Complement Susceptibility in Relation to Genome Sequence of RecentKlebsiella pneumoniaeIsolates from Thai Hospitals

ABSTRACTThe capacity to resist the bactericidal action of complement (C′) is a strong but poorly understood virulence trait inKlebsiellaspp. Killing requires activation of one or more C′ pathways, assembly of C5b-9 membrane attack complexes (MACs) on the surface of the outer membrane (OM), and penetration of MACs into the target bilayer. We interrogated whole-genome sequences of 164Klebsiellaisolates from three tertiary hospitals in Thailand for genes encoding surface-located macromolecules considered to play a role in determination of C′ resistance. Most isolates (154/164) were identified asKlebsiella pneumoniae, and the collection conformed to previously established population structures and antibiotic resistance patterns. The distribution of sequence types (STs) and capsular (K) types were also typical of global populations. The majority (64%) of isolates were resistant to C′, and the remainder were either rapidly or slowly killed. All isolates carried genes encoding capsular polysaccharides (K antigens), which have been strongly linked to C′ resistance. In contrast to previous reports, there were no differences in the amount of capsule produced by C′-resistant isolates compared to C′-susceptible isolates, nor was there any correlation between serum reactivity and the presence of hypermucoviscous capsules. Similarly, there were no correlations between the presence of genes specifying lipopolysaccharide O-side chains or major OM proteins. Some virulence factors were found more frequently in C′-resistant isolates but were considered to reflect clonal ST expansion. Thus, no single gene accounts for the C′ resistance of the isolates sequenced in this study.IMPORTANCEMultidrug-resistantKlebsiella pneumoniaeis responsible for an increasing proportion of nosocomial infections, and emerging hypervirulentK. pneumoniaeclones now cause severe community-acquired infections in otherwise healthy individuals. These bacteria are adept at circumventing immune defenses, and most survive and grow in serum; their capacity to avoid C′-mediated destruction is correlated with their invasive potential. Killing of Gram-negative bacteria occurs following activation of the C′ cascades and stable deposition of C5b-9 MACs onto the OM. ForKlebsiella, studies with mutants and conjugants have invoked capsules, lipopolysaccharide O-side chains, and OM proteins as determinants of C′ resistance, although the precise roles of the macromolecules are unclear. In this study, we sequenced 164Klebsiellaisolates with different C′ susceptibilities to identify genes involved in resistance. We conclude that no single OM constituent can account for resistance, which is likely to depend on biophysical properties of the target bilayer.

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Coexistence of aminoglycoside resistance genes in CTX-M-producing isolates of Klebsiella pneumoniae in Bushehr province, Iran

Iranian Journal of Microbiology ◽

10.18502/ijm.v13i2.5975 ◽

2021 ◽

Author(s):

Behrouz Latifi ◽

Saeed Tajbakhsh ◽

Leila Ahadi ◽

Forough Yousefi

Keyword(s):

Klebsiella Pneumoniae ◽

Resistance Genes ◽

Confirmatory Test ◽

M Gene ◽

Aminoglycoside Resistance ◽

Genetic Groups ◽

Genes Encoding ◽

Resistance Patterns ◽

Aminoglycoside Resistance Genes ◽

Antibiotic Resistance Patterns

Background and Objectives: Increasing the rate of extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae has given rise to a major healthcare issue in clinical settings over the past few years. Treatment of these strains is hardly effective since the plasmid encoding ESBL may also carry other resistance genes including aminoglycosides. The current study aimed to evaluate the prevalence of ESBL-producing K. pneumoniae and investigate the coexistence of Cefoxitamase-Munich (bla ) with aminoglycoside-modifying enzyme (AME) genes, aac(3)IIa as well as aac(6′)Ib, in CTX‑M‑producing K. pneumoniae isolated from patients in Bushehr province, Iran. Materials and Methods: A total of 212 K. pneumoniae isolates were collected and confirmed using polymerase chain re‑ action (PCR) of the malate dehydrogenase gene. Isolates were screened for production of ESBL. Phenotypic confirmatory test was performed using combined disk test. The genes encoding CTX-M groups and AME genes, aac(3)IIa and aac(6′)Ib, were investigated by PCR. Results: The ESBL phenotype was detected in 56 (26.4%) K. pneumoniae isolates. Moreover, 83.9% of ESBL-producing isolates carried the genes for CTX-M type β-lactamases, which were distributed into the two genetic groups of CTX-M-1 (97.8%)- and CTX-M-2 (2.1%)-related enzymes. Notably, among K. pneumoniae isolates containing the blaCTX‑M gene, 68.08% of isolates harbored AME genes. In addition, the coexistence of bla in 46.8% of CTX-M-producing K. pneumoniae isolates. Conclusion: This study provides evidence of a high prevalence of AME genes in CTX-M- producing K. pneumoniae iso‑ lates; therefore, in the initial empirical treatment of infections caused by ESBL-KP in regions with such antibiotic resistance patterns, aminoglycoside combination therapy should be undertaken carefully.

