Molecular characterization of clinical carbapenem-resistant Enterobacterales from Qatar

AbstractOne hundred forty-nine carbapenem-resistant Enterobacterales from clinical samples obtained between April 2014 and November 2017 were subjected to whole genome sequencing and multi-locus sequence typing. Klebsiella pneumoniae (81, 54.4%) and Escherichia coli (38, 25.5%) were the most common species. Genes encoding metallo-β-lactamases were detected in 68 (45.8%) isolates, and OXA-48-like enzymes in 60 (40.3%). blaNDM-1 (45; 30.2%) and blaOXA-48 (29; 19.5%) were the most frequent. KPC-encoding genes were identified in 5 (3.6%) isolates. Most common sequence types were E. coli ST410 (8; 21.1%) and ST38 (7; 18.4%), and K. pneumoniae ST147 (13; 16%) and ST231 (7; 8.6%).

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Molecular characterization of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae among the pediatric population in Qatar

10.21203/rs.3.rs-29509/v1 ◽

2020 ◽

Author(s):

Andres Perez-Lopez ◽

Sathyavathi Sundararaju ◽

Hassan Al-Mana ◽

Kin Ming Tsui ◽

Mohammad Hasan ◽

...

Keyword(s):

Pediatric Patients ◽

Arabian Peninsula ◽

Pediatric Population ◽

Public Health Problem ◽

E Coli ◽

Extended Spectrum ◽

Genes Encoding ◽

Sequence Types ◽

Esbl Producers

Abstract Background: Although extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae are a public health problem in the Arabian Peninsula, data on the molecular characteristic of their antimicrobial resistance determinants in children is limited.Methods: Whole-genome sequencing (WGS) was performed on ESBL-producing E. coli and K. pneumoniae isolates recovered from screening and clinical specimens from pediatric patients at Sidra Medicine in Doha from January to December 2018.Results: WGS was performed on 327 ESBL producers: 255 E. coli and 72 K. pneumoniae. The most common sequence types (ST) were ST131 (16.5%), ST38 and ST10 (8.2 each%) in E. coli and ST307 (9.7%), ST45 and ST268 (6.9% each) in K. pneumoniae. CTX-M type ESBL were found in all but one isolate, with CTX-M-15 accounting for 87.8%. Co-carriage of OXA-1 alone or in combination with TEM-1B was associated with reduced susceptibility toamoxicillin/clavulanate (P=0.002 and P<0.0001) and piperacillin/tazobactam (P=0.02 and P=0.004). The most common plasmid-mediated quinolone resistance genes co-carried were qnr A/B/E/S (45.3%). Ninety percent of gentamicin non-susceptible isolates harboured genes encoding AAC(3) enzymes, mainly aac(3)-IIa. Only 2 of 57 isolates harbouring aac(6’)-Ib-cr were non-susceptible to amikacin. Eighty-five percent of isolates carried IncF plasmids. Conclusions: Our data show that CTX-M is largely the most prevalent ESBL type in the pediatric population in Qatar with a predominance of CTX-M-15. Carbapenem-sparing options to treat ESBL infections are limited given the frequent co-production of OXA-1 and TEM-1B enzymes and co-resistance to antibiotic classes other than β-lactams.

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Genomic and Molecular Characterization of Clinical Isolates of Enterobacteriaceae Harboring mcr-1 in Colombia, 2002 to 2016

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00841-17 ◽

2017 ◽

Vol 61 (12) ◽

Cited By ~ 28

Author(s):

Sandra Yamile Saavedra ◽

Lorena Diaz ◽

Magdalena Wiesner ◽

Adriana Correa ◽

Stefany Alejandra Arévalo ◽

...

