scholarly journals Genomic Analysis and Antimicrobial Resistance of Campylobacter jejuni and Campylobacter coli in Peru

2022 ◽  
Vol 12 ◽  
Author(s):  
Willi Quino ◽  
Junior Caro-Castro ◽  
Verónica Hurtado ◽  
Diana Flores-León ◽  
Narjol Gonzalez-Escalona ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
Virulence Factors ◽  
In Silico ◽  
Genomic Analysis ◽  
23S Rrna ◽  
Campylobacter Coli ◽  
Global Public Health ◽  
Emerging Pathogens ◽  
High Genetic Diversity

Campylobacter is the leading cause of human bacterial gastroenteritis worldwide and has a major impact on global public health. Whole Genome Sequencing (WGS) is a powerful tool applied in the study of foodborne pathogens. The objective of the present study was to apply WGS to determine the genetic diversity, virulence factors and determinants of antimicrobial resistance of the populations of C. jejuni and C. coli in Peru. A total of 129 Campylobacter strains (108 C. jejuni and 21 C. coli) were sequenced using Illumina Miseq platform. In silico MLST analysis identified a high genetic diversity among those strains with 30 sequence types (STs), several of them within 11 clonal complexes (CC) for C. jejuni, while the strains of C. coli belonged to a single CC with 8 different STs. Phylogeny analysis showed that Peruvian C. jejuni strains were divided into 2 clades with 5 populations, while C. coli formed a single clade with 4 populations. Furthermore, in silico analyses showed the presence of several genes associated with adherence, colonization and invasion among both species: cadF (83.7%), jlpA (81.4%), racR (100%), dnaJ (83.7%), pebA (83.7%), pldA (82.1%), porA (84.5%), ceuE (82.9%), ciaB (78.3%), iamB (86.8%), and flaC (100%). The majority (82.9%) of the Campylobacter strains carried the cdtABC operon which code for cytolethal distending toxin (CDT). Half of them (50.4%) carried genes associated with the presence of T6SS, while the frequency of genes associated with T4SS were relatively low (11.6%). Genetic markers associated with resistance to quinolones, tetracycline (tetO, tetW/N/W), beta-lactamases (blaoxa–61), macrolides (A2075G in 23S rRNA) were found in 94.5, 21.7, 66.7, 6.2, 69.8, and 18.6% of strains, respectively. The cmeABC multidrug efflux operon was present in 78.3% of strains. This study highlights the importance of using WGS in the surveillance of emerging pathogens associated with foodborne diseases, providing genomic information on genetic diversity, virulence mechanisms and determinants of antimicrobial resistance. The description of several Campylobacter genotypes having many virulence factors and resistance to quinolones and tetracyclines circulating in Peru provides important information which helps in the monitoring, control and prevention strategies of this emerging pathogen in our country.

scholarly journals Genomic analysis of the diversity, antimicrobial resistance and virulence potential of clinical Campylobacter jejuni and Campylobacter coli strains from Chile

2020 ◽  
Author(s):  
Veronica Bravo ◽  
Assaf Katz ◽  
Lorena Porte ◽  
Thomas Weitzel ◽  
Carmen Varela ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
South America ◽  
Campylobacter Jejuni ◽  
Virulence Factors ◽  
Epidemiological Data ◽  
Campylobacter Coli ◽  
Genome Sequences ◽  
High Genetic Diversity ◽  
Clinical Strains

ABSTRACTCampylobacter jejuni and Campylobacter coli are the leading cause of human gastroenteritis in the industrialized world and an emerging threat in developing countries. The incidence of campylobacteriosis in South America is greatly underestimated, mostly due to the lack of adequate diagnostic methods. Accordingly, there is limited genomic and epidemiological data from this region. In the present study, we performed a genome-wide analysis of the genetic diversity, virulence, and antimicrobial resistance of the largest collection of clinical C. jejuni and C. coli strains from Chile available to date (n=81), collected in 2017-2019 in Santiago, Chile. This culture collection accounts for over a third of the genome sequences available of clinical strains from South America. cgMLST analysis identified high genetic diversity as well as 13 novel STs and alleles in both C. jejuni and C. coli. Pangenome and virulome analyses showed a differential distribution of virulence factors, including both plasmid and chromosomally encoded T6SSs and T4SSs. Resistome analysis predicted widespread resistance to fluoroquinolones, but low rates of erythromycin resistance. This study provides valuable genomic and epidemiological data and highlights the need for further genomic epidemiology studies in Chile and other South American countries to better understand molecular epidemiology and antimicrobial resistance of this emerging intestinal pathogen.AUTHOR SUMMARYCampylobacter is the leading cause of bacterial gastroenteritis worldwide and an emerging and neglected pathogen in South America. In this study, we performed an in-depth analysis of the genome sequences of 69 C. jejuni and 12 C. coli clinical strains isolated from Chile, which account for over a third of the sequences from clinical strains available from South America. We identified a high genetic diversity among C. jejuni strains and the unexpected identification of clade 3 C. coli strains, which are infrequently isolated from humans in other regions of the world. Most strains harbored the virulence factors described for Campylobacter. While ~40% of strains harbored mutation in the gyrA gene described to confer fluoroquinolone resistance, very few strains encoded the determinants linked to macrolide resistance, currently used for the treatment of campylobacteriosis. Our study contributes to our knowledge of this important foodborne pathogen providing valuable data from South America.

