Antimicrobial Resistance Profiles and Phylogenetic Analysis of Campylobacter jejuni Strains Isolated in Brazil by Whole Genome Sequencing

2020 ◽  
Author(s):  
Miliane Rodrigues Frazão ◽  
Guojie Cao ◽  
Marta Inês Cazentini Medeiros ◽  
Sheila da Silva Duque ◽  
Marc William Allard ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Campylobacter Jejuni ◽  
Genome Sequencing ◽  
Whole Genome

scholarly journals Prediction of antimicrobial resistance in clinical Campylobacter jejuni isolates from whole-genome sequencing data

2020 ◽  
Author(s):  
Louise Gade Dahl ◽  
Katrine Grimstrup Joensen ◽  
Mark Thomas Østerlund ◽  
Kristoffer Kiil ◽  
Eva Møller Nielsen
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Campylobacter Jejuni ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Point Mutations ◽  
23S Rrna ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data

Abstract Campylobacter jejuni is recognised as the leading cause of bacterial gastroenteritis in industrialised countries. Although the majority of Campylobacter infections are self-limiting, antimicrobial treatment is necessary in severe cases. Therefore, the development of antimicrobial resistance (AMR) in Campylobacter is a growing public health challenge and surveillance of AMR is important for bacterial disease control. The aim of this study was to predict antimicrobial resistance in C. jejuni from whole-genome sequencing data. A total of 516 clinical C. jejuni isolates collected between 2014 and 2017 were subjected to WGS. Resistance phenotypes were determined by standard broth dilution, categorising isolates as either susceptible or resistant based on epidemiological cutoffs for six antimicrobials: ciprofloxacin, nalidixic acid, erythromycin, gentamicin, streptomycin, and tetracycline. Resistance genotypes were identified using an in-house database containing reference genes with known point mutations and the presence of resistance genes was determined using the ResFinder database and four bioinformatical methods (modified KMA, ABRicate, ARIBA, and ResFinder Batch Upload). We identified seven resistance genes including tet(O), tet(O/32/O), ant(6)-Ia, aph(2″)-If, blaOXA, aph(3′)-III, and cat as well as mutations in three genes: gyrA, 23S rRNA, and rpsL. There was a high correlation between phenotypic resistance and the presence of known resistance genes and/or point mutations. A correlation above 98% was seen for all antimicrobials except streptomycin with a correlation of 92%. In conclusion, we found that WGS can predict antimicrobial resistance with a high degree of accuracy and have the potential to be a powerful tool for AMR surveillance.

scholarly journals Monitoring of Antimicrobial Resistance to Aminoglycosides and Macrolides in Campylobacter coli and Campylobacter jejuni From Healthy Livestock in Spain (2002–2018)

2021 ◽  
Vol 12 ◽  
Author(s):  
Vicente Lopez-Chavarrias ◽  
Maria Ugarte-Ruiz ◽  
Carmen Barcena ◽  
Adolfo Olarra ◽  
Maria Garcia ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Campylobacter Jejuni ◽  
Genome Sequencing ◽  
Synonymous Codon ◽  
Bacterial Species ◽  
Simultaneous Presentation ◽  
Surveillance Program ◽  
Campylobacter Coli ◽  
Whole Genome

