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PubMed2026

Whole-Genome Analysis Reveals Antimicrobial Resistance and Population Structure of Environmental and Veterinary Acinetobacter baumannii.

Acinetobacter (A.) baumannii is an important multidrug-resistant pathogen increasingly recognized across animal and environmental settings, and carbapenem-resistant A. baumannii (CRAB) is classified as a critical-priority pathogen by the World Health Organization. This study investigated the antimicrobial resistance (AMR) and genomic characteristics of 122 A. baumannii isolates comprising 72 veterinary and 50 environmental isolates collected in Andhra Pradesh, India. Antimicrobial susceptibility testing, whole-genome sequencing (WGS), resistance and virulence gene profiling, multilocus sequence typing (MLST), core-genome analysis, single nucleotide polymorphism (SNP) phylogeny, and pan-genome analysis were performed. Overall, 58.2% of isolates were multidrug-resistant (MDR), and 41.8% were extensively drug-resistant (XDR). Sequence type (ST) 52 predominated among veterinary isolates, whereas ST2 was more frequent among environmental isolates. The presence of carbapenem-resistant isolates along with the ST2 lineage enhances the similarity to clinical A. baumannii. Several intrinsic resistance genes, including blaOXA-23, armA, aph(3″)-Ib, aph(6)-Id, tet(B), mph(E), and msr(E), were more prevalent in the ST2-associated population. Virulence-associated determinants were widely conserved. Core-genome MLST (cgMLST) and core-genome SNP (cgSNP) analyses identified highly related isolates within both lineages, while pairwise SNP differences were 0-7. Pan-genome analysis identified 4204 gene clusters and distinct accessory gene patterns between ST2 and ST52. These findings indicate that resistance gene distribution was closely associated with lineage structure and support integrated genomic surveillance of A. baumannii across animal and environmental reservoirs.

Acinetobacter baumannii↗
PubMed1990

Genetic population structure, clonal phylogeny, and pathogenicity of Salmonella paratyphi B.

Genetic diversity and relationships among 123 strains of Salmonella paratyphi B (serotype 1,4,[5],12:b:[1,2]) were estimated from an assessment of electrophoretically demonstrable allelic variation at 24 chromosomal enzyme gene loci. Fourteen electrophoretic types, marking clones, were distinguished, the phylogeny of the clonal lineages was reconstructed, and biotype and other phenotypic characters were mapped onto this structure. Most d-tartrate-negative strains are members of an abundant, globally distributed clone (Pb 1) that is polymorphic for many biotype characters (including d-tartrate utilization), bacteriophage type, rRNA pattern, and colicin M and phage ES18 sensitivity. This clone is largely responsible for S. paratyphi B enteric fever in humans. In contrast, d-tartrate-positive strains (formerly known as S. java) occurred in all seven of the clonal lineages identified by population genetic analysis, although most d-tartrate-positive isolates belong to only two clones (Pb 3 and Pb 4), which vary in frequency geographically. Monophasic strains represent four closely related clones forming a distinctive phylogenetic lineage. The Kauffmann hypothesis of convergence in serotype among distantly related cell lineages through recombination (via phage transduction or other means) may account for the considerable genotypic diversity among clones of S. paratyphi B. Pb 4, Pb 6, and Pb 7 are more closely allied with clones of S. typhimurium and S. saintpaul than with other clones of S. paratyphi B. Sensitivity or resistance to colicin M and phage ES18 and the electrophoretic pattern of the rRNA, which were incorporated into a recently proposed scheme for the identification of types of S. paratyphi B, individually or in combination fail to mark clones or other meaningful phylogenetic subdivisions.

Colicins↗
PubMed2006

Population structure of Francisella tularensis.

We have sequenced fragments of five metabolic housekeeping genes and two genes encoding outer membrane proteins from 81 isolates of Francisella tularensis, representing all four subspecies. Phylogenetic clustering of gene sequences from F. tularensis subsp. tularensis and F. tularensis subsp. holarctica aligned well with subspecies affiliations. In contrast, F. tularensis subsp. novicida and F. tularensis subsp. mediasiatica were indicated to be phylogenetically incoherent taxa. Incongruent gene trees and mosaic structures of housekeeping genes provided evidence for genetic recombination in F. tularensis.

Animals↗
PubMed1998

Clonal population structure of Colombian sylvatic Trypanosoma cruzi.