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Elucidating the Regulon of Multidrug Resistance Regulator RarA in Klebsiella pneumoniae

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01998-12 ◽

2013 ◽

Vol 57 (4) ◽

pp. 1603-1609 ◽

Cited By ~ 31

Author(s):

Shyamasree De Majumdar ◽

Mark Veleba ◽

Sarah Finn ◽

Séamus Fanning ◽

Thamarai Schneiders

Keyword(s):

Klebsiella Pneumoniae ◽

Cell Envelope ◽

Polymyxin B ◽

Multidrug Resistant ◽

Protein Synthesis Inhibitors ◽

Content Type ◽

Phenotypic Microarray ◽

Genes Encoding ◽

Clusters Of Orthologous Groups ◽

Microarray Analyses

ABSTRACTRarA is an AraC-type regulator inKlebsiella pneumoniae, which, when overexpressed, confers a low-level multidrug-resistant (MDR) phenotype linked to the upregulation of both theacrABandoqxABefflux genes. IncreasedrarAexpression has also been shown to be integral in the development of tigecycline resistance in the absence oframAinK. pneumoniae. Given its phenotypic role in MDR, microarray analyses were performed to determine the RarA regulon. Transcriptome analysis was undertaken using strains Ecl8ΔrarA/pACrarA-2 (rarA-expressing construct) and Ecl8ΔrarA/pACYC184 (vector-only control) using bespoke microarray slides consisting of probes derived from the genomic sequences ofK. pneumoniaeMGH 78578 (NC_009648.1) and Kp342 (NC_011283.1). Our results show thatrarAoverexpression resulted in the differential expression of 66 genes (42 upregulated and 24 downregulated). Under the COG (clusters of orthologous groups) functional classification, the majority of affected genes belonged to the category of cell envelope biogenesis and posttranslational modification, along with genes encoding the previously uncharacterized transport proteins (e.g., KPN_03141,sdaCB, andleuE) and the porin OmpF. However, genes associated with energy production and conversion and amino acid transport/metabolism (e.g.,nuoA,narJ, andproWX) were found to be downregulated. Biolog phenotype analyses demonstrated thatrarAoverexpression confers enhanced growth of the overexpresser in the presence of several antibiotic classes (i.e., beta-lactams and fluoroquinolones), the antifungal/antiprotozoal compound clioquinol, disinfectants (8-hydroxyquinoline), protein synthesis inhibitors (i.e., minocycline and puromycin), membrane biogenesis agents (polymyxin B and amitriptyline), DNA synthesis (furaltadone), and the cytokinesis inhibitor (sanguinarine). Both our transcriptome and phenotypic microarray data support and extend the role of RarA in the MDR phenotype ofK. pneumoniae.