Antimicrobial resistance (AMR) in Campylobacter spp. (Campylobacter coli and Campylobacter jejuni) is a concern due to its importance in public health, particularly when it involves aminoglycosides and macrolides, drugs of choice for treatment of human cases. Co-resistance to these two antimicrobial classes involves transfer of genetic elements and/or acquisition of mutations in different genetic loci, which can in turn spread through vertical or horizontal gene transfer (HGT) phenomena, with each route having different potential implications. This study aimed at evaluating the association between the presence of phenotypic resistance to these two antimicrobial classes in C. coli and C. jejuni recovered from livestock at slaughterhouses in Spain (as part of the AMR surveillance program), and at assessing the genetic heterogeneity between resistant and susceptible isolates by analysing the “short variable region” (SVR) of the flaA gene. Over the 2002–2018 period, antimicrobial susceptibility test results from 10,965 Campylobacter isolates retrieved from fecal samples of broilers, turkeys, pigs and cattle were collected to compare the proportion of resistant isolates and the Minimum Inhibitory Concentrations (MICs) against six antimicrobials including gentamicin (GEN), streptomycin (STR), and erythromycin (ERY). AMR-associated genes were determined for a group of 51 isolates subjected to whole genome sequencing, and the flaA SVR of a subset of 168 isolates from all hosts with different resistotypes was used to build a Neighbor-Joining-based phylogenetic tree and assess the existence of groups by means of “relative synonymous codon usage” (RSCU) analysis. The proportion of antimicrobial resistant isolates to both, aminoglycosides and macrolides, varied widely for C. coli (7–91%) and less for C. jejuni (all hosts 0–11%). Across hosts, these proportions were 7–56% in poultry, 12–82% in cattle, and 22–91% in pigs for C. coli and 0–8% in poultry and 1–11% in cattle for C. jejuni. Comparison of the MIC distributions revealed significant host-specific differences only for ERY in C. jejuni (p = 0.032). A significant association in the simultaneous presentation of AMR to both antimicrobial classes was observed across hosts/bacterial species. The flaA gene analysis showed clustering of isolates sharing resistotype and to a lesser degree bacterial species and host. Several resistance markers associated with resistance to aminoglycosides and macrolides were found among the sequenced isolates. The consistent association between the simultaneous presentation of AMR to aminoglycosides and macrolides in all hosts could be due to the persistence of strains and/or resistance mechanisms in Campylobacter populations in livestock over time. Further studies based on whole genome sequencing are needed to assess the epidemiological links between hosts and bacterial strains.

scholarly journals Antimicrobial resistance profiling and phylogenetic analysis of Neisseria gonorrhoeae clinical isolates from Kenya in a resource-limited setting

2020 ◽  
Author(s):  
Meshack O Juma ◽  
Arun Sankaradoss ◽  
Redcliff Ndombi ◽  
Patrick Mwaura ◽  
Tina Damodar ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Phylogenetic Analysis ◽  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Resource Limited Settings ◽  
Resource Limited ◽  
The World

Background Africa has one of the highest incidences of gonorrhoea, but not much information is available on the relatedness with strains from other geographical locations. Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a major public health threat, with the bacteria gaining resistance to most of the available antibiotics, compromising treatment across the world. Whole-genome sequencing is an efficient way of predicting AMR determinants and their spread in the human population. Previous studies on Kenyan gonococcal samples have focused on plasmid-mediated drug resistance and fluoroquinolone resistance using Illumina sequencing. Recent advances in next-generation sequencing technologies like Oxford Nanopore Technology (ONT) have helped in the generation of longer reads of DNA in a shorter duration with lower cost. However, long-reads are error-prone. The increasing accuracy of base-calling algorithms, high throughput, error-correction strategies, and ease of using the mobile sequencer in remote areas is leading to the adoption of the MinION sequencer (ONT), for routine microbial genome sequencing. Methods To investigate whether MinION-only sequencing is sufficient for diagnosis, genome sequencing and downstream analysis like inferring phylogenetic relationships and detection of AMR in resource-limited settings, we sequenced the genomes of fourteen clinical isolates suspected to be N. gonorrhoeae from Nairobi, Kenya. The isolates were tested using standard bacteriological methods for identification, interpretted using analytical profile index and antibiotic susceptibility tests had indicated ciprofloxacin and gentamycin resistance. Using whole genome sequencing, the isolates were confirmed to be cases of N. gonorrhoeae (n=12), Additionally, we identified reads from N. meningitidis (n=2) and both of N. gonorrhoeae and Moraxella osloensis (n=3) in the sample (co-infections) respectively, which have been implicated in sexually transmitted infections in the recent years. The near-complete N. gonorrhoeae genomes (n=10) were anaysed further for mutations/factors causing AMR using an in-house database of mutations curated from the literature. We attempted to understand the basis of drug resistance using homology modelling of AMR proteins, using known structures from other bacteria. Results We observe that Ciprofloxacin resistance is associated with multiple mutations in both gyrA and parC. We identified mutations conferring tetracycline (rpsJ) and Sulfonamide (folA) resistance in all the isolates and plasmids encoding beta-lactamase and tet(M) were identified in almost all of the strains. Phylogenetic analysis clustered the nine isolates into clades containing previously sequenced genomes from Kenya and countries across the world. Conclusion Here, we demonstrate the utility of mobile DNA sequencing technology supplemented with reference-based assembly in sequence typing and elucidating the basis of AMR. Bioinformatics profiling to predict AMR can be used along with routine AMR susceptibily tests in clinics. The workflow followed in the study, including AMR mutation dataset creation and the genome identification, assembly and analysis, can be used for the genome assembly and analysis of any clinical isolate. Further studies are required to determine the utility of real-time sequencing in the outbreak investigations, diagnosis and management of infections, especially in resource-limited settings.