Isoenzyme variability and evidence of genetic exchange were evaluated in 75 wild stocks of Trypanosoma cruzi obtained from different hosts from 5 geographical regions within the endemic area in Colombia. Cluster analysis of genetic variability was attempted. Thirty-three multilocus enzyme genotypes (clonets) were identified from 75 stocks, 27 of which clustered with zymodeme Z1 and 6 with zymodeme Z3. Two stocks isolated from human infections showed the potential risk to rural communities in Colombia. The stocks exhibited departures from Hardy-Weinberg expectations, including both fixed heterozygote and fixed homozygote demes, where both segregation and recombination were absent. To inspect for population subdivision that might falsely imply clonality in these stocks, Wright's F statistics were calculated. Theta values (Fst) were significantly different from 0 when 33 clonets, 27 Z1-like clonets, and 5 geographical subpopulations were compared; thus, a significant amount of divergence has occurred between and within them. In addition, linkage disequilibrium was detected for most possible pairwise comparisons of loci. In conclusion, the above results all support a scenario of long-term clonal evolution in Colombian sylvatic T. cruzi populations.

Animals↗
PubMed1999

Genetic population structure of two African-Ecuadorian communities of Esmeraldas.

The genetic structure of two African-Ecuadorian communities, Rio Cayapas and Viche (Esmeraldas province, northwest Ecuador), was studied on the basis of ACP1, ADA, AK1, CA2, ESD, GLO1, G6PD, PGD, and PGM1 subtypes and thermostability, PGM2, HBbeta, F13A, F13B, ORM1, AHSG, C6, C7, and APOC2 gene frequency, and migration data on 255 individuals. The fixation index of Wright (F(ST)), correspondence, and genetic distance analysis were applied to compare the genetic relationships between these communities and other American populations of African ancestry. F(ST) values from the migration data and surname origins suggest that Rio Cayapas is genetically more isolated and shows less mobility and admixture than does Viche. The genetic admixture estimates indicate a large contribution of African genes to the gene pool of both communities (74.3% to 58.4%), whereas the proportion of the Amerindian component differs significantly (14.5% in Rio Cayapas to 27.6% in Viche).

Africa↗
PubMed2002

Population structure of the African savannah elephant inferred from mitochondrial control region sequences and nuclear microsatellite loci.

Two hundred and thirty-six mitochondrial DNA nucleotide sequences were used in combination with polymorphism at four nuclear microsatellite loci to assess the amount and distribution of genetic variation within and between African savannah elephants. They were sampled from 11 localities in eastern, western and southern Africa. In the total sample, 43 haplotypes were identified and an overall nucleotide diversity of 2.0% was observed. High levels of polymorphism were also observed at the microsatellite loci both at the level of number of alleles and gene diversity. Nine to 14 alleles per locus across populations and 44 alleles in the total sample were found. The gene diversity ranged from 0.51 to 0.72 in the localities studied. An analysis of molecular variance showed significant genetic differentiation between populations within regions and also between regions. The extent of subdivision between populations at the mtDNA control region was approximately twice as high as shown by the microsatellite loci (mtDNA F(ST) = 0.59; microsatellite R(ST) = 0.31). We discuss our results in the light of Pleistocene refugia and attribute the observed pattern to population divergence in allopatry accompanied by a recent population admixture following a recent population expansion.

Africa↗
PubMed2007

Absence of population structure of turbot (Psetta maxima) in the Baltic Sea.

We found low, albeit significant, genetic differentiation among turbot (Psetta maxima) in the Baltic Sea but in contrast to earlier findings we found no evidence of isolation by distance. In fact temporal variation among years in one locality exceeded spatial variation among localities. This is an unexpected result since adult turbot are sedentary and eggs are demersal at the salinities occurring in the Baltic. Our findings are most likely explained by the fact that we sampled fish that were born after/during a large influx of water to the Baltic Sea, which may have had the consequence that previously locally and relatively sedentary populations became admixed. These results suggest that populations that colonize relatively variable habitats, like the Baltic, face problems. Any adaptations to local conditions that may build up during stable periods may quickly become eroded when conditions change and/or when populations become admixed. Our results indicate that the ability of turbot to survive and reproduce at the low salinity in the Baltic is more likely due to phenotypic plasticity than a strict genetic adaptation to low salinity.

Adaptation, Biological↗
PubMed2004

Analysis of population structure of Aspergillus flavus from peanut based on vegetative compatibility, geographic origin, mycotoxin and sclerotia production.