scholarly journals Genomic analysis of the diversity, antimicrobial resistance and virulence potential of clinical Campylobacter jejuni and Campylobacter coli strains from Chile

2021 ◽  
Vol 15 (2) ◽  
pp. e0009207
Author(s):  
Veronica Bravo ◽  
Assaf Katz ◽  
Lorena Porte ◽  
Thomas Weitzel ◽  
Carmen Varela ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
Campylobacter Jejuni ◽  
Epidemiological Data ◽  
Diagnostic Methods ◽  
Campylobacter Coli ◽  
South American ◽  
Differential Distribution ◽  
High Genetic Diversity ◽  
A Genome

Campylobacter jejuni and Campylobacter coli are the leading cause of human gastroenteritis in the industrialized world and an emerging threat in developing countries. The incidence of campylobacteriosis in South America is greatly underestimated, mostly due to the lack of adequate diagnostic methods. Accordingly, there is limited genomic and epidemiological data from this region. In the present study, we performed a genome-wide analysis of the genetic diversity, virulence, and antimicrobial resistance of the largest collection of clinical C. jejuni and C. coli strains from Chile available to date (n = 81), collected in 2017–2019 in Santiago, Chile. This culture collection accounts for more than one third of the available genome sequences from South American clinical strains. cgMLST analysis identified high genetic diversity as well as 13 novel STs and alleles in both C. jejuni and C. coli. Pangenome and virulome analyses showed a differential distribution of virulence factors, including both plasmid and chromosomally encoded T6SSs and T4SSs. Resistome analysis predicted widespread resistance to fluoroquinolones, but low rates of erythromycin resistance. This study provides valuable genomic and epidemiological data and highlights the need for further genomic epidemiology studies in Chile and other South American countries to better understand molecular epidemiology and antimicrobial resistance of this emerging intestinal pathogen.

scholarly journals Virulence and Antimicrobial Resistance inCampylobacterspp. from a Peruvian Pediatric Cohort

Scientifica ◽  
2017 ◽  
Vol 2017 ◽  
pp. 1-8 ◽  
Author(s):  
Angela Lluque ◽  
Maribel Riveros ◽  
Ana Prada ◽  
Theresa J. Ochoa ◽  
Joaquim Ruiz
Keyword(s):  
Cohort Study ◽  
Antimicrobial Resistance ◽  
Nalidixic Acid ◽  
Campylobacter Jejuni ◽  
Virulence Factors ◽  
Antimicrobial Agents ◽  
23S Rrna ◽  
Campylobacter Coli ◽  
Ciprofloxacin Resistance ◽  
Almost All

The presence of virulence factors (VFs) and mechanisms of quinolones and macrolide resistance was analyzed inCampylobacterspp. from a pediatric cohort study in Lima. In 149 isolates (39Campylobacter jejuniand 24Campylobacter colifrom diarrheic cases; 57C. jejuniand 29C. colifrom controls), the presence of thecdtABCandcadFgenes andiammarker was established. Nalidixic acid, ciprofloxacin, erythromycin, and azithromycin susceptibilities were established in 115 isolates and tetracycline-susceptibility was established in 100 isolates. The presence of mutations in thegyrA,parC,and23S rRNAgenes was determined. ThecadFgene and all genes from thecdtABCoperon were significantly more frequent amongC. jejuni(P<0.0001); theiammarker was more frequent inC. coli(P<0.0001). No differences were observed in VFs between cases and controls. Almost all isolates were tetracycline-resistant; nalidixic acid and ciprofloxacin resistance reached levels of 90.4% and 88.7%, respectively. Resistance to macrolides was 13% (C. jejuni4.3%;C. coli26.1%). Resistance to ciprofloxacin was related to GyrA Thr86 substitutions, while 13 of 15 macrolide-resistant isolates possessed a23S rRNAmutation (A2075G). Differences in the presence of VFs and alarming levels of resistance to tested antimicrobial agents were observed amongC. jejuniandC. coli.

scholarly journals Prevalence, Population Diversity and Antimicrobial Resistance of Campylobacter coli Isolated in Italian Swine at Slaughterhouse

