scholarly journals Large-scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Nazreen F. Hadjirin ◽  
Eric L. Miller ◽  
Gemma G. R. Murray ◽  
Phung L. K. Yen ◽  
Ho D. Phuc ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Large Scale ◽  
Genomic Analysis ◽  
Streptococcus Suis ◽  
Multidrug Resistant ◽  
Beta Lactam ◽  
Contributing Factors ◽  
Usage Patterns ◽  
Natural Separation ◽  
Serious Disease

Abstract Background Antimicrobial resistance (AMR) is among the gravest threats to human health and food security worldwide. The use of antimicrobials in livestock production can lead to emergence of AMR, which can have direct effects on humans through spread of zoonotic disease. Pigs pose a particular risk as they are a source of zoonotic diseases and receive more antimicrobials than most other livestock. Here we use a large-scale genomic approach to characterise AMR in Streptococcus suis, a commensal found in most pigs, but which can also cause serious disease in both pigs and humans. Results We obtained replicated measures of Minimum Inhibitory Concentration (MIC) for 16 antibiotics, across a panel of 678 isolates, from the major pig-producing regions of the world. For several drugs, there was no natural separation into ‘resistant’ and ‘susceptible’, highlighting the need to treat MIC as a quantitative trait. We found differences in MICs between countries, consistent with their patterns of antimicrobial usage. AMR levels were high even for drugs not used to treat S. suis, with many multidrug-resistant isolates. Similar levels of resistance were found in pigs and humans from regions associated with zoonotic transmission. We next used whole genome sequences for each isolate to identify 43 candidate resistance determinants, 22 of which were novel in S. suis. The presence of these determinants explained most of the variation in MIC. But there were also interesting complications, including epistatic interactions, where known resistance alleles had no effect in some genetic backgrounds. Beta-lactam resistance involved many core genome variants of small effect, appearing in a characteristic order. Conclusions We present a large dataset allowing the analysis of the multiple contributing factors to AMR in S. suis. The high levels of AMR in S. suis that we observe are reflected by antibiotic usage patterns but our results confirm the potential for genomic data to aid in the fight against AMR.

scholarly journals Evaluation of antimicrobial resistance, biofilm forming potential, and the presence of biofilm-related genes among clinical isolates of Pseudomonas aeruginosa

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Esmat Kamali ◽  
Ailar Jamali ◽  
Abdollah Ardebili ◽  
Freshteh Ezadi ◽  
Alireza Mohebbi
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antimicrobial Resistance ◽  
Multidrug Resistant ◽  
Infection Prevention And Control ◽  
Beta Lactam ◽  
Antimicrobial Susceptibility Pattern ◽  
Combination Strategies ◽  
High Standards ◽  
And Control ◽  
Genotypic Characteristics

Abstract Objectives Pseudomonas aeruginosa is known as a leading cause of nosocomial infections worldwide. Antimicrobial resistance and biofilm production, as two main virulence factors of P. aeruginosa, are responsible for the persistence of prolonged infections. In this study, antimicrobial susceptibility pattern and phenotypic and genotypic characteristics of biofilm of P. aeruginosa were investigated. Results A total of 80 clinical P. aeruginosa isolates were obtained. Isolates showed resistance to all antibiotics with a rate from 12.5% (n = 10) against amikacin and piperacillin/tazobactam to 23.75% (n = 19) to levofloxacin. Multidrug-resistant P. aeruginosa accounted for 20% (n = 16). 83.75% (n = 67) of isolates showed biofilm phenotype. All three biofilm-related genes were found simultaneously in 87.5% (n = 70) of P. aeruginosa and 13.5% (n = 10) of the isolates had none of the genes tested. From the results of the present study, combination therapy including an anti-pseudomonal beta-lactam (piperacillin/tazobactam or ceftazidime) and an aminoglycoside or carbapenems (imipenem, meropenem) with fluoroquinolones in conjunction with an aminoglycoside can be used against Pseudomonas infections. However, reasonable antimicrobial use and high standards of infection prevention and control are essential to prevent further development of antimicrobial resistance. Combination strategies based on the proper anti-pseudomonal antibiotics along with anti-biofilm agents can also be selected to eradicate biofilm-associated infections.

