scholarly journals Molecular Characterization and Antimicrobial Susceptibility of C. jejuni Isolates from Italian Wild Bird Populations

Pathogens ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 304 ◽  
Author(s):  
Francesca Marotta ◽  
Anna Janowicz ◽  
Lisa Di Marcantonio ◽  
Claudia Ercole ◽  
Guido Di Donato ◽  
...  
Keyword(s):  
Nalidixic Acid ◽  
Point Mutations ◽  
Bird Species ◽  
Acid Resistance ◽  
Wild Birds ◽  
23S Rrna ◽  
The Novel ◽  
Phenotypic Resistance ◽  
Bird Populations ◽  
Sequence Types

Poultry is considered a major reservoir of human campylobacteriosis. It also been reported that not only poultry, but also wild birds, are capable of carrying C. jejuni, thus demonstrating to be a risk of spreading the bacteria in the environment. To gain insight into the population structure and investigate the antimicrobial resistance genotypes and phenotypes, we analyzed a collection of 135 C. jejuni from 15 species of wild birds in Italy. MLST revealed the presence of 41 sequence types (STs) and 13 clonal complexes (CCs). ST-179 complex and the generalist ST-45 complex were the most prevalent. Core genome MLST revealed that C. jejuni from ST-45 complex clustered according to the bird species, unlike the ST-179 complex which featured 3 different species in the same cluster. Overall we found a moderate prevalence of resistance to tetracycline (12.5%), ciprofloxacin and nalidixic acid (10%). The novel ST isolated from one pigeon showed resistance to all the antibiotics tested. The ST-179 complex (33.3%) was identified with significantly higher nalidixic acid resistance relative to other tested STs. Nine AMR genes (tet(O), cmeA, cmeB, cmeC, cmeR, aad, blaOXA-61, blaOXA-184 and erm(B)) and 23S rRNA and gyrA-associated point mutations were also described, indicating a concordance level between genotypic and phenotypic resistance of 23.3%, 23.4% and of 37.5% for streptomycin, tetracycline and quinolones/fluoroquinolones, respectively. We recommend that particular attention should be given to wild birds as key sentinel animals for the ecosystem contamination surveillance.

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 Genotypic Resistance inHelicobacter pyloriStrains Correlates with Susceptibility Test and Treatment Outcomes after Levofloxacin- and Clarithromycin-Based Therapies

2010 ◽  
Vol 55 (3) ◽  
pp. 1123-1129 ◽  
Author(s):  
Jyh-Ming Liou ◽  
Chi-Yang Chang ◽  
Wang-Huei Sheng ◽  
Yu-Chi Wang ◽  
Mei-Jyh Chen ◽  
...  
Keyword(s):  
Treatment Outcomes ◽  
Triple Therapy ◽  
Direct Sequencing ◽  
Point Mutations ◽  
Kappa Coefficient ◽  
23S Rrna ◽  
Genotypic Resistance ◽  
Phenotypic Resistance ◽  
Therapeutic Outcomes ◽  
H Pylori

ABSTRACTThe accuracy of genotypic resistance to levofloxacin (gyrAmutations) and its agreement with treatment outcomes after levofloxacin-based therapy have not been reported. We aimed to assess the correlation.Helicobacter pyloristrains isolated from patients who received levofloxacin-based and clarithromycin-based triple therapies in a previous randomized trial were analyzed for point mutations ingyrAand 23S rRNA. PCR followed by direct sequencing was used to assess thegyrAand 23S rRNA mutations. An agar dilution test was used to determine the MICs of clarithromycin and levofloxacin. We found that the agreement between genotypic and phenotypic resistance to levofloxacin was best when the MIC breakpoint was >1 μg/ml (kappa coefficient, 0.754). The eradication rates in patients with and withoutgyrAmutations were 41.7% and 82.7%, respectively (P= 0.003). The agreement between genotypic and phenotypic resistance to clarithromycin was best when the MIC breakpoint was >2 μg/ml (kappa, 0.694). The eradication rates in patients with and without 23S rRNA mutations were 7.7% and 93.5%, respectively (P< 0.001). The agreements (kappa coefficient) between therapeutic outcomes after clarithromycin-based triple therapy and genotypic and phenotypic resistance were 0.671 and 0.356, respectively. The agreements (kappa coefficient) between therapeutic outcomes after levofloxacin-based triple therapy and genotypic and phenotypic resistance were 0.244 and 0.190, respectively. In conclusion,gyrAand 23S rRNA mutations inH. pyloristrains appeared to be better markers than phenotypic resistance in the prediction of treatment outcomes. The optimal breakpoints for levofloxacin and clarithromycin resistance appeared to be >1 μg/ml and >2 μg/ml, respectively.