Isolates of Aspergillus flavus obtained from a new growing peanut region in Argentina (Formosa province) were examined for aflatoxin types B and G and cyclopiazonic acid (CPA) production. Sclerotia diameters and the number of sclerotia produced per square centimetre were also determined for each isolate. They were tested by vegetative compatibility group analysis to investigate their genetic relatedness and correlate the results with vegetative compatibility groups previously described from the major peanut-growing area (Córdoba province) in our country. Two isolates were considered atypical because they simultaneously produce aflatoxins B and G and CPA. A. flavus population from Formosa province was very diverse genetically. Vegetative compatibility groups (VCGs) formed by typical isolations of A. flavus were different among agroecological sites. Formosa isolates could not be grouped to any of the Córdoba VCGs, while that one of the VCGs that contain atypical isolates included strains from the two geographical regions. Each VCG included isolates of the same mycotoxin and sclerotia production pattern. The two regions analysed have different climatic conditions, soil type, crop sequence history and also are in different latitude. These parameters may reflect different geographic adaptation between isolates from both sites.

Adaptation, Physiological↗
PubMed2026

Two domesticated species of rice shaped the population structure of Xanthomonas oryzae pv. oryzae in Africa.

African rice (Oryza glaberrima) was independently domesticated in West Africa around 3000 years ago, and has long been intertwined in the history of the region. Asian rice (Oryza sativa), which was introduced in Africa when European settlers arrived, gradually replaced African rice and has since dominated rice cultivation in the continent. Domesticated rice species are affected by bacterial leaf blight (BLB), which is caused by the pathogen Xanthomonas oryzae pv. oryzae (Xoo). Here we show that the bacterial leaf blight pathogen in Africa (AfXoo) belongs to a distinct phylogroup from the one circulating in Asia (AsXoo), and has a different evolutionary history. Analysis of 87 AfXoo genomes identified five main populations, including highly clonal ones, and a more diverse and recombinant population. Tip-dating analysis revealed that the AfXoo population went through a period of expansion, then decline and more recent recovery. We hypothesize this followed the rise and fall of African rice, and that the introduction of O. sativa served as a bottleneck leading to the emergence of current AfXoo populations. We show that AfXoo has a highly conserved repertoire of type III effectors (T3E), but that nonetheless there is variation especially between populations. In the case of transcription activator-like effectors (TALEs), variation can arise quickly through rearrangements, and we hypothesize that the TALE repertoire of AfXoo has been selected to allow the bacteria to colonize both species of cultivated rice found in the continent. Our research provides an attempt to decipher the genetic history of bacterial blight in West Africa, and its past and present impact on rice cultivation in the region.

Journal Article↗
PubMed2003

A test for deviation from island-model population structure.

The neutral island model forms the basis for several estimation models that relate patterns of genetic structure to microevolutionary processes. Estimates of gene flow are often based on this model and may be biased when the model's assumptions are violated. An appropriate test for violations is to compare FST scores for individual loci to a null distribution based on the average FST taken over multiple loci. A parametric bootstrap method is described here based on Wright's beta-distribution to generate null distributions of FST for each locus. These null distributions account for error introduced by sampling populations, individuals and loci, and also biological sources of error, including variable alleles/locus and inbreeding. Confidence limits can be obtained directly from these distributions. Significant deviations from the island model may be the result of selection, deviations from the island model's migration pattern, nonequilibrium conditions, or other deviations from island-model assumptions. Only strong biases are likely to be detected because of the inherently large sampling variation of FST. Nevertheless, a coefficient, Nb, describing bias in the spread of the beta-distribution in units comparable to the gene flow parameter, Nm, can be obtained for each locus. In samples from populations of the butterfly Coenonympha tullia, the loci Idh-1, Mdh-1, Pgi and Pgm showed significantly lower FST than expected.

Animals↗
PubMed2004

Phylogenetic analysis of multiple loci reveal the population structure within Letharia in the Caucasus and Morocco.

The sequence variation within the genus Letharia in the Caucasus and Morocco was investigated. Twelve thalli from each area were sequenced at eight different loci. Phylogenetic analysis of the multiple loci data revealed the cryptic species Letharia 'lupina' in Morocco, previously known only from western North America. The two cryptic species L. vulpina and L. 'lupina' locally share the same ecology but are genetically isolated from each other. In the Caucasus, five different haplotypes of L. vulpina were detected, and in Morocco four L. vulpina haplotypes and six L. 'lupina' haplotypes were found. For L. vulpina, allelic differences were detected at five of the eight loci in the Caucasus and Morocco. The populations of L. vulpina in both the Caucasus and Morocco contain more genetic variation than those previously investigated in Europe, which indicates that the Caucasus and Morocco acted as refugia during quaternary glaciations, and that central and northern Europe may have been recolonised from one or both of these areas.

Alleles↗
PubMedDate not supplied

Population structure and Mdh-1 locus variation in Apis mellifera ligustica.