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Genotypes of Esbl Producing Escherichia Coli and Klebsiella Pneumoniae in Relation to Resistance to Antimicrobial Drugs

PRILOZI ◽

10.2478/prilozi-2014-0004 ◽

2014 ◽

Vol 35 (2) ◽

pp. 31-38

Author(s):

Ana Kaftandzieva ◽

Elena Trajkovska-Dokic ◽

Vesna Kotevska ◽

Zaklina Cekovska ◽

Gordana Jankoska

Keyword(s):

Antibiotic Resistance ◽

Klebsiella Pneumoniae ◽

Antimicrobial Agents ◽

Single Gene ◽

Tracheal Aspirate ◽

Beta Lactams ◽

Antimicrobial Drugs ◽

E Coli ◽

Resistance Patterns ◽

Antibiotic Resistance Patterns

Abstract The aim of the study was to evaluate the association of drug resistance with β-lactamase gene types in ESBL positive E. coli and Klebsiella pneumoniae-Kp. Material and methods: A total of 251 ESBL-positive E. coli and Kp isolates obtained from urine, tracheal aspirate, wound swab and blood from patients hospitalised at the University Clinics in Skopje were detected using the ESBL set and automated Vitek 2 system. Vitek was also used for susceptibility testing (determination of MIC of 17 antimicrobial agents). Multiplex PCR was used to identify genes for different types of ESBLs in a 100 randomly selected, ESBL positive strains. Results: More of the 87 ESBL typeable isolates (61%) harbour two or more bla genes and the frequency of antibiotic resistance was high in these isolates, compared to those with a single gene. Isolates with ≥ 3 genes were highly resistant to beta-lactams and non-beta lactams used. The degree of resistance to 3rd generation cephalosporins was also high in these isolates (MIC ≥ 64). More of the ESBL-positive isolates showed higher resistance to cefotaxime than to ceftazidime. Conclusion: Identification of the genes is necessary for the surveillance of their transmission in hospitals. Surveillance of antibiotic resistance patterns are crucial to overcome the problems associated with ESBLs.

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Epidemiology and Outcomes of Nontyphoidal Salmonella Bacteremias from England, 2004 to 2015

Journal of Clinical Microbiology ◽

10.1128/jcm.01189-18 ◽

2018 ◽

Vol 57 (1) ◽

Cited By ~ 1

Author(s):

Shannon Katiyo ◽

Berit Muller-Pebody ◽

Mehdi Minaji ◽

David Powell ◽

Alan P. Johnson ◽

...

Keyword(s):

Antimicrobial Agents ◽

High Morbidity ◽

First Line ◽

Data Set ◽

Content Type ◽

Increased Risk ◽

Resistance Patterns ◽

Prolonged Hospital ◽

Antibiotic Resistance Patterns ◽

Emergence Of Resistance

ABSTRACT Nontyphoidal Salmonella (NTS) bacteremia causes hospitalization and high morbidity and mortality. We linked Gastrointestinal Bacteria Reference Unit (GBRU) data to the Hospital Episode Statistics (HES) data set to study the trends and outcomes of NTS bacteremias in England between 2004 and 2015. All confirmed NTS isolates from blood from England submitted to GBRU between 1 January 2004 and 31 December 2015 were deterministically linked to HES records. Adjusted odds ratios (AOR), proportions, and confidence intervals (CI) were calculated to describe differences in age, sex, antibiotic resistance patterns, and serotypes over time. Males, neonates, and adults above 65 years were more likely to have NTS bacteremia (AOR, 1.54 [95% CI, 1.46 to 1.67]; 2.57 [95% CI, 1.43 to 4.60]; and 3.56 [95% CI, 3.25 to 3.90], respectively). Proportions of bacteremia increased from 1.41% in 2004 to 2.67% in 2015. Thirty-four percent of all blood isolates were resistant to a first-line antibiotic, and 1,397 (56%) blood isolates were linked to an HES record. Of the patients with NTS bacteremia, 969 (69%) had a cardiovascular condition and 155 (12%) patients died, out of which 120 (77%) patients were age 65 years and above. NTS bacteremia mainly affects older people with comorbidities placing them at increased risk of prolonged hospital stay and death. Resistance of invasive NTS to first-line antimicrobial agents appeared to be stable in England, but the emergence of resistance to last-resort antibiotics, such as colistin, requires careful monitoring.

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Comparison of Genotypes and Antibiotic Resistances of Campylobacter jejuni and Campylobacter coli on Chicken Retail Meat and at Slaughter

Applied and Environmental Microbiology ◽

10.1128/aem.00493-13 ◽

2013 ◽

Vol 79 (12) ◽

pp. 3875-3878 ◽

Cited By ~ 13

Author(s):

Sonja Kittl ◽

Bożena M. Korczak ◽

Lilian Niederer ◽

Andreas Baumgartner ◽

Sabina Buettner ◽

...