scholarly journals Genotypes and antibiotic resistance of bovineCampylobacterand their contribution to human campylobacteriosis

2014 ◽  
Vol 143 (11) ◽  
pp. 2373-2380 ◽  
Author(s):  
R. JONAS ◽  
S. KITTL ◽  
G. OVERESCH ◽  
P. KUHNERT
Keyword(s):  
Antibiotic Resistance ◽  
Point Mutations ◽  
Human Infection ◽  
Rrna Genes ◽  
23S Rrna ◽  
Campylobacter Coli ◽  
Source Attribution ◽  
23S Rrna Genes ◽  
Sequence Types ◽  
Human Campylobacteriosis

SUMMARYCampylobacter jejuniandCampylobacter coliare the most important bacterial causes of human gastroenteritis. Chicken has been recognized as a major source for human infection, whereas cattle might also contribute to a lesser extent. However, there is a paucity of information available regardingCampylobacterin Swiss cattle and their role for human campylobacteriosis. To gain more information on genotypes and antibiotic resistance of bovineC. jejuniandC. coliand on their contribution to human disease, 97 cattle isolates were analysed. Multilocus sequence typing (MLST) andflaBtyping were applied and thegyrAand 23S rRNA genes were screened for point mutations responsible for quinolone and macrolide resistance, respectively. A total of 37 sequence types (STs) and 44flaBtypes were identified, including two sequence types and fiveflaBtypes not previously described. Most common sequence types were ST21 (21%), ST61 (12%) and ST48 (11%). Only one isolate was macrolide resistant while 31% (n= 30) were quinolone resistant. Source attribution indicated chicken as the main source of human infection with cattle being second. In conclusion, cattle should not be underestimated as a potential source of human campylobacteriosis.

scholarly journals Molecular Epidemiology and Characterization of Campylobacter spp. Isolated from Wild Bird Populations in Northern England

2009 ◽  
Vol 75 (10) ◽  
pp. 3007-3015 ◽  
Author(s):  
Laura A. Hughes ◽  
Malcolm Bennett ◽  
Peter Coffey ◽  
John Elliott ◽  
Trevor R. Jones ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Wild Bird ◽  
Bird Species ◽  
Domestic Animal ◽  
Wild Birds ◽  
Campylobacter Coli ◽  
Coastal Habitat ◽  
Cross Sectional ◽  
Bird Populations

ABSTRACT Campylobacter infections have been reported at prevalences ranging from 2 to 50% in a range of wild bird species, although there have been few studies that have investigated the molecular epidemiology of Campylobacter spp. Consequently, whether wild birds are a source of infection in humans or domestic livestock or are mainly recipients of domestic animal strains and whether separate cycles of infection occur remain unknown. To address these questions, serial cross-sectional surveys of wild bird populations in northern England were carried out over a 2-year period. Fecal samples were collected from 2,084 wild bird individuals and screened for the presence of Campylobacter spp. A total of 56 isolates were recovered from 29 birds sampled at 15 of 167 diverse locales. Campylobacter jejuni, Campylobacter lari, and Campylobacter coli were detected by PCR, and the prevalences of different Campylobacter spp. in different avian families ranged from 0% to 33%. Characterization of 36 C. jejuni isolates by multilocus sequence typing revealed that wild birds carry both livestock-associated and unique strains of C. jejuni. However, the apparent absence of unique wild bird strains of C. jejuni in livestock suggests that the direction of infection is predominantly from livestock to wild birds. C. lari was detected mainly in wild birds sampled in an estuarine or coastal habitat. Fifteen C. lari isolates were analyzed by macrorestriction pulsed-field gel electrophoresis, which revealed genetically diverse populations of C. lari in Eurasian oystercatchers (Haematopus ostralegus) and clonal populations in magpies (Pica pica).