2020 ◽  
Vol 8 (2) ◽  
pp. 222 ◽  
Author(s):  
Guido Di Donato ◽  
Francesca Marotta ◽  
Roberta Nuvoloni ◽  
Katiuscia Zilli ◽  
Diana Neri ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
Population Diversity ◽  
Campylobacter Coli ◽  
Gyra Gene ◽  
Genotypic Resistance ◽  
High Genetic Diversity ◽  
Genetic Profiles ◽  
Carcass Contamination ◽  
Sequence Types

Campylobacter spp. are among the microorganisms most commonly associated with foodborne disease. Swine are known to be the main reservoir of Campylobacter coli and a possible source infection of humans as a result of carcass contamination at slaughter. The aim of this study was to evaluate the prevalence of C. coli contamination in swine carcasses, the antimicrobial resistance (AMR) patterns of isolates and the genetic diversity between strains obtained from swine and those isolated from humans. The prevalence of contamination was higher on carcasses (50.4%) than in faeces (32.9%). The 162 C. coli isolated from swine were examined by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The results of PFGE indicated a high genetic diversity among the isolates, with 25 different PFGE types. MLST assigned 51 sequence types (STs) to isolates. The most common genotype was ST-854 (16.04%), ST-9264 (10.49 %) and ST-1016 (6.08 %). Results of AMR showed a high resistance to quinolones and fluoroquinolones together with aminoglycosides and tetracycline. Many strains were multi-resistant with predominant R-type TeSCipNa (57%). Five resistance genes were detected along with mutation in the gyrA gene. A strong correlation between phenotypic and genotypic resistance was found for fluoroquinolone and tetracycline. Genetic profiles obtained in swine isolates were compared to those of 11 human strains. All human strains and 64.19% of animal strains (104/162) were assigned to the ST-828 clonal complex.

scholarly journals Whole genome-based characterisation of antimicrobial resistance and genetic diversity in Campylobacter jejuni and Campylobacter coli from ruminants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Medelin Ocejo ◽  
Beatriz Oporto ◽  
José Luis Lavín ◽  
Ana Hurtado
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
Campylobacter Jejuni ◽  
Resistance Genes ◽  
Campylobacter Coli ◽  
Whole Genome ◽  
Northern Spain ◽  
Sequence Alignments ◽  
Phenotypic Data ◽  
Wide Range

AbstractCampylobacter, a leading cause of gastroenteritis in humans, asymptomatically colonises the intestinal tract of a wide range of animals.Although antimicrobial treatment is restricted to severe cases, the increase of antimicrobial resistance (AMR) is a concern. Considering the significant contribution of ruminants as reservoirs of resistant Campylobacter, Illumina whole-genome sequencing was used to characterise the mechanisms of AMR in Campylobacter jejuni and Campylobacter coli recovered from beef cattle, dairy cattle, and sheep in northern Spain. Genome analysis showed extensive genetic diversity that clearly separated both species. Resistance genotypes were identified by screening assembled sequences with BLASTn and ABRicate, and additional sequence alignments were performed to search for frameshift mutations and gene modifications. A high correlation was observed between phenotypic resistance to a given antimicrobial and the presence of the corresponding known resistance genes. Detailed sequence analysis allowed us to detect the recently described mosaic tet(O/M/O) gene in one C. coli, describe possible new alleles of blaOXA-61-like genes, and decipher the genetic context of aminoglycoside resistance genes, as well as the plasmid/chromosomal location of the different AMR genes and their implication for resistance spread. Updated resistance gene databases and detailed analysis of the matched open reading frames are needed to avoid errors when using WGS-based analysis pipelines for AMR detection in the absence of phenotypic data.

scholarly journals Genomic Analysis of Antimicrobial Resistance Genotype-to-Phenotype Agreement in Helicobacter pylori

2020 ◽  
Vol 9 (1) ◽  
pp. 2
Author(s):  
Tal Domanovich-Asor ◽  
Yair Motro ◽  
Boris Khalfin ◽  
Hillary A. Craddock ◽  
Avi Peretz ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Antimicrobial Resistance ◽  
Point Mutations ◽  
Genomic Analysis ◽  
23S Rrna ◽  
Phenotype Correlation ◽  
Bioinformatics Pipeline ◽  
Phenotypic Resistance ◽  
Commercial Kits ◽  
H Pylori