Keyword(s):

Campylobacter Jejuni ◽

Human Infection ◽

Chicken Meat ◽

Campylobacter Coli ◽

Production Chain ◽

Content Type ◽

Resistance Patterns ◽

Retail Meat ◽

Retail Chicken Meat ◽

Antibiotic Resistance Patterns

ABSTRACTMultilocus sequence typing (MLST) and antibiotic resistance patterns ofCampylobacter jejuniandCampylobacter colifrom retail chicken meat showed high overlap with isolates collected at slaughterhouses, indicating little selection along the production chain. They also showed significant common sequence types with human clinical isolates, revealing chicken meat as a likely source for human infection.

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Antimicrobial Activity of Ceftazidime-Avibactam Tested against Multidrug-Resistant Enterobacteriaceae and Pseudomonas aeruginosa Isolates from U.S. Medical Centers, 2013 to 2016

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01045-17 ◽

2017 ◽

Vol 61 (11) ◽

Cited By ~ 52

Author(s):

Helio S. Sader ◽

Mariana Castanheira ◽

Dee Shortridge ◽

Rodrigo E. Mendes ◽

Robert K. Flamm

Keyword(s):

Pseudomonas Aeruginosa ◽

Multidrug Resistant ◽

Drug Resistant ◽

Large Collection ◽

Content Type ◽

Negative Results ◽

Medical Centers ◽

Extensively Drug Resistant ◽

Genes Encoding

ABSTRACT The in vitro activity of ceftazidime-avibactam and many comparator agents was determined against various resistant subsets of organisms selected among 36,380 Enterobacteriaceae and 7,868 Pseudomonas aeruginosa isolates. The isolates were consecutively collected from 94 U.S. hospitals, and all isolates were tested for susceptibility by reference broth microdilution methods in a central monitoring laboratory (JMI Laboratories). Enterobacteriaceae isolates resistant to carbapenems (CRE) and/or ceftazidime-avibactam (MIC ≥ 16 μg/ml) were evaluated for the presence of genes encoding extended-spectrum β-lactamases and carbapenemases. Ceftazidime-avibactam inhibited >99.9% of all Enterobacteriaceae at the susceptible breakpoint of ≤8 μg/ml and was active against multidrug-resistant (MDR; n = 2,953; MIC50/90, 0.25/1 μg/ml; 99.2% susceptible), extensively drug-resistant (XDR; n = 448; MIC50/90, 0.5/2 μg/ml; 97.8% susceptible), and CRE (n = 513; MIC50/90, 0.5/2 μg/ml; 97.5% susceptible) isolates. Only 82.2% of MDR Enterobacteriaceae (n = 2,953) and 64.2% of ceftriaxone-nonsusceptible Klebsiella pneumoniae (n = 1,063) isolates were meropenem susceptible. Among Enterobacter cloacae (22.2% ceftazidime nonsusceptible), 99.8% of the isolates, including 99.3% of the ceftazidime-nonsusceptible isolates, were ceftazidime-avibactam susceptible. Only 23 of 36,380 Enterobacteriaceae (0.06%) isolates were ceftazidime-avibactam nonsusceptible, including 9 metallo-β-lactamase producers and 2 KPC-producing strains with porin alteration; the remaining 12 strains showed negative results for all β-lactamases tested. Ceftazidime-avibactam showed potent activity against P. aeruginosa (MIC50/90, 2/4 μg/ml; 97.1% susceptible), including MDR (MIC50/90, 4/16 μg/ml; 86.5% susceptible) isolates, and inhibited 71.8% of isolates nonsusceptible to meropenem, piperacillin-tazobactam, and ceftazidime (n = 628). In summary, ceftazidime-avibactam demonstrated potent activity against a large collection (n = 44,248) of contemporary Gram-negative bacilli isolated from U.S. patients, including organisms resistant to most currently available agents, such as CRE and meropenem-nonsusceptible P. aeruginosa.