Whole Genome Sequencing and Phylogenetic Analysis of the Rabies Virus Strain Moscow 3253 Adapted to a Vero Cell Line

2020 ◽  
Vol 35 (4) ◽  
pp. 237-242
Author(s):  
Ya. M. Krasnov ◽  
Zh. V. Alkhova ◽  
S. V. Generalov ◽  
I. V. Tuchkov ◽  
E. A. Naryshkina ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Vero Cell ◽  
Whole Genome Sequencing ◽  
Cell Line ◽  
Rabies Virus ◽  
Genome Sequencing ◽  
Virus Strain ◽  
Whole Genome ◽  
Vero Cell Line ◽  
Rabies Virus Strain

Identification of multiple species and subpopulations among Australian clinical Sporothrix isolates using whole genome sequencing

2018 ◽  
Vol 57 (7) ◽  
pp. 905-908 ◽  
Author(s):  
David New ◽  
Alicia G Beukers ◽  
Sarah E Kidd ◽  
Adam J Merritt ◽  
Kerry Weeks ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Sporothrix Schenckii ◽  
Sensu Stricto ◽  
Northern Territory ◽  
Whole Genome ◽  
Phylogenetic Resolution ◽  
Genetic Clustering ◽  
Multiple Species

AbstractWhole genome sequencing (WGS) was used to demonstrate the wide genetic variability within Sporothrix schenckii sensu lato and establish that there are two main species of Sporothrix within Australian clinical isolates—S. schenckii sensu stricto and Sporothrix globosa. We also demonstrated southwest Western Australia contained genetically similar S. schenckii ss strains that are distinct from strains isolated in the eastern and northern states of Australia. Some genetic clustering by region was also noted for northern NSW, Queensland, and Northern Territory. Phylogenetic analysis of WGS data provided greater phylogenetic resolution compared to analysis of the calmodulin gene alone.

scholarly journals Putative Integrative Mobile Elements That Exploit the Xer Recombination Machinery Carrying blaIMI-Type Carbapenemase Genes in Enterobacter cloacae Complex Isolates in Singapore

2017 ◽  
Vol 62 (1) ◽  
Author(s):  
Tse H. Koh ◽  
Nurdyana Binte Abdul Rahman ◽  
Jeanette W. P. Teo ◽  
My-Van La ◽  
Balamurugan Periaswamy ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Multilocus Sequence Typing ◽  
Enterobacter Cloacae ◽  
Mobile Elements ◽  
Whole Genome ◽  
Content Type ◽  
Flanking Regions ◽  
Enterobacter Cloacae Complex

ABSTRACT Whole-genome sequencing was performed on 16 isolates of the carbapenemase-producing Enterobacter cloacae complex to determine the flanking regions of bla IMI-type genes. Phylogenetic analysis of multilocus sequence typing (MLST) targets separated the isolates into 4 clusters. The bla IMI-type genes were all found on Xer-dependent integrative mobile elements (IMEX). The IMEX elements of 5 isolates were similar to those described in Canada, while the remainder were novel. Five isolates had IMEX elements lacking a resolvase and recombinase.

scholarly journals Piglet Gut and in-Barn Manure from Farms on a Raised without Antibiotics Program Display Reduced Antimicrobial Resistance but an Increased Prevalence of Pathogens

Antibiotics ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1152
Author(s):  
Samuel M. Chekabab ◽  
John R. Lawrence ◽  
Alvin C. Alvarado ◽  
Bernardo Z. Predicala ◽  
Darren R. Korber
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Fecal Samples ◽  
Time Points ◽  
Conventional Farms ◽  
Production Practices ◽  
On Farm ◽  
The Impact