Keyword(s):

Antimicrobial Agents ◽

Clinical Isolates ◽

Gram Negative ◽

Content Type ◽

E Coli ◽

Carbapenem Resistant ◽

Serovar Typhimurium ◽

Chromosome Conjugation ◽

Sequence Types

ABSTRACT Polymyxins are last-resort antimicrobial agents used to treat infections caused by carbapenem-resistant Enterobacteriaceae. Due to the worldwide dissemination of polymyxin resistance in animal and human isolates, we aimed to characterize polymyxin resistance associated with the presence of mcr-1 in Enterobacteriaceae and nonfermenter Gram-negative bacilli, using isolates collected retrospectively in Colombia from 2002 to 2016. A total of 5,887 Gram-negative clinical isolates were studied, and 513 were found to be resistant to the polymyxins. Susceptibility to colistin was confirmed by broth microdilution for all mcr-1-positive isolates, and these were further subjected to whole-genome sequencing (WGS). The localization of mcr-1 was confirmed by S1 pulsed-field gel electrophoresis (S1-PFGE) and CeuI-PFGE hybridization. Transferability was evaluated by mating assays. A total of 12 colistin-resistant isolates recovered after 2013 harbored mcr-1, including 8 Escherichia coli, 3 Salmonella enterica serovar Typhimurium, and 1 Klebsiella pneumoniae isolate. E. coli isolates were unrelated by PFGE and belonged to 7 different sequence types (STs) and phylogroups. S. Typhimurium and K. pneumoniae isolates belonged to ST34 and ST307, respectively. The mcr-1 gene was plasmid borne in all isolates but two E. coli isolates which harbored it on the chromosome. Conjugation of mcr-1 was successful in 8 of 10 isolates (8.2 × 10−5 to 2.07 × 10−1 cell per recipient). Plasmid sequences showed that the mcr-1 plasmids belonged to four different Inc groups (a new IncP-1 variant and the IncFII, IncHI1, and IncH families). Our results indicate that mcr-1 is circulating in clinical isolates of colistin-resistant Enterobacteriaceae in Colombia and is mainly harbored in transferable plasmids.

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Dissemination of Carbapenemases (OXA-48, NDM and VIM) Producing Enterobacteriaceae Isolated from the Mohamed VI University Hospital in Marrakech, Morocco

Antibiotics ◽

10.3390/antibiotics10050492 ◽

2021 ◽

Vol 10 (5) ◽

pp. 492

Author(s):

Souad Loqman ◽

Nabila Soraa ◽

Seydina M. Diene ◽

Jean-Marc Rolain

Keyword(s):

Clinical Problem ◽

Common Species ◽

University Hospital ◽

Disc Diffusion ◽

E Coli ◽

Carbapenem Resistant ◽

One Year ◽

Encoding Genes ◽

Major Clinical Problem ◽

Carbapenem Resistant Enterobacteriaceae

The emergence and spread of carbapenem-resistant Enterobacteriaceae (CRE) represent a major clinical problem and raise serious health concerns. The present study aimed to investigate and ascertain the occurrence of CRE among hospitalized patients of Mohamed VI University Hospital, Marrakech, Morocco. Biological samples were collected over a one-year period (2018). The bacterial isolates were identified by MALDI-TOF-MS. Antibiotic susceptibility testing was performed using disc diffusion and Etest. The modified Hodge test and combined disc diffusion test were used for phenotypic detection. CRE hydrolyzing enzyme encoding genes: blaOXA-48, blaKPC, blaIMP, blaVIM, and blaNDM were characterized by PCR and DNA sequencing. In total, 131 non-duplicate CRE clinical strains resistant to Ertapenem were isolated out of 1603 initial Enterobacteriaceae. Klebsiella pneumoniae was the most common species (59%), followed by Enterobacter cloacae (24%), E. coli (10%), Citrobacter freundii (3%), Klebsiellaoxycota (2%), Serratia marcescens (1%), and Citrobacter braakii (1%). Of these, 56.49%, 21.37%, 15.27%, 3.38%, and 3.05% were collected from blood, urine, pus, catheters and respiratory samples, respectively. Approximately 85.5% (112/131) of the isolates were carbapenemase producers (40 blaOXA-48, 27 blaNDM, 38 blaOXA-48 + blaNDM and 7 blaVIM). All metallo-β-lactamases isolates were NDM-1 and VIM-1 producers. This is the first documentation of blaOXA-48 genes from C. freundii and C. braakii in Morocco.