In a wide area of the Piedmont of Italy the apiaries of Apis mellifera ligustica Spin., (the Italian bee) show homogeneous allelic frequency distributions at the Mdh-1 locus, the only one known to be polymorphic in worker bees. This can be explained by considering that an apiary is not a closed genetic system and that among apiaries gene flow is sufficient to overcome the different forces of inbreeding and random genetic drift. Nevertheless there is some evidence for partial subdivision because the pooled samples show a weak Wahlund effect. Moreover, the M allele at the same locus can be used as a diagnostic marker to distinguish A. m. ligustica populations (M absent or at very low frequencies) from A. m. mellifera French populations (monomorphic for M). The two honey-bee varieties, almost entirely separated by the Alps, hybridize with each other in very limited alpine areas. Hybrid populations show intermediate M frequencies.

Animals↗
PubMed2001

Population structure in two sympatric species of the Lake Tanganyika cichlid tribe Eretmodini: evidence for introgression.

Patterns of genetic differentiation were analysed and compared in two sympatric species of the endemic Lake Tanganyika cichlid tribe Eretmodini by means of mitochondrial DNA (mtDNA) sequences of the control region and six microsatellite DNA loci. The sample area covers a total of 138 km of mostly uninterrupted rocky shoreline in the Democratic Republic of Congo and includes the entire distribution range of Tanganicodus cf. irsacae that stretches over a distance of 35 km. Both markers detected significant genetic differentiation within and between the two species. T. cf. irsacae contained lower overall genetic variation than Eretmoduscyanostictus, possibly due to its more restricted range of distribution and its smaller effective population sizes. Complete fixation of Tanganicodus mtDNA haplotypes was observed in Eretmodus at two localities, while at two other localities some Tanganicodus individuals possessed Eretmodus mtDNA haplotypes. Taking into account the relatively large average sequence divergence of 6.2% between the two species, as well as the geographical distribution of mtDNA haplotypes in the lake, the observed pattern is more likely to be a consequence of asymmetric introgression than of shared ancestral polymorphism. As there is significant population differentiation between sympatric Tanganicodus and Eretmodus populations, the events of introgressions may have happened after secondary contact, but our data provide no evidence for ongoing gene flow and suggest that both species are reproductively isolated at present time.

Animals↗
PubMed1996

Population structure of Streptococcus agalactiae reveals an association between specific evolutionary lineages and putative virulence factors but not disease.

To evaluate the genetic diversity and relationships in a collection of 85 Danish strains of Streptococcus agalactiae (group B streptococcus) we have performed restriction fragment length polymorphism analysis on EcoRI- and MspI-digested whole-cell DNA using as probes rRNA, DNA fragments representing the genes encoding hyaluronidase, C5a-peptidase, alpha-antigen, and beta-antigen as well as two randomly selected genomic DNA fragments for which the coding potential is unknown. In addition, we have assayed for expression of hyaluronidase activity and beta-antigen. Combined analyses of our data and those previously obtained by multilocus enzyme electrophoresis and serotyping revealed a population separating into six major lineages that correlate with individual serotypes. The significant linkage disequilibrium of alleles indicates that the S. agalactiae population examined is predominantly clonal. Notably, strains expressing the serotype III capsule divide into two distant evolutionary lineages, of which one lacks expression of hyaluronidase activity. Six North American isolates of serotype III clustered together with multiple Danish serotype III strains, showing that the combinations of characters on which the phylogenetic tree was based are conserved worldwide. Occurrence of beta-antigen correlated with a specific version of the alpha-antigen gene and was exclusively associated with a single major phylogenetic lineage. Comparisons with the clinical history of the strains revealed no evidence of differences in pathogenic potential among the six major genetic divisions.

Adhesins, Bacterial↗
PubMed1983

Enzyme polymorphism and genetic population structure in Escherichia coli and Shigella.

