scholarly journals RNA markers for ultra-rapid molecular antimicrobial susceptibility testing in fluoroquinolone-treated Klebsiella pneumoniae

2020 ◽  
Vol 75 (7) ◽  
pp. 1747-1755 ◽  
Author(s):  
Xi Yang ◽  
Marjan M Hashemi ◽  
Nadya Andini ◽  
Michelle M Li ◽  
Shuzhen Kuang ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Rna Sequencing ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Expression Profiles ◽  
Transcript Level ◽  
Bioinformatic Analysis ◽  
Antimicrobial Susceptibility Testing ◽  
Marker Selection ◽  
Appropriate Treatment

Abstract Objectives Traditional antimicrobial susceptibility testing (AST) is growth dependent and time-consuming. With rising rates of drug-resistant infections, a novel diagnostic method is critically needed that can rapidly reveal a pathogen’s antimicrobial susceptibility to guide appropriate treatment. Recently, RNA sequencing has been identified as a powerful diagnostic tool to explore transcriptional gene expression and improve AST. Methods RNA sequencing was used to investigate the potential of RNA markers for rapid molecular AST using Klebsiella pneumoniae and ciprofloxacin as a model. Downstream bioinformatic analysis was applied for optimal marker selection. Further validation on 11 more isolates of K. pneumoniae was performed using quantitative real-time PCR. Results From RNA sequencing, we identified RNA signatures that were induced or suppressed following exposure to ciprofloxacin. Significant shifts at the transcript level were observed as early as 10 min after antibiotic exposure. Lastly, we confirmed marker expression profiles with concordant MIC results from traditional culture-based AST and validated across 11 K. pneumoniae isolates. recA, coaA and metN transcripts harbour the most sensitive susceptibility information and were selected as our top markers. Conclusions Our results suggest that RNA signature is a promising approach to AST development, resulting in faster clinical diagnosis and treatment of infectious disease. This approach is potentially applicable in other models including other pathogens exposed to different classes of antibiotics.

Prevalence and molecular epidemiology of mcr-1-positive Klebsiella pneumoniae in healthy adults from China

2020 ◽  
Vol 75 (9) ◽  
pp. 2485-2494 ◽  
Author(s):  
Jiayue Lu ◽  
Ning Dong ◽  
Congcong Liu ◽  
Yu Zeng ◽  
Qiaoling Sun ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Mainland China ◽  
Healthy Adults ◽  
Antimicrobial Susceptibility Testing ◽  
Pcr Analysis ◽  
Resistant Bacteria ◽  
Healthy Individuals ◽  
Low Prevalence

Abstract Objectives To investigate the nationwide prevalence of mcr-1-positive Klebsiella pneumoniae (MCRPKP) strains among healthy adults in China and identify their phenotypic and genomic characterizations. Methods A total of 7401 rectal swab samples were collected from healthy individuals in 30 hospitals located in 30 provinces and municipalities of mainland China in 2016. Colistin-resistant bacteria were enriched in colistin-supplemented lysogeny broth. MCRPKP strains were isolated and characterized with MALDI-TOF MS, PCR analysis and antimicrobial susceptibility testing. The genomic characteristics of MCRPKP strains were determined by WGS and bioinformatics analysis. Results Seven MCRPKP strains and one mcr-1-positive Klebsiella variicola strain were selectively isolated from six locales (three from Henan and one from each of Tianjin, Jiangxi, Yunnan, Gansu and Tibet). Antimicrobial susceptibility testing results indicated that all mcr-1-positive strains were susceptible to meropenem, aztreonam and ceftazidime/avibactam. WGS analysis suggested these strains belonged to seven distinct STs: ST15, ST1425, ST1462, ST273, ST307, ST391 and ST37-SLV. mcr-1 genes were carried by diverse plasmids, including IncHI2 (n = 3), IncX4 (n = 2), IncHI2/IncN (n = 1), IncFIB (n = 1) and one other plasmid type. Two ST15 strains harboured both mcr-1 and mcr-8 genes, which has not been reported before. Conclusions Our data indicated a low prevalence of mcr-1-positive Klebsiella strains (0.11%, 8/7401) in healthy individuals in mainland China and most of these strains remained susceptible to clinically important antibiotics. The prevalence and coexistence of mcr-1 and mcr-8 in K. pneumoniae may further threaten public health through either the food chain or environmental routes.

scholarly journals Genomic evolution of the globally disseminated multidrug-resistant Klebsiella pneumoniae clonal group 147