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Genomic evolution and local epidemiology of Klebsiella pneumoniae from a major hospital in Beijing, China, over a 15 year period: dissemination of known and novel high-risk clones

Microbial Genomics ◽

10.1099/mgen.0.000520 ◽

2021 ◽

Author(s):

Mattia Palmieri ◽

Kelly L. Wyres ◽

Caroline Mirande ◽

Zhao Qiang ◽

Ye Liyan ◽

...

Keyword(s):

High Risk ◽

Klebsiella Pneumoniae ◽

Type Species ◽

Treatment Options ◽

Multidrug Resistant ◽

Virulence Plasmid ◽

Content Type ◽

Origin And Evolution ◽

Link Type ◽

Beijing China

Klebsiella pneumoniae is a frequent cause of nosocomial and severe community-acquired infections. Multidrug-resistant (MDR) and hypervirulent (hv) strains represent major threats, and tracking their emergence, evolution and the emerging convergence of MDR and hv traits is of major importance. We employed whole-genome sequencing (WGS) to study the evolution and epidemiology of a large longitudinal collection of clinical K. pneumoniae isolates from the H301 hospital in Beijing, China. Overall, the population was highly diverse, although some clones were predominant. Strains belonging to clonal group (CG) 258 were dominant, and represented the majority of carbapenemase-producers. While CG258 strains showed high diversity, one clone, ST11-KL47, represented the majority of isolates, and was highly associated with the KPC-2 carbapenemase and several virulence factors, including a virulence plasmid. The second dominant clone was CG23, which is the major hv clone globally. While it is usually susceptible to multiple antibiotics, we found some isolates harbouring MDR plasmids encoding for ESBLs and carbapenemases. We also reported the local emergence of a recently described high-risk clone, ST383. Conversely to strains belonging to CG258, which are usually associated to KPC-2, ST383 strains seem to readily acquire carbapenemases of different types. Moreover, we found several ST383 strains carrying the hypervirulence plasmid. Overall, we detected about 5 % of simultaneous carriage of AMR genes (ESBLs or carbapenemases) and hypervirulence genes. Tracking the emergence and evolution of such strains, causing severe infections with limited treatment options, is fundamental in order to understand their origin and evolution and to limit their spread. This article contains data hosted by Microreact.

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Report of Antibiotic Resistance in Urban and Rural Wastewaters from West Bengal, India

Journal of Pharmaceutical Research International ◽

10.9734/jpri/2021/v33i53a33660 ◽

2021 ◽

pp. 274-285

Author(s):

Meesha Singh ◽

Rupsha Karmakar ◽

Sayak Ganguli ◽

Mahashweta Mitra Ghosh

Keyword(s):

Antibiotic Resistance ◽

Biochemical Characterization ◽

Chemical Properties ◽

Multidrug Resistant ◽

Resistant Bacteria ◽

Medical Facility ◽

Antibiotic Resistant ◽

Two Samples ◽

Resistance Patterns ◽

Antibiotic Resistance Patterns

Aims: This study aims at comparative identification of antibiotic resistance patterns in bacteria isolated from samples collected from rural environment (LS) and urban environments (SS). Metagenomic profiling gave us insights into the microbial abundance of the two samples. This study focused on culture-based methods for complete identification of antibiotic resistant isolates and estimation of comparative antibiotic resistance among the two samples. Study Design: Untreated medical waste and anthropogenic waste disposal can lead to the propagation of different antibiotic resistant strains in wastewater environments both in urban and rural set ups which provide an insight towards this study approach mentioned in the methodology segment. Place and Duration of Study: Sewer system of a medical facility located in Purulia, India was the collection site for liquid sludge. Solid sludge and associated wastewater were collected in vicinity of a large urban medical facility from central Kolkata, India. Methodology: Physico-chemical properties were analyzed followed by microbiological and biochemical characterization. The antibiotic resistance patterns were determined by Kirby-Bauer disc diffusion assay. Potent multidrug resistant isolates were identified using 16srRNA gene amplification followed by Phylogenetic profiling, using CLC Genomics workbench. Results: We observed maximum resistance in an E. coli isolate which was resistant up to 22 antibiotics. Combined data for resistance from urban and rural samples were found to exhibit 83.9% resistance to beta lactams, 85.7% to macrolides, 44.2% to fluoroquinolones, 50% to glycopeptides and cephalosporins, 35.7 % to carbapenems and sulfonamides, 28.5 % to tetracycline, and 23.8 % to aminoglycosides. Conclusion: The high prevalence of antibiotic-resistant bacteria harbouring diverse resistance traits across samples indicated towards probable horizontal gene transfer across environmental niches. This study can prove to be useful to understand and map the patterns of resistance and stringently apply the counter measures related to public health practices.

