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.

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 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 Whole Genome Sequence-Based Prediction of Resistance Determinants in High-Level Multidrug-Resistant Campylobacter jejuni Isolates in Lithuania

2020 ◽  
Vol 9 (1) ◽  
pp. 66
Author(s):  
Jurgita Aksomaitiene ◽  
Aleksandr Novoslavskij ◽  
Egle Kudirkiene ◽  
Ausra Gabinaitiene ◽  
Mindaugas Malakauskas
Keyword(s):  
Antibiotic Resistance ◽  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Campylobacter Jejuni ◽  
Mobile Genetic Elements ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Genome Sequences ◽  
Resistance Determinants ◽  
High Level

Spread of antibiotic resistance via mobile genetic elements associates with transfer of genes providing resistance against multiple antibiotics. Use of various comparative genomics analysis techniques enables to find intrinsic and acquired genes associated with phenotypic antimicrobial resistance (AMR) in Campylobacter jejuni genome sequences with exceptionally high-level multidrug resistance. In this study, we used whole genome sequences of seven C. jejuni to identify isolate-specific genomic features associated with resistance and virulence determinants and their role in multidrug resistance (MDR). All isolates were phenotypically highly resistant to tetracycline, ciprofloxacin, and ceftriaxone (MIC range from 64 to ≥256 µg/mL). Besides, two C. jejuni isolates were resistant to gentamicin, and one was resistant to erythromycin. The extensive drug-resistance profiles were confirmed for the two C. jejuni isolates assigned to ST-4447 (CC179). The most occurring genetic antimicrobial-resistance determinants were tetO, beta-lactamase, and multidrug efflux pumps. In this study, mobile genetic elements (MGEs) were detected in genomic islands carrying genes that confer resistance to MDR, underline their importance for disseminating antibiotic resistance in C. jejuni. The genomic approach showed a diverse distribution of virulence markers, including both plasmids and phage sequences that serve as horizontal gene transfer tools. The study findings describe in silico prediction of AMR and virulence genetics determinants combined with phenotypic AMR detection in multidrug-resistant C. jejuni isolates from Lithuania.

scholarly journals First detection of a plasmid-encoded New-Delhi metallo-beta-lactamase-1 (NDM-1) producing Acinetobacter baumannii using whole genome sequencing, isolated in a clinical setting in Benin

2020 ◽  
Author(s):  
Carine Laurence Yehouenou ◽  
Bert Bogaerts ◽  
Kevin Vanneste ◽  
Nancy H.C. Roosens ◽  
Sigrid C.J. De Keersmaecker ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
World Health ◽  
New Delhi ◽  
Whole Genome ◽  
Beta Lactamase ◽  
Drug Resistant ◽  
Extensively Drug Resistant

Abstract Background: Carbapenem-resistant Acinetobacter baumannii is considered a top priority pathogen by the World Health Organization for combatting increasing antibiotic resistance and development of new drugs. Since it was originally reported in Klebsiella pneumoniae in 2009, the quick spread of the blaNDM-1 gene encoding a New-Delhi metallo-beta-lactamase-1 (NDM-1) is increasingly recognized as a serious threat. This gene is usually carried by large plasmids and has already been documented in diverse bacterial species, including A. baumannii. Here, we report the first detection of a NDM-1-producing A. baumannii strain isolated in Benin.Case presentation: A 31-year-old woman was admitted to a surgical unit with a diagnosis of post-cesarean hematoma. An extensively-drug resistant A. baumannii strain solely susceptible to amikacin, colistin and ciprofloxacin, and resistant to several other antibiotics including ceftazidime, imipenem, meropenem, gentamicin, tobramycin, ceftazidime/avibactam, and sulfamethoxazole-trimethoprim, was isolated from the wound. Production of NDM-1 was demonstrated by immunochromatographic testing. Whole genome sequencing of the isolate confirmed the presence of blaNDM-1, but also antibiotic resistance genes against multiple beta-lactamases and other classes of antibiotics, in addition to several virulence genes. Moreover, the blaNDM-1 gene was found to be present in a Tn125 transposon integrated on a plasmid.Conclusions: The discovery of this extensively-drug resistant A. baumannii strain carrying blaNDM-1 in Benin is worrying, especially because of its high potential risk of horizontal gene transfer due to being integrated in a transposon located on a plasmid. Strict control and prevention measures should be taken, once NDM-1 positive A. baumannii has been identified to prevent transfer of this resistance gene to other Enterobacterales. Capacity building is required by governmental agencies to provision suitable antibiotic treatment options and strategies, in combination with strengthening laboratory services for detection and surveillance of this pathogen.

scholarly journals Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent

mBio ◽  
2019 ◽  
Vol 10 (6) ◽  
Author(s):  
Eike J. Steinig ◽  
Sebastian Duchene ◽  
D. Ashley Robinson ◽  
Stefan Monecke ◽  
Maho Yokoyama ◽  
...  
Keyword(s):  
Health Care ◽  
Staphylococcus Aureus ◽  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Genome Sequencing ◽  
Indian Subcontinent ◽  
Community Setting ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Content Type