scholarly journals Increase in Nalidixic Acid Resistance among Non-Typhi Salmonella enterica Isolates in the United States from 1996 to 2003

2006 ◽  
Vol 51 (1) ◽  
pp. 195-197 ◽  
Author(s):  
Jennifer E. Stevenson ◽  
Kathryn Gay ◽  
Timothy J. Barrett ◽  
Felicita Medalla ◽  
Tom M. Chiller ◽  
...  
Keyword(s):  
Public Health ◽  
United States ◽  
Nalidixic Acid ◽  
Salmonella Enterica ◽  
Susceptibility Testing ◽  
Point Mutations ◽  
Acid Resistance ◽  
The United States ◽  
Control And Prevention ◽  
Nalidixic Acid Resistance

ABSTRACT Fluoroquinolones commonly are used to treat adult Salmonella infections. Fluoroquinolone treatment has failed for persons infected with nalidixic acid-resistant Salmonella. From 1996 to 2003, state public health laboratories forwarded 12,252 non-Typhi Salmonella enterica isolates to the Centers for Disease Control and Prevention for antimicrobial susceptibility testing; 203 (1.6%) of the isolates were nalidixic acid resistant, and 14 (7%) of those were ciprofloxacin resistant. Resistance to nalidixic acid significantly increased from 0.4% in 1996 to 2.3% in 2003. All ciprofloxacin-resistant isolates had at least one point mutation in the quinolone resistance determining region (QRDR) of gyrA and did not harbor qnr or have point mutations in the QRDR of gyrB, parC, or parE. Continued surveillance of antimicrobial resistance among non-Typhi S. enterica isolates is needed to mitigate the increasing prevalence of nalidixic acid resistance.

scholarly journals Quinolones resistance in Salmonella spp. isolated from broilers and chickens’ carcasses under federal inspection

2020 ◽  
Vol 40 (7) ◽  
pp. 519-524
Author(s):  
Ana Luisa O.C. Carneiro ◽  
Rosiane L. Silva ◽  
Isabela B.B.E. Rodrigues ◽  
Simone C. Machado ◽  
Nathalie C. Cunha ◽  
...  
Keyword(s):  
Nalidixic Acid ◽  
Salmonella Enterica ◽  
Mutation Screening ◽  
Saint Paul ◽  
Point Mutations ◽  
Salmonella Spp ◽  
Gyra Gene ◽  
Disk Diffusion Test ◽  
Genetic Sequencing ◽  
Phenotypic Resistance

ABSTRACT: We analyzed 77 Salmonella spp. strains, from which 20 were isolated from broilers (cloacal swabs) and 57 from chickens from slaughterhouses under federal inspection. The following serotypes were identified: Salmonella Saint Paul (29), Salmonella Heidelberg (27), Salmonella Anatum (9), Salmonella Cerro (5), Salmonella Senftenberg (5), Salmonella enterica (O: 4,5) (1) and Salmonella enterica (O: 9.12) (1). Fifteen strains (19.5%) were resistant to enrofloxacin, six (7.8%) to ciprofloxacin, and 26 (33.8%) to nalidixic acid in the Disk Diffusion Test. The fifteen enrofloxacin resistant strains were selected for the PCR to detect the genes gyrA, gyrB, parC, and parE, and genetic sequencing to identify mutations in these genes. Five strains (33.3%) had point mutations in the gyrA gene, and one (6.7%) presented a point mutation in the parC gene. None of the 15 strains had mutations in the gyrB and parE genes, and none had more than one mutation in the gyrA gene or the other genes. The presence of point mutations in the strains studied corroborates with the phenotypic resistance observed to nalidixic acid. However, it did not explain the resistance to fluoroquinolones found in the 15 strains. Other mechanisms may be related to the fluoroquinolones resistance, highlighting the need for additional mutation screening.

scholarly journals Genotype profiles of Helicobacter pylori from gastric biopsies and strains with antimicrobial-induced resistance