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Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains

Microbial Genomics ◽

10.1099/mgen.0.000474 ◽

2020 ◽

Vol 6 (12) ◽

Author(s):

Katlego Kopotsa ◽

Nontombi M. Mbelle ◽

John Osei Sekyere

Keyword(s):

Klebsiella Pneumoniae ◽

Multidrug Resistant ◽

Type I ◽

Bacteriophage Therapy ◽

Content Type ◽

Carbapenem Resistant ◽

Plasmid Replicon ◽

Size Number ◽

Plasmid Size ◽

Epidemiological Trends

Carbapenem-resistant Klebsiella pneumoniae (CRKP) remains a major clinical pathogen and public health threat with few therapeutic options. The mobilome, resistome, methylome, virulome and phylogeography of CRKP in South Africa and globally were characterized. CRKP collected in 2018 were subjected to antimicrobial susceptibility testing, screening by multiplex PCR, genotyping by repetitive element palindromic (REP)-PCR, plasmid size, number, incompatibility and mobility analyses, and PacBio’s SMRT sequencing (n=6). There were 56 multidrug-resistant CRKP, having bla OXA-48-like and bla NDM-1/7 carbapenemases on self-transmissible IncF, A/C, IncL/M and IncX3 plasmids endowed with prophages, traT, resistance islands, and type I and II restriction modification systems (RMS). Plasmids and clades detected in this study were respectively related to globally established/disseminated plasmids clades/clones, evincing transboundary horizontal and vertical dissemination. Reduced susceptibility to colistin occurred in 23 strains. Common clones included ST307, ST607, ST17, ST39 and ST3559. IncFIIk virulent plasmid replicon was present in 56 strains. Whole-genome sequencing of six strains revealed least 41 virulence genes, extensive ompK36 mutations, and four different K- and O-loci types: KL2, KL25, KL27, KL102, O1, O2, O4 and O5. Types I, II and III RMS, conferring m6A (G A TC, G A TGNNNNNNTTG, CA A NNNNNNCATC motifs) and m4C (C C WGG) modifications on chromosomes and plasmids, were found. The nature of plasmid-mediated, clonal and multi-clonal dissemination of blaOXA-48-like and blaNDM-1 mirrors epidemiological trends observed for closely related plasmids and sequence types internationally. Worryingly, the presence of both bla OXA-48 and bla NDM-1 in the same isolates was observed. Plasmid-mediated transmission of RMS, virulome and prophages influence bacterial evolution, epidemiology, pathogenicity and resistance, threatening infection treatment. The influence of RMS on antimicrobial and bacteriophage therapy needs urgent investigation.

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Complete Genome Sequence of Klebsiella pneumoniae Phage Sweeny

Microbiology Resource Announcements ◽

10.1128/mra.01047-19 ◽

2019 ◽

Vol 8 (39) ◽

Cited By ~ 1

Author(s):

Nicholas Martinez ◽

Eric Williams ◽

Heather Newkirk ◽

Mei Liu ◽

Jason J. Gill ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Complete Genome Sequence ◽

Protein Level ◽

Multidrug Resistant ◽

Content Type ◽

Hospital Acquired Infections ◽

Multidrug Resistant Bacterium ◽

Protein Encoding ◽

Hospital Acquired ◽

Encoding Genes

Klebsiella pneumoniae is a multidrug-resistant bacterium causing many severe hospital-acquired infections. Here, we describe siphophage Sweeny that infects K. pneumoniae. Of its 78 predicted protein-encoding genes, a functional assignment was given to 36 of them. Sweeny is most closely related to T1-like phages at the protein level.

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