scholarly journals Whole genomic sequencing based genotyping reveals a specific X3 sublineage restricted to Mexico and related with multidrug resistance

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ana Cristina Jiménez-Ruano ◽  
Carlos Francisco Madrazo-Moya ◽  
Irving Cancino-Muñoz ◽  
Paulina M. Mejía-Ponce ◽  
Cuauhtémoc Licona-Cassani ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Multidrug Resistant ◽  
Genomic Sequencing ◽  
Whole Genome ◽  
Drug Resistant ◽  
The Past ◽  
High Prevalence ◽  
Genomic Cluster

AbstractWhole genome sequencing (WGS) has been shown to be superior to traditional procedures of genotyping in tuberculosis (TB), nevertheless, reports of its use in drug resistant TB (DR-TB) isolates circulating in Mexico, are practically unknown. Considering the above the main of this work was to identify and characterize the lineages and genomic transmission clusters present in 67 DR-TB isolates circulating in southeastern Mexico. The results show the presence of three major lineages: L1 (3%), L2 (3%) and L4 (94%), the last one included 16 sublineages. Sublineage 4.1.1.3 (X3) was predominant in 18 (27%) of the isolates, including one genomic cluster, formed by eleven multidrug resistant isolates and sharing the SIT 3278, which seems to be restricted to Mexico. By the use of WGS, it was possible to identify the high prevalence of L4 and a high number of sublineages circulating in the region, also was recognized the presence of a novel X3 sublineage, formed exclusively by multidrug resistant isolates and with restrictive circulation in Mexico for at least the past 17 years.

scholarly journals The use of whole-genome sequencing in cluster investigation of a multidrug-resistant tuberculosis outbreak

2018 ◽  
Vol 51 (6) ◽  
pp. 1702313 ◽  
Author(s):  
Maeve K. Lalor ◽  
Nicola Casali ◽  
Timothy M. Walker ◽  
Laura F. Anderson ◽  
Jennifer A. Davidson ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Multidrug Resistant ◽  
Epidemiological Methods ◽  
Whole Genome ◽  
Transmission Network ◽  
Drug Resistant ◽  
Nucleotide Polymorphisms ◽  
The Uk ◽  
Epidemiological Information

We used whole-genome sequencing (WGS) to delineate transmission networks and investigate the benefits of WGS during cluster investigation.We included clustered cases of multidrug-resistant (MDR) tuberculosis (TB)/extensively drug-resistant (XDR) TB linked by mycobacterial interspersed repetitive unit variable tandem repeat (MIRU-VNTR) strain typing or epidemiological information in the national cluster B1006, notified between 2007 and 2013 in the UK. We excluded from further investigation cases whose isolates differed by greater than 12 single nucleotide polymorphisms (SNPs). Data relating to patients' social networks were collected.27 cases were investigated and 22 had WGS, eight of which (36%) were excluded as their isolates differed by more than 12 SNPs to other cases. 18 cases were ruled into the transmission network based on genomic and epidemiological information. Evidence of transmission was inconclusive in seven out of 18 cases (39%) in the transmission network following WGS and epidemiological investigation.This investigation of a drug-resistant TB cluster illustrates the opportunities and limitations of WGS in understanding transmission in a setting with a high proportion of migrant cases. The use of WGS should be combined with classical epidemiological methods. However, not every cluster will be solvable, regardless of the quality of genomic data.

Whole genome analysis of extensively drug-resistant Acinetobacter bau-mannii clinical isolates in Thailand

2020 ◽  
Vol 20 ◽  
Author(s):  
Peechanika Chopjitt ◽  
Anusak Kerdsin ◽  
Dan Takeuchi ◽  
Rujirat Hatrongjit ◽  
Parichart Boueroy ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Efflux Pump ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Drug Resistant ◽  
Resistant Genes ◽  
Extensively Drug Resistant ◽  
Antibiotic Efflux

Background:: Acinetobacter baumannii is recognized as a majority opportunistic nosocomial pathogen and caus-ing hospital-acquired infection worldwide. The increasing prevalence of extensively drug-resistant Acinetobacter baumannii (XDRAB) has become a rising concern in healthcare facilities and has impeded public health due to limitation of therapeutic options and are associated with high morbidity and mortality as well as longer hospitalization. Whole-genome sequencing of highly multidrug resistant A. baumannii will increase understanding of resistant mechanisms, the emergence of novel re-sistance, genetic relationships among the isolates, source tracking, and treatment decisions in selected patients. Objective:: This study revealed the genomic analysis to explore blaOXA-23 harboring XDRAB isolates in Thailand. Methods:: Whole-genome sequencing of the two XDRAB isolates was carried out on a HiSeq2000 Illumina platform and susceptibility on antimicrobials was conducted. Results:: Both isolates revealed sequence types of international, clone II-carrying, multiple antimicrobial-resistant genes—ST195 and ST451. They were resistant to antimicrobial agents in all drug classes tested for Acinetobacter spp. They carried 18 antimicrobial-resistant genes comprising of 4 -lactamase genes (blaOXA-23, blaOXA-66, blaTEM-1D, blaADC-25), 4 aminogly-coside-resistant genes (armA, aph(3')-Ia, aph(3'')-Ib, aph(6)-Id), 3 macrolide-resistant genes (amvA, mphE, msrE), 1 sulfon-amide-resistant gene (sul-2), 2 tetracycline-resistant genes (tetB, tetR), 1 resistant-nodulation-cell division (RND) antibiotic efflux pump gene cluster, 2 major facilitator superfamily (MFS) antibiotic efflux pump genes (abaF, abaQ), and 1 small multidrug-resistant (SMR) antibiotic efflux pump gene (abeS). Mutation of gyrA (S81L) occurred in both isolates. Conclusions:: Whole-genome sequencing revealed both blaOXA-23 harboring XDRAB isolates were clustered under interna-tional clone II with difference STs and carrying multiple antimicrobial-resistant genes conferred their resistance to antimi-crobial agents. Inactivation of antimicrobials and target modification by enzymes, and pumping antibiotics by efflux pump are mainly resistance mechanism of the XDRAB in this study.