ABSTRACT The evolution and global transmission of antimicrobial resistance have been well documented for Gram-negative bacteria and health care-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. In this study, we traced the recent origins and global spread of a multidrug-resistant, community-associated Staphylococcus aureus lineage 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 show that the clone emerged on the Indian subcontinent in the early 1960s and disseminated rapidly in the 1990s. Short-term outbreaks in community and health care 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 emergence 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 health care-associated clones with the epidemiological transmission of community-associated methicillin-resistant S. aureus (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. IMPORTANCE The Bengal Bay clone (ST772) is a community-associated and multidrug-resistant Staphylococcus aureus lineage first isolated from Bangladesh and India in 2004. In this study, we showed 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 health care outbreaks. The Bengal Bay clone therefore combines the virulence potential and epidemiology of community-associated clones with the multidrug resistance of health care-associated S. aureus lineages. 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 Genomic Investigation of Salmonella Isolates Recovered From a Pig Slaughtering Process in Hangzhou, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Beibei Wu ◽  
Abdelaziz Ed-Dra ◽  
Hang Pan ◽  
Chenghang Dong ◽  
Chenghao Jia ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Critical Points ◽  
Food Chain ◽  
Antimicrobial Agents ◽  
Multidrug Resistant ◽  
Dilution Method ◽  
Whole Genome ◽  
Antimicrobial Resistance Genes

The pig industry is the principal source of meat products in China, and the presence of pathogens in pig-borne meat is a crucial threat to public health. Salmonella is the major pathogen associated with pig-borne diseases. However, route surveillance by genomic platforms along the food chain is still limited in China. Here, we conducted a study to evaluate the dynamic prevalence of Salmonella in a pig slaughtering process in Hangzhou, Zhejiang Province, China. Fifty-five of 226 (24.37%) samples were positive for Salmonella; from them, 78 different isolates were selected and subjected to whole genome sequencing followed by bioinformatics analyses to determine serovar distribution, MLST patterns, antimicrobial resistance genes, plasmid replicons, and virulence factors. Moreover, phenotypic antimicrobial resistance was performed using the broth dilution method against 14 antimicrobial agents belonging to 10 antimicrobial classes. Our results showed that samples collected from the dehairing area (66.66%) and the splitting area (57.14%) were the most contaminated. Phenotypic antimicrobial resistance classified 67 of 78 isolates (85.90%) as having multidrug resistance (MDR), while the highest resistance was observed in tetracycline (85.90%; 67/78) followed by ampicillin (84.62%; 66/78), chloramphenicol (71.80%; 56/78), and nalidixic acid (61.54%; 48/78). Additionally, serovar prediction showed the dominance of Salmonella Typhimurium ST19 (51.28%; 40/78) among the 78 studied isolates, while plasmid prediction reported the dominance of IncHI2A_1 (20.51%; 16/78), followed by IncX1_1 (17.95%; 14/78) and IncHI2_1 (11.54%; 9/78). Virulence factor prediction showed the detection of cdtB gene encoding typhoid toxins in two Salmonella Goldcoast ST358 and one Salmonella Typhimurium ST19, while one isolate of Salmonella London ST155 was positive for genes encoding for the siderophore “yersiniabactin” and the gene senB encoding for enterotoxin production. From this study, we conclude that pig slaughterhouses are critical points for the dissemination of virulent and multidrug-resistant Salmonella isolates along the food chain which require the implementation of management systems to control the critical points. Moreover, there is an urgent need for the implementation of the whole genome sequencing platform to monitor the emergence of virulent and multidrug-resistant clones along the food chain.

scholarly journals Genetic features of Multi Drug Resistant (MDR) Klebsiella pneumoniae and its Plasmids

2019 ◽  
Author(s):  
Begoña Fuster ◽  
Nuria Tormo ◽  
Carme Salvador ◽  
Neris García ◽  
Fernando González-Candelas ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clinical Microbiology ◽  
New Technologies ◽  
World Health ◽  
Whole Genome ◽  
Resistance Determinants ◽  
Antimicrobial Resistance Genes

Klebsiella pneumoniae, a major cause of both hospital and community-acquired infections, is listed by the World Health Organization as a critical priority antibiotic- resistant bacterial pathogen. With the appearance of sequencing techniques such as Next-generation Sequencing (NGS), there is the possibility to obtain the whole genome of the bacteria, getting to know all antimicrobial resistance determinants. The purpose of this study has been to apply this new technology to clinical microbiology, in order to characterize the resistome present in carbapenem-resistant K.pneumoniae strains isolated in a tertiary hospital in Valencia, Spain. A total of 234 isolates were prepared for whole-genome sequencing with Ilumina MiSeq, and sequences were later studied for antimicrobial resistance genes, sequence-typing and plasmids. Sequence-typing showed four major circulating clones in our hospital settings: ST11, ST307, ST101 and ST147, carrying different plasmids and different resistance determinants such as OXA-48 and NDM-1 carbapenemase. Application of new technologies such as whole-genome sequencing in clinical microbiology gives advantages when it comes to rapid therapy adjustment, consequently improving the patient’s clinical outcomes.

scholarly journals Whole-Genome Sequencing of Pathogenic Bacteria—New Insights into Antibiotic Resistance Spreading

2021 ◽  
Vol 9 (12) ◽  
pp. 2624
Author(s):  
Andrey Shelenkov
Keyword(s):  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
World Health Organization ◽  
Genome Sequencing ◽  
Pathogenic Bacteria ◽  
World Health ◽  
Whole Genome ◽  
Opportunistic Bacteria ◽  
The World ◽  
Health Organization

In recent years, the acquisition of antimicrobial resistance (AMR) by both pathogenic and opportunistic bacteria has become a major problem worldwide, which was already noticed as a global healthcare threat by the World Health Organization [...]

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