2020 ◽  
Vol 13 ◽  
pp. 175628482095259
Author(s):  
You-hua Wang ◽  
Fang-fei Wang ◽  
Xiao-ling Gong ◽  
Li-li Yan ◽  
Qiao-yun Zhao ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Induced Resistance ◽  
Antibiotic Susceptibility ◽  
Point Mutations ◽  
Test Method ◽  
23S Rrna ◽  
Sequencing Analysis ◽  
Gyra Gene ◽  
Phenotypic Resistance ◽  
Gastric Biopsies

Background and aims: The genotypic method could significantly shorten the time needed to obtain antibiotic susceptibility data for Helicobacter pylori. The aim of this study was to explore the profile of H. pylori from gastric biopsies and strains with antibiotic-induced resistance. Methods: A total of 124 gastric biopsies were used to perform gene sequencing and to perform bacterial culture and susceptibility testing. Seven susceptible strains were selected to develop resistance to clarithromycin, levofloxacin, and metronidazole. Four susceptible strains were selected to transfer candidate mutations. The genotype profiles of these groups were analyzed by sequencing analysis. The antibiotic susceptibility of these strains was detected using the E-test method. Results: Phenotypic resistance to clarithromycin, levofloxacin, and metronidazole was observed in 35.5%, 40.0%, and 79.8% strains, respectively. Point mutations in 23 S rRNA, gyrA, and rdxA genes were observed in 39.5%, 38.7%, and 86.3% of gastric biopsies, respectively. The A2143G mutation in the 23S rRNA occurs in most clarithromycin-resistant samples. The A2142C point mutation showed a higher efficacy than A2142G and A2143G for inducing clarithromycin resistance. The D91N and N87K mutations in gyrA occurs in most levofloxacin-resistant samples, and double point mutations showed a higher efficacy than single mutations for inducing levofloxacin resistance. Phenotypic resistance and mutations in rdxA lacked consistency. Conclusion: Genotype-based gastric biopsy analysis was reliable for determining clarithromycin and levofloxacin resistance. A2143G in 23S rRNA and N87K/D91N in the gyrA gene occurred in most resistant strains. Mutations in the rdxA gene were not good indicators of metronidazole resistance.

scholarly journals Rare alternative second line injectable drug resistance markers identified by gene-wise genome wide association in M. tuberculosis with unexplained resistance

2021 ◽  
Author(s):  
Derek Vanian Conkle-Gutierrez ◽  
Calvin Kim ◽  
Sarah M Ramirez-Busby ◽  
Samuel J Modlin ◽  
Mikael Mansjö ◽  
...  
Keyword(s):  
Statistical Power ◽  
Point Mutations ◽  
Kanamycin Resistance ◽  
The Novel ◽  
Second Line ◽  
Mechanisms Of Resistance ◽  
Phenotypic Resistance ◽  
Genomic Markers ◽  
Novel Association ◽  
Promoter Mutations

Point mutations in the rrs gene and eis promoter are known to confer resistance to second-line injectable drugs (SLIDs) amikacin (AMK), capreomycin (CAP), and kanamycin (KAN). While mutations in these canonical genes confer a majority of SLID-resistance, alternative mechanisms of resistance are not uncommon and threaten effective treatment decisions when using conventional molecular diagnostics. In total, 1184 clinical M. tuberculosis isolates from 7 countries were studied for genomic markers associated with phenotypic resistance. The markers rrs:A1401G and rrs:G1484T were associated with resistance to all three SLIDs, and three known markers in the eis promoter (eis:G-10A, eis:C-12T, and eis:C-14T) were similarly associated with kanamycin resistance (KAN-R). Among 325, 324, 270 AMK-R, CAP-R, and KAN-R isolates, 264 (81.2%), 250 (77.2%), and 249 (92.3%) harbored canonical mutations, respectively. Thirteen isolates harbored more than one canonical mutation. Canonical mutations did not account for 111 of the phenotypically resistant isolates. A gene-wise method identified three genes and promoters with mutations that, on aggregate, associated with unexplained resistance to at least one SLID. Our analysis associated whiB7 promoter mutations with KAN resistance, supporting clinical relevance for the previously demonstrated role of whiB7 overexpression in KAN resistance. We also provide evidence for the novel association of ppe51 (a gene previously associated with various antimicrobial compounds) with AMK resistance, and for the novel association of thrB with AMK and CAP resistance. The use of gene-wise association can provide additional insight, and therefore is recommended for identification of rare mechanisms of resistance when individual mutations carry insufficient statistical power.