2022 ◽  
Vol 8 (1) ◽  
Author(s):  
Carla Rodrigues ◽  
Siddhi Desai ◽  
Virginie Passet ◽  
Devarshi Gajjar ◽  
Sylvain Brisse
Keyword(s):  
Klebsiella Pneumoniae ◽  
Resistance Genes ◽  
Antimicrobial Susceptibility ◽  
Type Species ◽  
Susceptibility Testing ◽  
Multidrug Resistant ◽  
Antimicrobial Susceptibility Testing ◽  
Content Type ◽  
Genetic Elements ◽  
Link Type

The rapid emergence of multidrug-resistant Klebsiella pneumoniae is being driven largely by the spread of specific clonal groups (CGs). Of these, CG147 includes 7-gene multilocus sequence typing (MLST) sequence types (STs) ST147, ST273 and ST392. CG147 has caused nosocomial outbreaks across the world, but its global population dynamics remain unknown. Here, we report a pandrug-resistant ST147 clinical isolate from India (strain DJ) and define the evolution and global emergence of CG147. Antimicrobial-susceptibility testing following European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines and genome sequencing (Illumina and Oxford Nanopore Technologies, Unicycler assembly) were performed on strain DJ. Additionally, we collated 217 publicly available CG147 genomes [National Center for Biotechnology Information (NCBI), May 2019]. CG147 evolution was inferred within a temporal phylogenetic framework (beast) based on a recombination-free sequence alignment (Roary/Gubbins). Comparative genomic analyses focused on resistance and virulence genes and other genetic elements (BIGSdb, Kleborate, PlasmidFinder, phaster, ICEfinder and CRISPRCasFinder). Strain DJ had a pandrug-resistance phenotype. Its genome comprised the chromosome, seven plasmids and one linear phage-plasmid. Four carbapenemase genes were detected: bla NDM-5 and two copies of bla OXA-181 in the chromosome, and a second copy of bla NDM-5 on an 84 kb IncFII plasmid. CG147 genomes carried a mean of 13 acquired resistance genes or mutations; 63 % carried a carbapenemase gene and 83 % harboured bla CTX-M. All CG147 genomes presented GyrA and ParC mutations and a common subtype I-E CRISPR-Cas system. ST392 and ST273 emerged in 2005 and 1995, respectively. ST147, the most represented phylogenetic branch, was itself divided into two main clades with distinct capsular loci: KL64 (74 %, DJ included, emerged in 1994 and disseminated worldwide, with carbapenemases varying among world regions) and KL10 (20 %, emerged in 2002, predominantly found in Asian countries, associated with carbapenemases NDM and OXA-48-like). Furthermore, subclades within ST147-KL64 differed at the yersiniabactin locus, OmpK35/K36 mutations, plasmid replicons and prophages. The absence of IncF plasmids in some subclades was associated with a possible activity of a CRISPR-Cas system. K. pneumoniae CG147 comprises pandrug-resistant or extensively resistant isolates, and carries multiple and diverse resistance genes and mobile genetic elements, including chromosomal bla NDM-5. Its emergence is being driven by the spread of several phylogenetic clades marked by their own genomic features and specific temporo–spatial dynamics. These findings highlight the need for precision surveillance strategies to limit the spread of particularly concerning CG147 subsets.

scholarly journals Effect of Antimicrobial Stewardship with Rapid MALDI-TOF Identification and Vitek 2 Antimicrobial Susceptibility Testing on Hospitalization Outcome

2019 ◽  
Author(s):  
Stephen J Cavalieri ◽  
Seunghyug Kwon ◽  
Renuga Vivekanandan ◽  
Sumaya Ased ◽  
Cassara Carroll ◽  
...  
Keyword(s):  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Length Of Hospital Stay ◽  
Antimicrobial Susceptibility Testing ◽  
Maldi Tof ◽  
Motion Study ◽  
Appropriate Treatment ◽  
Appropriate Therapy ◽  
Vitek 2 ◽  
Organism Identification

AbstractIntroductionRapid organism identification (ID) and antimicrobial susceptibility testing (AST) along with antibiotic stewardship (ASP) are critical to appropriate treatment. We sought to capture time for bacterial culture and initiation of appropriate therapy for patients, from 2017 (without MALDI-TOF/Vitek 2 and ASP) and 2018 (with MALDI-TOF/Vitek 2 and ASP).MethodsEligible patients admitted to our hospital with a positive sputum, blood, or urine culture. Sequential patients were retrospectively obtained from March 1 to May 31, 2017. Seventy-seven patients from 2017 were compared to 77 patients from 2018. A time-in-motion study was performed to compare time to identification (ID), AST results, and ASP team intervention for the two periods. Data were entered into SPSS (ver 25) for analysis. Results are reported as mean (± SD) or percentage.ResultsTime to organism ID was significantly faster in 2018 (2018 24.9 ± 14.4, 2017 33.8 ± 17 h, p=0.001). Time to AST results was also significantly faster for patients in 2018 compared to 2017 (18.2 ± 14 compared to 28.5 ± 14.9 h, p<0.001). ASP team recommended significantly more adjustments to empiric antimicrobial therapy in 2018 (28% of 2018 vs. 2% in 2017, p< 0.001). Length of hospital stay was significantly shorter in 2018 compared to 2017 (2018 10.7 ± 11.1 days and 2017 15.5 ± 18.1 days, p=0.05).ConclusionsUse of MALDI-TOF/Vitek 2 leads to an average 21.5 h faster ID and AST results that can be acted upon by ASP for appropriate antimicrobial recommendations.