Lesion Heterogeneity and Long-Term Heteroresistance in Multidrug-Resistant Tuberculosis

2021 ◽  
Author(s):  
Yiwang Chen ◽  
Lecai Ji ◽  
Qingyun Liu ◽  
Jinli Li ◽  
Chuangyue Hong ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Drug Resistant ◽  
Treatment Regimens ◽  
Resistant Tuberculosis ◽  
Multidrug Resistant Tuberculosis

Abstract Tuberculosis heteroresistance, in which only a fraction of the bacteria in a patient with tuberculosis contains drug-resistant mutations, has been a rising concern. However, its origins and prevalence remain elusive. Here, whole-genome sequencing was performed on 83 serial isolates from 31 patients with multidrug-resistant tuberculosis, and heteroresistance was detected in isolates from 21 patients (67.74%). Heteroresistance persisted in the host for long periods, spanning months to years, and was associated with having multiple tubercular lesions. Our findings indicate that heteroresistance is common and persistent in patients with multidrug-resistant tuberculosis and may affect the success of their treatment regimens.

scholarly journals Contamination of street food with multidrug-resistant Salmonella, in Ouagadougou, Burkina Faso

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0253312
Author(s):  
Marguerite E. M. Nikiema ◽  
Maria Pardos de la Gandara ◽  
Kiswensida A. M. Compaore ◽  
Absétou Ky Ba ◽  
Karna D. Soro ◽  
...  
Keyword(s):  
Burkina Faso ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Public Health Problem ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Global Public Health ◽  
Gastrointestinal Infections ◽  
Street Food ◽  
High Prevalence

Background Gastrointestinal infections are a global public health problem. In Burkina Faso, West Africa, exposure to Salmonella through the consumption of unhygienic street food represents a major risk of infection requiring detailed evaluation. Methods Between June 2017 and July 2018, we sampled 201 street food stalls, in 11 geographic sectors of Ouagadougou, Burkina Faso. We checked for Salmonella contamination in 201 sandwiches (one per seller), according to the ISO 6579:2002 standard. All Salmonella isolates were characterized by serotyping and antimicrobial susceptibility testing, and whole-genome sequencing was performed on a subset of isolates, to investigate their phylogenetic relationships and antimicrobial resistance determinants. Results The prevalence of Salmonella enterica was 17.9% (36/201) and the Salmonella isolates belonged to 16 different serotypes, the most frequent being Kentucky, Derby and Tennessee, with five isolates each. Six Salmonella isolates from serotypes Brancaster and Kentucky were multidrug-resistant (MDR). Whole-genome sequencing revealed that four of these MDR isolates belonged to the emergent S. enterica serotype Kentucky clone ST198-X1 and to an invasive lineage of S. enterica serotype Enteritidis (West African clade). Conclusion This study reveals a high prevalence of Salmonella spp. in sandwiches sold in Ouagadougou. The presence of MDR Salmonella in food on sale detected in this study is also matter of concern.

scholarly journals Evolution and global transmission of a multidrug-resistant, community-associated MRSA lineage from the Indian subcontinent

2017 ◽  
Author(s):  
Eike J. Steinig ◽  
Sebastian Duchene ◽  
D. Ashley Robinson ◽  
Stefan Monecke ◽  
Maho Yokoyama ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Indian Subcontinent ◽  
Community Setting ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Healthcare Associated