scholarly journals Salmonella in Retail Food and Wild Birds in Singapore—Prevalence, Antimicrobial Resistance, and Sequence Types

2019 ◽  
Vol 16 (21) ◽  
pp. 4235 ◽  
Author(s):  
Aung ◽  
Chen ◽  
Chau ◽  
Yap ◽  
Lim ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Food Samples ◽  
Wild Birds ◽  
Whole Genome Analysis ◽  
Specific Sequence ◽  
Phenotypic Resistance ◽  
Faecal Samples ◽  
High Prevalence ◽  
Sequence Types ◽  
Retail Food

Non-typhoidal salmonellosis is a leading cause of foodborne zoonosis. To better understand the epidemiology of human salmonellosis, this study aimed to determine the prevalence, antimicrobial resistance and sequence types of Salmonella in retail food and wild birds (proximity to humans) in Singapore. We analyzed 21,428 cooked and ready-to-eat food and 1,510 residual faecal samples of wild birds collected during 2010–2015. Thirty-two Salmonella isolates from food and wild birds were subjected to disc diffusion and multi-locus sequence typing (MLST). Salmonella was isolated from 0.08% (17/21,428) of food and 0.99% (15/1510) of wild birds. None of the isolates from wild birds (n = 15) exhibited phenotypic resistance, while the isolates from food (47.1%, 8/17) showed a high prevalence of phenotypic resistance to, at least, one antimicrobial. These findings suggested that the avian Salmonella isolates had been subjected to less antimicrobial selection pressure than those from food samples. MLST revealed specific sequence types found in both food and wild birds. The study can guide future studies with whole-genome analysis on a larger number of isolates from various sectors for public health measures.

scholarly journals Antimicrobial Resistance Profiles and Macrolide Resistance Mechanisms of Campylobacter coli Isolated from Pigs and Chickens

2021 ◽  
Vol 9 (5) ◽  
pp. 1077
Author(s):  
Ji-Hyun Choi ◽  
Dong Chan Moon ◽  
Abraham Fikru Mechesso ◽  
Hee Young Kang ◽  
Su-Jeong Kim ◽  
...  
Keyword(s):  
Nalidixic Acid ◽  
Ribosomal Proteins ◽  
Resistance Mechanisms ◽  
23S Rrna ◽  
Considerable Proportion ◽  
Rrna Gene ◽  
Campylobacter Coli ◽  
Erythromycin Resistance ◽  
Public Health Hazards ◽  
Resistance Rates

We identified 1218 Campylobacter coli isolates from fecal and carcass samples of pigs (n = 643) and chickens (n = 575) between 2010 and 2018. About 99% of the isolates were resistant to at least one antimicrobial agent. The isolates exhibited high resistance rates (>75%) to ciprofloxacin, nalidixic acid, and tetracycline. Azithromycin and erythromycin resistance rates were the highest in isolates from pigs (39.7% and 39.2%, respectively) compared to those of chickens (15.8% and 16.3%, respectively). Additionally, a low-to-moderate proportion of the isolates were resistant to florfenicol, gentamicin, clindamycin, and telithromycin. Multidrug resistance (MDR) was found in 83.1% of the isolates, and profiles of MDR usually included ciprofloxacin, nalidixic acid, and tetracycline. We found point mutation (A2075G) in domain V of the 23S rRNA gene in the majority of erythromycin-resistant isolates. Multilocus sequence typing of 137 erythromycin-resistant C. coli isolates revealed 37 previously reported sequence types (STs) and 8 novel STs. M192I, A103VI, and G74A substitutions were frequently noted in the ribosomal proteins L4 or L22. Further, we identified a considerable proportion (>90%) of erythromycin-resistant isolates carrying virulence factor genes: flaA, cadF, ceuE, and VirB. The prudent use of antimicrobials and regular microbiological investigation in food animals will be vital in limiting the public health hazards of C. coli in Korea.

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