scholarly journals Characterization of Multidrug Resistant Extended-Spectrum Beta-Lactamase-ProducingEscherichia coliamong Uropathogens of Pediatrics in North of Iran

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Mohammad Sadegh Rezai ◽  
Ebrahim Salehifar ◽  
Alireza Rafiei ◽  
Taimour Langaee ◽  
Mohammadreza Rafati ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Multidrug Resistant ◽  
Beta Lactamase ◽  
Beta Lactam ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli ◽  
Beta Lactam Antibiotics ◽  
Extended Spectrum ◽  
Extended Spectrum Beta Lactamases ◽  
North Of Iran

Escherichia coliremains as one of the most important bacteria causing infections in pediatrics and producing extended-spectrum beta-lactamases (ESBLs) making them resistant to beta-lactam antibiotics. In this study we aimed to genotype ESBL-producingE. coliisolates from pediatric patients for ESBL genes and determine their association with antimicrobial resistance. One hundred of theE. coliisolates were initially considered ESBL producing based on their MIC results. These isolates were then tested by polymerase chain reaction (PCR) for the presence or absence ofCTX,TEM,SHV,GES, andVEBbeta-lactamase genes. About 30.5% of isolatedE. coliwas ESBL-producing strain. TheTEMgene was the most prevalent (49%) followed bySHV(44%),CTX(28%),VEB(8%), andGES(0%) genes. The ESBL-producingE. coliisolates were susceptible to carbapenems (66%) and amikacin (58%) and showed high resistance to cefixime (99%), colistin (82%), and ciprofloxacin (76%). In conclusion, carbapenems were the most effective antibiotics against ESBl-producingE. coliin urinary tract infection in North of Iran. The most prevalent gene is the TEM-type, but the other resistant genes and their antimicrobial resistance are on the rise.

scholarly journals Emergence and Evolution of Multidrug-Resistant Klebsiella pneumoniae with both blaKPC and blaCTX-M Integrated in the Chromosome

2017 ◽  
Vol 61 (7) ◽  
Author(s):  
Weihua Huang ◽  
Guiqing Wang ◽  
Robert Sebra ◽  
Jian Zhuge ◽  
Changhong Yin ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
Resistance Genes ◽  
De Novo ◽  
Genomic Analysis ◽  
Multidrug Resistant ◽  
Comparative Genomic ◽  
Type I ◽  
Content Type ◽  
Antimicrobial Resistance Genes

ABSTRACT The extended-spectrum-β-lactamase (ESBL)- and Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae represent serious and urgent threats to public health. In a retrospective study of multidrug-resistant K. pneumoniae, we identified three clinical isolates, CN1, CR14, and NY9, carrying both bla CTX-M and bla KPC genes. The complete genomes of these three K. pneumoniae isolates were de novo assembled by using both short- and long-read whole-genome sequencing. In CR14 and NY9, bla CTX-M and bla KPC were carried on two different plasmids. In contrast, CN1 had one copy of bla KPC-2 and three copies of bla CTX-M-15 integrated in the chromosome, for which the bla CTX-M-15 genes were linked to an insertion sequence, ISEcp1, whereas the bla KPC-2 gene was in the context of a Tn4401a transposition unit conjugated with a PsP3-like prophage. Intriguingly, downstream of the Tn4401a-bla KPC-2-prophage genomic island, CN1 also carried a clustered regularly interspaced short palindromic repeat (CRISPR)-cas array with four spacers targeting a variety of K. pneumoniae plasmids harboring antimicrobial resistance genes. Comparative genomic analysis revealed that there were two subtypes of type I-E CRISPR-cas in K. pneumoniae strains and suggested that the evolving CRISPR-cas, with its acquired novel spacer, induced the mobilization of antimicrobial resistance genes from plasmids into the chromosome. The integration and dissemination of multiple copies of bla CTX-M and bla KPC from plasmids to chromosome depicts the complex pandemic scenario of multidrug-resistant K. pneumoniae. Additionally, the implications from this study also raise concerns for the application of a CRISPR-cas strategy against antimicrobial resistance.

