializing bacterial strains, likeBacillusspp., for feed applications or plant bioprotection, it is required that the strains are free of acquired antimicrobial resistance genes that could potentially spread to pathogenic bacteria, thereby adding to the pool of resistance genes that may cause treatment failures in humans or animals. Conversely, if antimicrobial resistance is intrinsic to a bacterial species, the risk of spreading horizontally to other bacteria is considered very low. Reliable susceptibility test methods and interpretation criteria at the species level are needed to accurately assess antimicrobial resistance levels. In the present study, tentative ECOFFs for fiveBacillusspecies were determined, and the results showed that the variation in MICs followed the respective species. Moreover, putative resistance genes, which were detected by whole-genome sequencing and suggested to be intrinsic rather that acquired, could explain the resistance phenotypes in most cases.


2018 ◽  
Vol 65 (3-4) ◽  
pp. 129-146 ◽  
Author(s):  
Tamar Krugman ◽  
Eviatar Nevo ◽  
Alex Beharav ◽  
Hanan Sela ◽  
Tzion Fahima

The Institute of Evolution Wild Cereal Gene Bank (ICGB) at the University of Haifa, Israel, harbors extensive collections of wild emmer wheat (WEW), Triticum dicoccoides, and wild barley (WB), Hordeum spontaneum, the primary progenitors of wheat and barley, respectively. The ICGB also includes minor collections of 10 species of Aegilops, wild oat (Avena barbata), and Brachypodium stacei and B. hybridum (previously distachyon). Here, we describe the WEW and WB collections, explain sampling strategies, and introduce related studies. Natural populations were sampled across Israel along aridity gradients, occurring from north to south and from west to east, and in local microsites with variable (or contrasting) ecological factors. The collection sites varied greatly in terms of climatic (rainfall, temperature and humidity), edaphic (soil types), and topography (altitude, slope) variables. Thus, the ICGB collections represent wild cereals adapted to a wide range of habitats and eco-geographical conditions. We have collected and preserved these unique gene pools since mid-70th, and further used them for theoretical and applied studies in population genetics, evolution, domestication, adaptation to local and regional habitats, and coping mechanisms for a plethora of biotic and abiotic stresses. Our studies revealed that WEW and WB populations from Israel harbor high adaptive genetic diversity that can serve as a reservoir of beneficial alleles to improve important agronomic traits such as disease resistance, drought tolerance and improved grain protein content. These mostly untapped genetic resources could contribute to increasing world food production for the constantly rising human population.


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