Antimicrobial resistance (AMR) in Helicobacter pylori is increasing and can result in treatment failure and inappropriate antibiotic usage. This study used whole genome sequencing (WGS) to comprehensively analyze the H. pylori resistome and phylogeny in order to characterize Israeli H. pylori. Israeli H. pylori isolates (n = 48) underwent antimicrobial susceptibility testing (AST) against five antimicrobials and WGS analysis. Literature review identified 111 mutations reported to correlate with phenotypic resistance to these antimicrobials. Analysis was conducted via our in-house bioinformatics pipeline targeting point mutations in the relevant genes (pbp1A, 23S rRNA, gyrA, rdxA, frxA, and rpoB) in order to assess genotype-to-phenotype correlation. Resistance rates of study isolates were as follows: clarithromycin 54%, metronidazole 31%, amoxicillin 10%, rifampicin 4%, and levofloxacin 2%. Genotype-to-phenotype correlation was inconsistent; for every analyzed gene at least one phenotypically susceptible isolate was found to have a mutation previously associated with resistance. This was also observed regarding mutations commonly used in commercial kits to diagnose AMR in H. pylori cases. Furthermore, 11 novel point mutations associated with a resistant phenotype were detected. Analysis of a unique set of H. pylori isolates demonstrates that inferring resistance phenotypes from WGS in H. pylori remains challenging and should be optimized further.

scholarly journals Genetic diversity and drug susceptibility patterns of the Mycobacterium tuberculosis complex in Yunnan, China

2019 ◽  
Vol 39 (5) ◽  
Author(s):  
Ruolan Bai ◽  
Shuijing Chi ◽  
Xiaofei Li ◽  
Xiting Dai ◽  
Zhenhua Ji ◽  
...  
Keyword(s):  
Public Health ◽  
Genetic Diversity ◽  
Mycobacterium Tuberculosis ◽  
Public Health Problem ◽  
Drug Susceptibility ◽  
Drug Resistant ◽  
Global Public Health ◽  
High Genetic Diversity ◽  
Dominant Feature ◽  
Mdr Tb

AbstractTuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb) which has been threatening global public health for many years. High genetic diversity is dominant feature of Mtb. Increasing cases of multidrug-resistant (MDR) tuberculosis (MDR-TB) is a serious public health problem to TB control in China. Spontaneous mutations in the Mtb genome can alter proteins which are the target of drugs, making the bacteria drug resistant. The purpose of the present study was to analyze the genotype of Mtb isolates from some areas in Yunnan, China and explore the association between genotypes and MDR-TB. Using spoligotyping, we identified Beijing genotypes, six non-Beijing genotypes and a number of orphan genotypes from 270 Mtb isolates from patients in Yunnan Province during 2014–2016. Of 270 Mtb isolates, 102 clinical Mtb strains were identified as drug-resistant (DR) by drug susceptibility testing (DST), among them, 52 MDR strains. Beijing genotypes occupied the highest MDR proportion (78.85%) followed by the orphan genotypes (15.38%). The characteristics of MDR strains showed high genetic diversity. The results will help to efficiently improve diagnosis and treatment and provide valuable information for Mtb molecular epidemiology.

scholarly journals Photobacterium damselaesubsp.damselae, a Generalist Pathogen with Unique Virulence Factors and High Genetic Diversity

2018 ◽  
Vol 200 (15) ◽  
Author(s):  
Carlos R. Osorio ◽  
Ana Vences ◽  
Xosé M. Matanza ◽  
Mateus S. Terceti
Keyword(s):  
Genetic Diversity ◽  
Virulence Factors ◽  
Cell Envelope ◽  
Fatal Outcome ◽  
Regulatory System ◽  
Cytolytic Activity ◽  
Conjugative Plasmid ◽  
Marine Animals ◽  
High Genetic Diversity ◽  
Content Type

ABSTRACTPhotobacterium damselaesubsp.damselaecauses vibriosis in a variety of marine animals, including fish species of importance in aquaculture. It also may cause wound infections in humans that can progress to a fatal outcome. Two major virulence factors are encoded within the large conjugative plasmid pPHDD1, the phospholipase D damselysin (Dly) and the pore-forming toxin phobalysin P (PhlyP). The two toxins exert hemolytic and cytolytic activities in a synergistic manner. Even though PhlyP has close homologues in manyVibriospecies, it has unique features that differentiate it from related toxins. Dly phospholipase constitutes a singular trait ofP. damselaesubsp.damselaeamong theVibrionaceae, although related toxins are found in members of theAeromonadaceae. Fish farm outbreaks can also be caused by plasmidless strains. Such observations led to the characterization of two ubiquitous chromosome-encoded toxins with lesser cytolytic activity, the pore forming-toxin phobalysin C (PhlyC) and the phospholipase-hemolysin PlpV. The high genetic diversity of this pathogen deserves special attention, as it has a number of strain-specific features, including the cell envelope polysaccharide synthesis clusters. Fish outbreaks are likely caused by multiclonal populations which contain both plasmidless and pPHDD1-harboring isolates and not by well-adapted clonal complexes. Still, among such genetic heterogeneity, it is feasible to identify conserved weak points in the biology of this bacterium: the two-component regulatory system RstAB (CarSR) was found to be necessary for the maximal production of virulence factors, and its inactivation severely impaired virulence.

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