scholarly journals Cyclic Avian Mass Mortality in the Northeastern United States Is Associated with a Novel Orthomyxovirus

2014 ◽  
Vol 89 (2) ◽  
pp. 1389-1403 ◽  
Author(s):  
Andrew B. Allison ◽  
Jennifer R. Ballard ◽  
Robert B. Tesh ◽  
Justin D. Brown ◽  
Mark G. Ruder ◽  
...  
Keyword(s):  
United States ◽  
Influenza A ◽  
Large Scale ◽  
Sequence Similarity ◽  
Genomic Analysis ◽  
Mass Mortality ◽  
Somateria Mollissima ◽  
Northeastern United States ◽  
Contributing Factors ◽  
Content Type

ABSTRACTSince 1998, cyclic mortality events in common eiders (Somateria mollissima), numbering in the hundreds to thousands of dead birds, have been documented along the coast of Cape Cod, MA, USA. Although longitudinal disease investigations have uncovered potential contributing factors responsible for these outbreaks, detecting a primary etiological agent has proven enigmatic. Here, we identify a novel orthomyxovirus, tentatively named Wellfleet Bay virus (WFBV), as a potential causative agent of these outbreaks. Genomic analysis of WFBV revealed that it is most closely related to members of theQuaranjavirusgenus within the familyOrthomyxoviridae. Similar to other members of the genus, WFBV contains an alphabaculovirus gp64-like glycoprotein that was demonstrated to have fusion activity; this also tentatively suggests that ticks (and/or insects) may vector the virus in nature. However, in addition to the six RNA segments encoding the prototypical structural proteins identified in other quaranjaviruses, a previously unknown RNA segment (segment 7) encoding a novel protein designated VP7 was discovered in WFBV. Although WFBV shows low to moderate levels of sequence similarity toQuaranfil virusandJohnston Atollvirus, the original members of theQuaranjavirusgenus, additional antigenic and genetic analyses demonstrated that it is closely related to the recently identified Cygnet River virus (CyRV) from South Australia, suggesting that WFBV and CyRV may be geographic variants of the same virus. Although the identification of WFBV in part may resolve the enigma of these mass mortality events, the details of the ecology and epidemiology of the virus remain to be determined.IMPORTANCEThe emergence or reemergence of viral pathogens resulting in large-scale outbreaks of disease in humans and/or animals is one of the most important challenges facing biomedicine. For example, understanding how orthomyxoviruses such as novel influenza A virus reassortants and/or mutants emerge to cause epidemic or pandemic disease is at the forefront of current global health concerns. Here, we describe the emergence of a novel orthomyxovirus, Wellfleet Bay virus (WFBV), which has been associated with cyclic large-scale bird die-offs in the northeastern United States. This initial characterization study provides a foundation for further research into the evolution, epidemiology, and ecology of newly emerging orthomyxoviruses, such as WFBV, and their potential impacts on animal and/or human health.

Multidrug-resistant Klebsiella pneumoniae: risks to food safety and public health

2020 ◽  
Vol 30 (Supplement_5) ◽  
Author(s):  
A Cornacchia ◽  
V Di Marzio ◽  
A Ciarrocchi ◽  
M A Saletti ◽  
C Marfoglia ◽  
...  
Keyword(s):  
Public Health ◽  
Food Safety ◽  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
Multidrug Resistant ◽  
Beta Lactam ◽  
Beta Lactams ◽  
Illumina Platform ◽  
Aminoglycoside Resistance ◽  
Consumer Safety