AbstractThe evolution and global transmission of antimicrobial resistance has been well documented in Gram-negative bacteria and healthcare-associated epidemic pathogens, often emerging from regions with heavy antimicrobial use. However, the degree to which similar processes occur with Gram-positive bacteria in the community setting is less well understood. Here, we trace the recent origins and global spread of a multidrug resistant, community-associatedStaphylococcus aureuslineage from the Indian subcontinent, the Bengal Bay clone (ST772). We generated whole genome sequence data of 340 isolates from 14 countries, including the first isolates from Bangladesh and India, to reconstruct the evolutionary history and genomic epidemiology of the lineage. Our data shows that the clone emerged on the Indian subcontinent in the early 1970s and disseminated rapidly in the 1990s. Short-term outbreaks in community and healthcare settings occurred following intercontinental transmission, typically associated with travel and family contacts on the subcontinent, but ongoing endemic transmission was uncommon. Acquisition of a multidrug resistance integrated plasmid was instrumental in the divergence of a single dominant and globally disseminated clade in the early 1990s. Phenotypic data on biofilm, growth and toxicity point to antimicrobial resistance as the driving force in the evolution of ST772. The Bengal Bay clone therefore combines the multidrug resistance of traditional healthcare-associated clones with the epidemiological transmission of community-associated MRSA. Our study demonstrates the importance of whole genome sequencing for tracking the evolution of emerging and resistant pathogens. It provides a critical framework for ongoing surveillance of the clone on the Indian subcontinent and elsewhere.ImportanceThe Bengal Bay clone (ST772) is a community-acquired and multidrug-resistantStaphylococcus aureuslineage first isolated from Bangladesh and India in 2004. In this study, we show that the Bengal Bay clone emerged from a virulent progenitor circulating on the Indian subcontinent. Its subsequent global transmission was associated with travel or family contact in the region. ST772 progressively acquired specific resistance elements at limited cost to its fitness and continues to be exported globally resulting in small-scale community and healthcare outbreaks. The Bengal Bay clone therefore combines the virulence potential and epidemiology of community-associated clones with the multidrug-resistance of healthcare-associatedS. aureuslineages. This study demonstrates the importance of whole genome sequencing for the surveillance of highly antibiotic resistant pathogens, which may emerge in the community setting of regions with poor antibiotic stewardship and rapidly spread into hospitals and communities across the world.

scholarly journals Emergence of dominant multidrug-resistant bacterial clades: Lessons from history and whole-genome sequencing

2018 ◽  
Vol 115 (51) ◽  
pp. 12872-12877 ◽  
Author(s):  
Elizabeth J. Klemm ◽  
Vanessa K. Wong ◽  
Gordon Dougan
Keyword(s):  
Antibiotic Resistance ◽  
Whole Genome Sequencing ◽  
Genome Evolution ◽  
Genome Sequencing ◽  
Bacterial Genome ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Bacterial Populations ◽  
Global Challenge ◽  
The Past

Antibiotic resistance in bacteria has emerged as a global challenge over the past 90 years, compromising our ability to effectively treat infections. There has been a dramatic increase in antibiotic resistance-associated determinants in bacterial populations, driven by the mobility and infectious nature of such determinants. Bacterial genome flexibility and antibiotic-driven selection are at the root of the problem. Genome evolution and the emergence of highly successful multidrug-resistant clades in different pathogens have made this a global challenge. Here, we describe some of the factors driving the origin, evolution, and spread of the antibiotic resistance genotype.

scholarly journals Detection of antimicrobial resistance, pathogenicity, and virulence potentials of non-typhoidal Salmonella isolates at the Yaounde abattoir using whole genome sequencing technique

2021 ◽  
Author(s):  
Chelea Matchawe ◽  
Eunice M Machuka ◽  
Martina Kyalo ◽  
Patrice Bonny ◽  
Nkeunen Gerard ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bacterial Pathogens ◽  
Critical Role ◽  
Multidrug Resistant ◽  
World Health ◽  
Whole Genome

One of the crucial public health problems today is emerging and re-emerging of multidrug-resistant bacterial pathogens coupled with a decline in the development of new antimicrobials. Non-typhoidal Salmonella is classified among the multidrug-resistant bacterial pathogens of international concern. To predict their multidrug resistance potentials, 19 assembled genomes (partial genomes) of 23 non-typhoidal Salmonella isolated at the Yaounde abattoir between December 2014 and November 2015 from live cattle (n=1), beef carcass (n=19), butchers' hands (n=1) and the beef processing environments (n=2) were explored using whole-genome sequencing. Phenotypically, while approximately 22% (n=5) of Salmonella isolates showed moderate resistance to streptomycin, 13.04 % (n=3) were multidrug-resistant. Genotypically, all the Salmonella isolates possessed high multidrug resistance potentials against several classes of antibiotics (third-generation cephalosporin and fluoroquinolone), which are assigned highest priority drugs by the World Health Organization. Moreover, more than 31% of the isolates exhibited resistance potentials to polymyxin, considered as the last resort drug with both clinical and veterinary relevance. Additionally, close to 80% of non-typhoidal Salmonella isolates in this study harbored "silent resistant genes" and thus constituted potential reservoirs of antibiotic resistance to other foodborne bacteria. Plasmids also appear to play a critical role in the horizontal transfer of antibiotic resistance genes of some isolates. The isolates showed a high degree of pathogenicity and possessed key effector proteins to establish infection in their hosts, including humans. The overall results demand prudent use of antibiotics and constant monitoring of antimicrobial resistance of non-typhoidal Salmonella in the Cameroonian abattoirs.

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