Electrophoretically demonstrable variation in 12 enzymes was studied in more than 1 600 isolates of Escherichia coli from human and animal sources and in 123 strains of the four species of Shigella. All 12 enzymes were polymorphic; and the number of allozymes (mobility variants), which were equated with alleles, averaged 9.3 per locus in E. coli. For Shigella species, the mean number of alleles was 2.9 per locus. Some 77% of the allozymes recorded in Shigella were shared with E. coli. A total of 302 unique genotypic combinations of alleles over the 12 loci (electrophoretic types, ETs) was distinguished, of which 279 represented E. coli and 23 were Shigella. Among electrophoretic types, mean allelic diversity per locus was 0.52 for E. coli and 0.29 for Shigella. It was estimated that there are, on the average, about 0.3 detectable codon differences per locus between pairs of strains of E. coli and Shigella, which is roughly equivalent to 1.2 amino acid differences per enzyme. Evidence that the enzyme loci studied are a random sample of the genome is provided by a significant positive correlation between estimates of genetic divergence between pairs of strains obtained by DNA reassociation tests and estimates of genetic distance between the same strains based on electrophoresis. A principal components analysis of allozyme profiles revealed that the 302 ETs fall into three overlapping clusters, reflecting strong non-random associations of alleles, largely at four loci. Each of the four ETs of E. coli that have been most frequently recovered from natural populations has an allozyme profile that is very similar to, or identical with, the hypothetical modal ET of one of the groups. ETs of Shigella fall into two of the groups. No biological significance can at present bbe attributed to the genetic structure revealed by Multilocus electrophoretic techniques. The electrophoretic data are fully compatible with other molecular and more conventional evidence of a close affinity between E. coli and Shigella, and they raise questions regarding the present assignments of certain strains to species. In support of evidence from DNA reassociation tests and serotyping, the present study suggests that S. sonnei is homogeneous in chromosomal genotype.

Adult↗
PubMed2002

Analysis of the population structure of Anopheles funestus (Diptera: Culicidae) from western and coastal Kenya using paracentric chromosomal inversion frequencies.

In total, 324 Anopheles funestus Giles specimens collected from seven houses in western Kenya and seven in coastal Kenya were scored for their paracentric chromosomal inversions with the aim of determining the level of genetic differentiation based on these inversions. Houses in each area were within a 2-km radius. The two areas are approximately 700 km apart. Only inversions 2a, 3a, 3b, and 5a were found to be polymorphic. Levels of polymorphism varied greatly between inversions. There were no significant deviations from Hardy-Weinberg expectations for samples from individual houses at one site or when data for houses in each area were pooled. Overall, the level of differentiation between western and coastal Kenya was significant, suggesting that the two populations are genetically isolated. Results based on inversion 2a alone were, however, not consistent with this conclusion. Founder effects and selection against the 2a inversion are discussed as possible explanations for this discrepancy.

Animals↗
PubMed2006

Synonymy of Calyptogena solidissima with Calyptogena kawamurai (Bivalvia: Vesicomyidae) and its population structure revealed by mitochondrial DNA sequences.

Nucleotide sequences of part (1,101 bp) of the mitochondrial cytochrome oxidase c subunit I (COI) gene were determined for two specimens of Calyptogena kawamurai collected in Kashima Nada and Suruga Bay, respectively. These sequences were identical to each other and to those from many individuals of Calyptogena solidissima, i.e., 11 of 12 specimens from a seep area in Nankai Trough, two of 20 from hydrothermal-vent fields in Okinawa Trough, and one of 14 from a seep area on Kuroshima Knoll. The nucleotide sequences of the 5' part (about 700 bp) of the first internal transcribed spacer (ITS-1) also showed a close relationship between C. kawamurai and C. solidissima. The radiating threads on the shell surface that were emphasized in describing C. solidissima are not consistent throughout these local populations. Variation in cardinal dentition was confirmed to be intraspecific by observations of a series of specimens. The shell length-height and shell length-width relationships of both species all fit a single regression line. These results suggest that C. solidissima is a junior synonym of C. kawamurai. The populations of Nankai Trough, Okinawa Trough, and Kuroshima Knoll were shown to be diverging genetically from each other. Populations of Okinawa Trough and Kuroshima Knoll are suggested to have derived independently from the most common haplotype of Nankai Trough.

Animals↗
PubMed2005

Repeat-induced point mutation and the population structure of transposable elements in Microbotryum violaceum.

Repeat-induced point mutation (RIP) is a genome defense in fungi that hypermutates repetitive DNA and is suggested to limit the accumulation of transposable elements. The genome of Microbotryum violaceum has a high density of transposable elements compared to other fungi, but there is also evidence of RIP activity. This is the first report of RIP in a basidiomycete and was obtained by sequencing multiple copies of the integrase gene of a copia-type transposable element and the helicase gene of a Helitron-type element. In M. violaceum, the targets for RIP mutations are the cytosine residues of TCG trinucleotide combinations. Although RIP is a linkage-dependent process that tends to increase the variation among repetitive sequences, a chromosome-specific substructuring was observed in the transposable element population. The observed chromosome-specific patterns are not consistent with RIP, but rather suggest an effect of gene conversion, which is also a linkage-dependent process but results in a homogenization of repeated sequences. Particular sequences were found more widely distributed within the genome than expected by chance and may reflect the recently active variants. Therefore, sequence variation of transposable elements in M. violaceum appears to be driven by selection for transposition ability in combination with the context-specific forces of the RIP and gene conversion.

Analysis of Variance↗