Abstract Background Klebsiella pneumoniae (Kp) is a Gram-negative hospital-acquired pathogen. Kp also poses a potential food safety hazard, since a significant increase of multidrug-resistant (MDR) Kp was observed in foods. The purpose of this study was to characterize MDR Kp strains in order to evaluate the presence of beta-lactams, quinolones and aminoglycosides resistance genes. Methods A total of 13 Kp strains, isolated from chicken (n.8), raw milk (n.2), waste water (n.2), human faeces (n.1), and identified as MDR by microdilution test, were selected to evaluate antimicrobial resistance profiles, focusing on beta-lactams, quinolones and aminoglycosides. Next Generation Sequencing (NGS), with NextSeq 500 Illumina platform, was performed to acquire genome sequences. The antimicrobial resistance profiles were obtained using ResFinder (https://cge.cbs.dtu.dk/services/ResFinder/). Results From the 13 Kp considered, 6 strains (46.2 %) showed the presence of several beta-lactam genes. The blaSHV gene was carried by 12 Kp (92.3%); of these strains, 5 also carried blaTEM (41.7%) and 3 also blaCTX-M (25.0%) genes. Only 1 Kp strain showed the presence of blaOKP-A gene. All the 13 Kp carried the oqxA and oqxB genes. Of these strains, 4 also highlighted the presence of qnrB or qnrS plasmid-mediated gene for quinolone resistance. Regarding aminoglycoside resistance, 6 Kp strains (46.2%) carried aph, aadA and aaC genes, linked to gentamicin and streptomycin resistance protein. Conclusions These preliminary results emphasize the need of further studies on more several samples, to better understand the antimicrobial resistance of Kp strains, the hypothetical transmission of MDR Kp from foods to consumers and the potential risk posed to food safety, environmental and public health. Key messages The increasing prevalence of multidrug-resistant Klebsiella pneumoniae requires the need to investigate more foods and environmental samples to ensure consumer safety and public health. Public health safety requires a major knowledge of the hypothetical mechanisms and routes of transmission of multidrug-resistant Klebsiella pneumoniae.

scholarly journals Paratype: A genotyping framework and an open-source tool for Salmonella Paratyphi A

2021 ◽  
Author(s):  
Arif M. Tanmoy ◽  
Yogesh Hooda ◽  
Mohammasd S. I. Sajib ◽  
Kesia E. da Silva ◽  
Junaid Iqbal ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Large Scale ◽  
Vaccine Development ◽  
Global Analysis ◽  
Treatment Strategies ◽  
Genomic Analysis ◽  
Genomic Variation ◽  
Global Database ◽  
Command Line Tool ◽  
Conserved Gene

Background: Salmonella enterica serovar Paratyphi A (Salmonella Paratyphi A) is the primary causative agent of paratyphoid fever, which is responsible for an estimated 3.4 million infections annually. However, little genomic information is available on population structure, antimicrobial resistance (AMR), and spatiotemporal distribution of the pathogen. With rising antimicrobial resistance and no licensed vaccines, genomic surveillance is important to track the evolution of this pathogen and monitor transmission. Results: We performed whole-genome sequencing of 817 Salmonella Paratyphi A isolates collected from Bangladesh, Nepal, and Pakistan and added publicly available 562 genomes to build a global database representing 37 countries, covering 1917-2019. To track the evolution of Salmonella Paratyphi A, we used the existing lineage scheme, developed earlier based on a small dataset, but certain sub-lineages were not homologous, and many isolates could not be assigned a lineage. Therefore, we developed a single nucleotide polymorphism based genotyping scheme, Paratype, a tool that segregates Salmonella Paratyphi A into three primary and nine secondary clades, and 18 genotypes. Each genotype has been assigned a unique allele definition located on a conserved gene. Using Paratype, we identified genomic variation between different sampling locations and specific AMR markers, and mutations in the O2-polysaccharide synthesis locus, a candidate for vaccine development. Conclusions: This large-scale global analysis proposes the first genotyping tool for Salmonella Paratyphi A. Paratype has already been released (https://github.com/CHRF-Genomics/Paratype) as an open-access, command-line tool and is being adopted for large scale genomic analysis. This tool will assist future genomic surveillance and help inform prevention and treatment strategies.

scholarly journals Resources for Genetic and Genomic Analysis of Emerging Pathogen Acinetobacter baumannii