scholarly journals Concomitant carriage of KPC-producing and non-KPC-producing Klebsiella pneumoniae ST512 within a single patient

2020 ◽  
Author(s):  
Agnès B Jousset ◽  
Rémy A Bonnin ◽  
Julie Takissian ◽  
Delphine Girlich ◽  
Liliana Mihaila ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Klebsiella Pneumoniae ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Antimicrobial Susceptibility Testing ◽  
Single Patient ◽  
Susceptible Population ◽  
First Case ◽  
Short Period

Abstract Background KPC-producing Klebsiella pneumoniae of clonal group 258 are prominent in healthcare settings in many regions of the world. The blaKPC gene is mostly carried by a multireplicon IncFIIk-IncFI plasmid suspected to be highly compatible and stable in this genetic background. Here, we analysed the genetic diversity of an ST512 K. pneumoniae population in a single patient. Methods Twelve K. pneumoniae isolates (n = 5 from urine samples and n = 7 from rectal swabs) were recovered from one patient over a 2 month period. Antimicrobial susceptibility testing, plasmid extraction and WGS were performed on all isolates. The first K. pneumoniae isolate, D1, was used as a reference for phylogenetic analysis. Results Antimicrobial susceptibility testing, plasmid analysis and WGS revealed concomitant carriage of carbapenem-resistant and carbapenem-susceptible K. pneumoniae isolates of ST512, with the absence of the entire blaKPC-carrying plasmid in the susceptible population. Furthermore, 14 other genetic events occurred within the genome, including 3 chromosomal deletions (of 71 kb, 33 kb and 11 bp), 2 different insertions of ISKpn26 and 9 SNPs. Interestingly, most of the events occurred in the same chromosomal region that has been deleted independently several times, probably after homologous recombination involving 259 bp repeated sequences. Conclusions Our study revealed (to the best of our knowledge) the first case of in vivo blaKPC-carrying plasmid curing and a wide within-patient genetic diversity of a single K. pneumoniae ST512 clone over a short period of carriage. This within-patient diversity must be taken into account when characterizing transmission chains using WGS during nosocomial outbreaks.

Pretreatment antimicrobial susceptibility testing is cost saving in the eradication of

2003 ◽  
Vol 1 (4) ◽  
pp. 273-278 ◽  
Author(s):  
Marco Romano ◽  
Riccardo Marmo ◽  
Antonio Cuomo ◽  
Teresa De Simone ◽  
Caterina Mucherino ◽  
...  
Keyword(s):  
Cost Saving ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Antimicrobial Susceptibility Testing

NGHIÊN CỨU SỰ NHẠY CẢM VỚI KHÁNG SINH CỦA MỘT SỐ CHỦNG VI KHUẨN GÂY VIÊM ĐƯỜNG HÔ HẤP CẤP Ở TRẺ EM DƯỚI 6 TUỔI TẠI BỆNH VIỆN NHI THANH HÓA 2009 - 2014

2020 ◽  
Vol 4 (3) ◽  
Author(s):  
Hoai Do Ngoc
Keyword(s):  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Antimicrobial Susceptibility Testing ◽  
High Rate ◽  
Isolation Rate

From 43.574 fluid nasopharynx speciments of  the chidren inpatient under six we isolated total 21.769 types bacteria with isolation rate : 49.95%. In which the highest isolation rate for H. influenza, S. pneumoniae and M. catarrhalis were 13,94%; 7,11%; 1,43% respectively. Antimicrobial susceptibility testing shown all the types of  for H. influenza, S. pneumoniae and M. catarrhalis good susses to Fosphomycine, S. pneumoniae and M. catarrhalis good susses to Imipenem, H. influenza good susses to Azithromycine, S. pneumoniae good susses to Penicilline and Piperacilline, M. catarrhalis good susses to Tobramycine and Ofloxacine. All of  H. influenza, S. pneumoniae and M. catarrhalis were reported resistance to Tri/Sulpha, Chloramphenicol, Erythromycine in high rate.

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