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Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals

International Journal of Molecular Sciences ◽

10.3390/ijms22115905 ◽

2021 ◽

Vol 22 (11) ◽

pp. 5905

Author(s):

Olivia M. Grünzweil ◽

Lauren Palmer ◽

Adriana Cabal ◽

Michael P. Szostak ◽

Werner Ruppitsch ◽

...

Keyword(s):

Escherichia Coli ◽

Marine Mammals ◽

Virulence Genes ◽

Multidrug Resistant ◽

Healthcare Sector ◽

Whole Genome ◽

E Coli ◽

High Prevalence ◽

Lactamase Gene ◽

Sequence Types

Marine mammals have been described as sentinels of the health of marine ecosystems. Therefore, the aim of this study was to investigate (i) the presence of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Enterobacterales, which comprise several bacterial families important to the healthcare sector, as well as (ii) the presence of Salmonella in these coastal animals. The antimicrobial resistance pheno- and genotypes, as well as biocide susceptibility of Enterobacterales isolated from stranded marine mammals, were determined prior to their rehabilitation. All E. coli isolates (n = 27) were screened for virulence genes via DNA-based microarray, and twelve selected E. coli isolates were analyzed by whole-genome sequencing. Seventy-one percent of the Enterobacterales isolates exhibited a multidrug-resistant (MDR) pheno- and genotype. The gene blaCMY (n = 51) was the predominant β-lactamase gene. In addition, blaTEM-1 (n = 38), blaSHV-33 (n = 8), blaCTX-M-15 (n = 7), blaOXA-1 (n = 7), blaSHV-11 (n = 3), and blaDHA-1 (n = 2) were detected. The most prevalent non-β-lactamase genes were sul2 (n = 38), strA (n = 34), strB (n = 34), and tet(A) (n = 34). Escherichia coli isolates belonging to the pandemic sequence types (STs) ST38, ST167, and ST648 were identified. Among Salmonella isolates (n = 18), S. Havana was the most prevalent serotype. The present study revealed a high prevalence of MDR bacteria and the presence of pandemic high-risk clones, both of which are indicators of anthropogenic antimicrobial pollution, in marine mammals.

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Molecular investigation of an outbreak associated with total parenteral nutrition contaminated with NDM-producing Leclercia adecarboxylata

BMC Infectious Diseases ◽

10.1186/s12879-021-05923-0 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Elvira Garza-González ◽

Paola Bocanegra-Ibarias ◽

Eduardo Rodríguez-Noriega ◽

Esteban González-Díaz ◽

Jesús Silva-Sanchez ◽

...

Keyword(s):

Comparative Genomics ◽

Carbapenem Resistance ◽

Clonal Diversity ◽

Molecular Characteristics ◽

Molecular Evidence ◽

Carbapenem Resistant ◽

Parental Nutrition ◽

Genes Encoding ◽

Main Lineage ◽

Encoding Genes

Abstract Background This study aimed to determine the epidemiological, microbiological, and molecular characteristics of an outbreak of carbapenem-resistant Leclercia adecarboxylata in three hospitals associated with the unintended use of contaminated total parental nutrition (TPN). Methods For 10 days, 25 patients who received intravenous TPN from the same batch of a formula developed sepsis and had blood cultures positive for L. adecarboxylata. Antimicrobial susceptibility and carbapenemase production were performed in 31 isolates, including one from an unopened bottle of TPN. Carbapenemase-encoding genes, extended-spectrum β-lactamase–encoding genes were screened by PCR, and plasmid profiles were determined. Horizontal transfer of carbapenem resistance was performed by solid mating. Clonal diversity was performed by pulsed-field gel electrophoresis. The resistome was explored by whole-genome sequencing on two selected strains, and comparative genomics was performed using Roary. Results All 31 isolates were resistant to aztreonam, cephalosporins, carbapenems, trimethoprim/sulfamethoxazole, and susceptible to gentamicin, tetracycline, and colistin. Lower susceptibility to levofloxacin (51.6%) and ciprofloxacin (22.6%) was observed. All the isolates were carbapenemase producers and positive for blaNDM-1, blaTEM-1B, and blaSHV-12 genes. One main lineage was detected (clone A, 83.9%; A1, 12.9%; A2, 3.2%). The blaNDM-1 gene is embedded in a Tn125-like element. Genome analysis showed genes encoding resistance for aminoglycosides, quinolones, trimethoprim, colistin, phenicols, and sulphonamides and the presence of IncFII (Yp), IncHI2, and IncHI2A incompatibility groups. Comparative genomics showed a major phylogenetic relationship among L. adecarboxylata I1 and USDA-ARS-USMARC-60222 genomes, followed by our two selected strains. Conclusion We present epidemiological, microbiological, and molecular evidence of an outbreak of carbapenem-resistant L. adecarboxylata in three hospitals in western Mexico associated with the use of contaminated TPN.