2015 ◽  
Vol 197 (12) ◽  
pp. 2027-2035 ◽  
Author(s):  
Larry A. Gallagher ◽  
Elizabeth Ramage ◽  
Eli J. Weiss ◽  
Matthew Radey ◽  
Hillary S. Hayden ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Large Scale ◽  
Experimental Studies ◽  
Bacterial Pathogen ◽  
Genomic Analysis ◽  
Multidrug Resistant ◽  
Health Care Facilities ◽  
High Coverage ◽  
Content Type ◽  
Genome Scale

ABSTRACTAcinetobacter baumanniiis a Gram-negative bacterial pathogen notorious for causing serious nosocomial infections that resist antibiotic therapy. Research to identify factors responsible for the pathogen's success has been limited by the resources available for genome-scale experimental studies. This report describes the development of several such resources forA. baumanniistrain AB5075, a recently characterized wound isolate that is multidrug resistant and displays robust virulence in animal models. We report the completion and annotation of the genome sequence, the construction of a comprehensive ordered transposon mutant library, the extension of high-coverage transposon mutant pool sequencing (Tn-seq) to the strain, and the identification of the genes essential for growth on nutrient-rich agar. These resources should facilitate large-scale genetic analysis of virulence, resistance, and other clinically relevant traits that makeA. baumanniia formidable public health threat.IMPORTANCEAcinetobacter baumanniiis one of six bacterial pathogens primarily responsible for antibiotic-resistant infections that have become the scourge of health care facilities worldwide. Eliminating such infections requires a deeper understanding of the factors that enable the pathogen to persist in hospital environments, establish infections, and resist antibiotics. We present a set of resources that should accelerate genome-scale genetic characterization of these traits for a reference isolate ofA. baumanniithat is highly virulent and representative of current outbreak strains.

scholarly journals Multidrug-resistant Staphylococcus cohnii and Staphylococcus urealyticus isolates from German dairy farms exhibit resistance to beta-lactam antibiotics and divergent penicillin-binding proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tobias Lienen ◽  
Arne Schnitt ◽  
Jens Andre Hammerl ◽  
Stephen F. Marino ◽  
Sven Maurischat ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Gene Prediction ◽  
Dairy Farms ◽  
Multidrug Resistant ◽  
Amino Acid Sequences ◽  
Penicillin Binding Protein ◽  
Beta Lactam ◽  
Penicillin Binding Proteins ◽  
Antimicrobial Substances ◽  
Beta Lactam Antibiotics

AbstractNon-aureus staphylococci are commonly found on dairy farms. Two rarely investigated species are Staphylococcus (S.) cohnii and S. urealyticus. Since multidrug-resistant S. cohnii and S. urealyticus are known, they may serve as an antimicrobial resistance (AMR) gene reservoir for harmful staphylococcal species. In our study, nine S. cohnii and six S. urealyticus isolates from German dairy farms were analyzed by whole-genome sequencing and AMR testing. The isolates harbored various AMR genes (aadD1, str, mecA, dfrC/K, tetK/L, ermC, lnuA, fexA, fusF, fosB6, qacG/H) and exhibited non-wildtype phenotypes (resistances) against chloramphenicol, clindamycin, erythromycin, fusidic acid, rifampicin, streptomycin, tetracycline, tiamulin and trimethoprim. Although 14/15 isolates lacked the blaZ, mecA and mecC genes, they showed reduced susceptibility to a number of beta-lactam antibiotics including cefoxitin (MIC 4–8 mg/L) and penicillin (MIC 0.25–0.5 mg/L). The specificity of cefoxitin susceptibility testing for mecA or mecC gene prediction in S. cohnii and S. urealyticus seems to be low. A comparison with penicillin-binding protein (PBP) amino acid sequences of S. aureus showed identities of only 70–80% with regard to PBP1, PBP2 and PBP3. In conclusion, S. cohnii and S. urealyticus from selected German dairy farms show multiple resistances to antimicrobial substances and may carry unknown antimicrobial resistance determinants.

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