In response to new stringent regulations in Canada regarding the use of antibiotics in animal production, many farms have implemented practices to produce animals that are raised without antibiotics (RWA) from birth to slaughter. This study aims to assess the impact of RWA production practices on reducing the actual total on-farm use of antibiotics, the occurrence of pathogens, and the prevalence of antimicrobial resistance (AMR). A 28-month longitudinal surveillance of farms that adopted the RWA program and conventional farms using antibiotics in accordance with the new regulations (non-RWA) was conducted by collecting fecal samples from 6-week-old pigs and composite manure from the barn over six time points and applying whole-genome sequencing (WGS) to assess the prevalence of AMR genes as well as the abundance of pathogens. Analysis of in-barn drug use records confirmed the decreased consumption of antibiotics in RWA barns compared to non-RWA barns. WGS analyses revealed that RWA barns had reduced the frequency of AMR genes in piglet feces and in-barn manure. However, metagenomic analyses showed that RWA barns had a significant increase in the frequency of pathogenic Firmicutes in fecal samples and pathogenic Proteobacteria in barn manure samples.

scholarly journals Serotype Diversity and Antimicrobial Resistance amongSalmonella entericaIsolates from Patients at an Equine Referral Hospital

2018 ◽  
Vol 84 (13) ◽  
pp. e02829-17 ◽  
Author(s):  
I. M. Leon ◽  
S. D. Lawhon ◽  
K. N. Norman ◽  
D. S. Threadgill ◽  
N. Ohta ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Referral Hospital ◽  
Whole Genome ◽  
Content Type ◽  
Genes Encoding ◽  
Life Threatening ◽  
Common Serotypes

ABSTRACTAlthoughSalmonella entericacan produce life-threatening colitis in horses, certain serotypes are more commonly associated with clinical disease. Our aim was to evaluate the proportional morbidity attributed to different serotypes, as well as the phenotypic and genotypic antimicrobial resistance (AMR) ofSalmonellaisolates from patients at an equine referral hospital in the southern United States. A total of 255Salmonellaisolates was obtained from clinical samples of patients admitted to the hospital between 2007 and 2015. Phenotypic resistance to 14 antibiotics surveilled by the U.S. National Antimicrobial Resistance Monitoring System was determined using a commercially available panel. Whole-genome sequencing was used to identify serotypes and genotypic AMR. The most common serotypes wereSalmonella entericaserotype Newport (18%),Salmonella entericaserotype Anatum (15.2%), andSalmonella entericaserotype Braenderup (11.8%). Most (n= 219) of the isolates were pansusceptible, while 25 were multidrug resistant (≥3 antimicrobial classes). Genes encoding beta-lactam resistance, such asblaCMY-2,blaSHV-12,blaCTX-M-27, andblaTEM-1B, were detected. TheqnrB2 andaac(6′)-Ib-crgenes were present in isolates with reduced susceptibility to ciprofloxacin. Genes encoding resistance to gentamicin (aph(3′)-Ia,aac(6′)-IIc), streptomycin (strA andstrB), sulfonamides (sul1), trimethoprim (dfrA), phenicols (catA), tetracyclines [tet(A) andtet(E)], and macrolides [ere(A)] were also identified. The main predicted incompatibility plasmid type was I1 (10%). Core genome-based analyses revealed phylogenetic associations between isolates of common serotypes. The presence of AMRSalmonellain equine patients increases the risk of unsuccessful treatment and causes concern for potential zoonotic transmission to attending veterinary personnel, animal caretakers, and horse owners. Understanding the epidemiology ofSalmonellain horses admitted to referral hospitals is important for the prevention, control, and treatment of salmonellosis.IMPORTANCEIn horses, salmonellosis is a leading cause of life-threatening colitis. At veterinary teaching hospitals, nosocomial outbreaks can increase the risk of zoonotic transmission, lead to restrictions on admissions, impact hospital reputation, and interrupt educational activities. The antimicrobials most often used in horses are included in the 5th revision of the World Health Organization's list of critically important antimicrobials for human medicine. Recent studies have demonstrated a trend of increasing bacterial resistance to drugs commonly used to treatSalmonellainfections. In this study, we identify temporal trends in the distribution ofSalmonellaserotypes and their mechanisms of antimicrobial resistance; furthermore, we are able to determine the likely origin of several temporal clusters of infection by using whole-genome sequencing. These data can be used to focus strategies to better contain the dissemination and enhance the mitigation ofSalmonellainfections and to provide evidence-based policies and guidelines to steward antimicrobial use in veterinary medicine.

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