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Resistome Profiles, Plasmid Typing, and Whole-Genome Phylogenetic Tree Analyses of BlaNDM-9 and Mcr-1 Co-Harboring Escherichia coli ST617 from a Patient without a History of Farm Exposure in Korea

Pathogens ◽

10.3390/pathogens8040212 ◽

2019 ◽

Vol 8 (4) ◽

pp. 212 ◽

Cited By ~ 3

Author(s):

Le Phuong Nguyen ◽

Naina Adren Pinto ◽

Thao Nguyen Vu ◽

Hung Mai ◽

An HT Pham ◽

...

Keyword(s):

Rectal Swab ◽

Asymptomatic Carrier ◽

University Hospital ◽

Surveillance Culture ◽

Whole Genome ◽

E Coli ◽

Carbapenem Resistant ◽

Plasmid Replicon ◽

Donor Cells ◽

History Of

Recently, a blaNDM-9 and mcr-1 co-harboring E. coli ST 617 isolate was identified from an asymptomatic carrier in Korea. An 81-year-old female was admitted to a university hospital for aortic cardiac valve repair surgery. Following surgery, she was admitted to the intensive care unit (ICU) for three days, and carbapenem-resistant E. coli YMC/2017/02/MS631 was isolated from a surveillance culture (rectal swab). Antimicrobial susceptibility testing (AST) for colistin was not performed at that time. Upon retrospective study, further AST revealed resistance to all tested antibiotics, including meropenem, imipenem, ceftazidime-avibactam, amikacin, gentamicin, ciprofloxacin, trimethoprim-sulfamethoxazole, and colistin, with the exception of tigecycline. Whole genome sequencing analyses showed that this strain belonged to the ST617 serotype O89/162: H10 and harbored three β-lactamase genes (blaTEM-1B, blaCTX-M-55, blaNDM-9), mcr-1, and 14 other resistance genes. Seven plasmid replicon types (IncB, IncFII, IncI2, IncN, IncY, IncR, IncX1) were identified. Horizontal transfer of blaNDM-9 and mcr-1 from donor cells to the recipient E. coli J53 has been observed. blaNDM-9 and mcr-1 were carried by IncB and IncI2 plasmids, respectively. To speculate on the incidence of this strain, routine rectal swab screening to identify asymptomatic carriers might be warranted, in addition to the screening of ICU patients.

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Enterobacteriaceae isolates carrying the New Delhi metallo-β-lactamase gene in Yemen

Journal of Medical Microbiology ◽

10.1099/jmm.0.073767-0 ◽

2014 ◽

Vol 63 (10) ◽

pp. 1316-1323 ◽

Cited By ~ 24

Author(s):

Alima Gharout-Sait ◽

Samer-Ahmed Alsharapy ◽

Lucien Brasme ◽

Abdelaziz Touati ◽

Rachida Kermas ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Susceptibility Testing ◽

Enterobacter Cloacae ◽

New Delhi ◽

Carbapenem Resistant ◽

Genes Encoding ◽

Phenotypic Tests ◽

Lactamase Gene ◽

Sequence Types

Ten carbapenem-resistant Enterobacteriaceae (eight Klebsiella pneumoniae isolates and two Enterobacter cloacae) isolates from Yemen were investigated using in vitro antimicrobial susceptibility testing, phenotypic carbapenemase detection, multilocus sequence typing (MLST) and replicon typing. Carbapenemase, extended-spectrum β-lactamase (ESBL) and plasmid-mediated quinolone resistance determinant genes were identified using PCR and sequencing. All of the 10 carbapenem-resistant Enterobacteriaceae were resistant to β-lactams, tobramycin, ciprofloxacin and cotrimoxazole. Imipenem, doripenem and meropenem MICs ranged from 2 to >32 mg l−1 and ertapenem MICs ranged from 6 to >32 mg l−1. All of the K. pneumoniae isolates showed ESBL activity in phenotypic tests. Genes encoding bla NDM were detected in all strains. All K. pneumoniae strains produced CTX-M-15 ESBL and SHV β-lactamases. TEM-1 β-lactamase was detected in seven isolates. Nine isolates were qnr positive including QnrB1, QnrA1 and QnrS1, and six isolates produced AAC-6′-Ib-cr. MLST identified five different sequence types (STs): ST1399, ST147, ST29, ST405 and ST340. Replicon typing showed the presence of IncFII1K plasmids in four transformants. To the best of our knowledge, this is the first report of NDM-1-producing Enterobacteriaceae isolates in Yemen.

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Phenotypic and Molecular Characteristics of the MDR Efflux Pump Gene-Carrying Stenotrophomonas maltophilia Strains Isolated in Warsaw, Poland

Biology ◽

10.3390/biology11010105 ◽

2022 ◽

Vol 11 (1) ◽

pp. 105

Author(s):

Olga M. Zając ◽

Stefan Tyski ◽

Agnieszka E. Laudy

Keyword(s):

Molecular Typing ◽

Stenotrophomonas Maltophilia ◽

Efflux Pump ◽

Pulsed Field Gel Electrophoresis ◽

Molecular Characteristics ◽

The World ◽

Genes Encoding ◽

Resistance Nodulation Division ◽

Sequence Types

An increase of nosocomial infections caused by Stenotrophomonas maltophilia strains has recently been observed all over the world. The isolation of these bacteria from the blood is of particular concern. In this study we performed the phenotypic and genotypic characterization of 94 S. maltophilia isolates, including isolates from patients hospitalized in a tertiary Warsaw hospital (n = 79) and from outpatients (n = 15). All isolates were found to be susceptible to trimethoprim-sulfamethoxazole and minocycline, while 44/94 isolates demonstrated a reduction in susceptibility to levofloxacin. A large genetic variation was observed among the isolates tested by pulsed-field gel electrophoresis. A clonal relationship with 100% similarity was observed between isolates within two sub-pulsotypes: the first included nine bloodstream isolates and the second involved six. Multilocus sequence typing showed two new sequence types (ST498 and ST499) deposited in public databases for molecular typing. Moreover, the presence of genes encoding ten different efflux pumps from the resistance-nodulation-division family and the ATP-binding cassette family was shown in the majority of the 94 isolates. The obtained knowledge about the prevalence of efflux pump genes in clinical S. maltophilia strains makes it possible to predict the scale of the risk of resistance emergence in strains as a result of gene overexpression.

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Identification and biochemical characterization of a novel PP2C-like Ser/Thr phosphatase inE. coli

10.1101/303594 ◽

2018 ◽

Author(s):

Krithika Rajagopalan ◽

Jonathan Dworkin

Keyword(s):

Biochemical Characterization ◽

Regulatory Protein ◽

Biochemical Properties ◽

Bacterial Genomes ◽

Phosphatase Inhibitors ◽

E Coli ◽

Specificity And Sensitivity ◽

Genes Encoding ◽

Number Of Bacteria

AbstractIn bacteria, signaling phosphorylation is thought to occur primarily on His and Asp residues. However, phosphoproteomic surveys in phylogenetically diverse bacteria over the past decade have identified numerous proteins that are phosphorylated on Ser and/or Thr residues. Consistently, genes encoding Ser/Thr kinases are present in many bacterial genomes such asE. coli,which encodes at least three Ser/Thr kinases. Since Ser/Thr phosphorylation is a stable modification, a dedicated phosphatase is necessary to allow reversible regulation. Ser/Thr phosphatases belonging to several conserved families are found in bacteria. One family of particular interest are Ser/Thr phosphatases which have extensive sequence and structural homology to eukaryotic Ser/Thr PP2C phosphatases. These proteins, called eSTPs (eukaryotic-like Ser/Thr phosphatases), have been identified in a number of bacteria, but not inE. coli.Here, we describe a previously unknown eSTP encoded by anE. coliORF,yegK,and characterize its biochemical properties including its kinetics, substrate specificity and sensitivity to known phosphatase inhibitors. We investigate differences in the activity of this protein in closely relatedE. colistrains. Finally, we demonstrate that this eSTP acts to dephosphorylate a novel Ser/Thr kinase which is encoded in the same operon.ImportanceRegulatory protein phosphorylation is a conserved mechanism of signaling in all biological systems. Recent phosphoproteomic analyses of phylogenetically diverse bacteria including the model Gram-negative bacteriumE. colidemonstrate that many proteins are phosphorylated on serine or threonine residues. In contrast to phosphorylation on histidine or aspartate residues, phosphorylation of serine and threonine residues is stable and requires the action of a partner Ser/Thr phosphatase to remove the modification. Although a number of Ser/Thr kinases have been reported inE. coli, no partner Ser/Thrphosphatases have been identified. Here, we biochemically characterize a novel Ser/Thr phosphatase that acts to dephosphorylate a Ser/Thr kinase that is encoded in the same operon.

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The characterization of ESBL genes in Escherichia coli and Klebsiella pneumoniae causing nosocomial infections in Vietnam

The Journal of Infection in Developing Countries ◽

10.3855/jidc.2938 ◽

2013 ◽

Vol 7 (12) ◽

pp. 922-928 ◽

Cited By ~ 15

Author(s):

Nguyen Hoang Thu Trang ◽

Tran Vu Thieu Nga ◽

James I Campbell ◽

Nguyen Trong Hiep ◽

Jeremy Farrar ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Klebsiella Pneumoniae ◽

Nosocomial Infections ◽

Enteric Bacteria ◽

E Coli ◽

Plasmid Analysis ◽

Resistance Plasmids ◽

Genes Encoding ◽

Third Generation Cephalosporins

Background: Extended-spectrum β-lactamases (ESBLs) are enzymes capable of hydrolyzing oxyimino-β-lactams and inducing resistance to third generation cephalosporins. The genes encoding ESBLs are widespread and generally located on highly transmissible resistance plasmids. We aimed to investigate the complement of ESBL genes in E. coli and Klebsiella pneumoniae causing nosocomial infections in hospitals in Ho Chi Minh City, Vietnam. Methodology: Thirty-two non-duplicate isolates of E. coli and Klebsiella pneumoniae causing nosocomial infections, isolated between March and June 2010, were subjected to antimicrobial susceptibility testing. All isolates were PCR-amplified to detect the blaSHV, blaTEM and blaCTX-M ESBL genes and subjected to plasmid analysis. Results: We found that co-resistance to multiple antimicrobials was highly prevalent, and we report the predominance of the blaCTX-M-15 and blaCTX-M-27 genes, located on highly transmissible plasmids ranging from 50 to 170 kb in size. Conclusions: Our study represents a snap shot of ESBL-producing enteric bacteria causing nosocomial infections in this setting. We suggest that antimicrobial resistance in nosocomial E. coli and Klebsiella pneumoniae is rampant in Vietnam and ESBL organisms are widespread. In view of these data and the dramatic levels of antimicrobial resistance reported in Vietnam we advocate an urgent review of antimicrobial use in the Vietnamese healthcare system.

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