scholarly journals Genomic Analysis of Carbapenemase-Producing Extensively Drug-Resistant Klebsiella pneumoniae Isolates Reveals the Horizontal Spread of p18-43_01 Plasmid Encoding blaNDM-1 in South Africa

2020 ◽  
Vol 8 (1) ◽  
pp. 137 ◽  
Author(s):  
Yogandree Ramsamy ◽  
Koleka P. Mlisana ◽  
Mushal Allam ◽  
Daniel G. Amoako ◽  
Akebe L. K. Abia ◽  
...  
Keyword(s):  
South Africa ◽  
Klebsiella Pneumoniae ◽  
Sequence Type ◽  
Control Measures ◽  
Whole Genome Sequence ◽  
Drug Resistant ◽  
Genotypic Resistance ◽  
Microbial Identification ◽  
Extensively Drug Resistant ◽  
Single Locus Variant

Whole-genome sequence (WGS) analyses were employed to investigate the genomic epidemiology of extensively drug-resistant Klebsiella pneumoniae strains, focusing on the carbapenem resistance-encoding determinants, mobile genetic support, clonal and epidemiological relationships. A total of ten isolates were obtained from patients admitted to the intensive care unit (ICU) in a public hospital in South Africa. Five isolates were from rectal swabs of colonized patients and five from blood cultures of patients with invasive carbapenem-resistant infections. Following microbial identification and antibiotic susceptibility tests, the isolates were subjected to WGS on the Illumina MiSeq platform. All the isolates showed genotypic resistance to tested β-lactams (NDM-1, OXA-1, CTX-M-15, TEM-1B, SHV-1) and other antibiotics. All but one isolate belonged to the ST152 with a novel sequence type, ST3136, differing by a single-locus variant. The isolates had the same plasmid multilocus sequence type (IncF[K12:A-:B36]) and capsular serotype (KL149), supporting the epidemiological linkage between the clones. Resistance to carbapenems in the 10 isolates was conferred by the blaNDM-1 mediated by the acquisition of multi-replicon [ColRNAI, IncFIB(pB171), Col440I, IncFII, IncFIB(K) and IncFII(Yp)] p18-43_01 plasmid. These findings suggest that the acquisition of blaNDM-1-bearing plasmid structure (p18-43_01), horizontal transfer and clonal dissemination facilitate the spread of carbapenemases in South Africa. This emphasizes the importance of targeted infection control measures to prevent dissemination.

scholarly journals Extensively drug-resistant Klebsiella pneumoniae ST307 outbreak, north-eastern Germany, June to October 2019

2019 ◽  
Vol 24 (50) ◽  
Author(s):  
Sebastian Haller ◽  
Rolf Kramer ◽  
Karsten Becker ◽  
Jürgen A Bohnert ◽  
Tim Eckmanns ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Sequence Type ◽  
Control Measures ◽  
Synergistic Activity ◽  
Drug Resistant ◽  
Eastern Germany ◽  
Extensively Drug Resistant ◽  
Medical Facilities ◽  
North Eastern ◽  
Genomic Analyses

From June to October 2019, 17 patients (six infected, 11 colonised) with an extensively drug-resistant (XDR) Klebsiella pneumoniae strain were notified from four Western Pomerania medical facilities. The XDR K. pneumoniae produced carbapenemases NDM-1 and OXA-48, and was only susceptible to chloramphenicol, tigecycline and cefiderocol. Synergistic activity was observed for the combination of aztreonam plus ceftazidime-avibactam. Genomic analyses showed all isolates belonged to K. pneumoniae sequence type 307. Control measures and further investigations are ongoing.

scholarly journals Whole-Genome Sequence of a Novel Sequence Type 3136 Carbapenem-Resistant Klebsiella pneumoniae Strain Isolated from a Hospitalized Patient in Durban, South Africa

2018 ◽  
Vol 7 (23) ◽  
Author(s):  
Yogandree Ramsamy ◽  
Koleka P. Mlisana ◽  
Mushal Allam ◽  
Arshad Ismail ◽  
Ravesh Singh ◽  
...  
Keyword(s):  
South Africa ◽  
Klebsiella Pneumoniae ◽  
Virulence Factors ◽  
Genome Sequence ◽  
Sequence Type ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Resistance Determinants ◽  
Carbapenem Resistant

Here, we describe the genome sequence of a novel sequence type 3136 (ST3136) Klebsiella pneumoniae strain isolated in South Africa. The 5,574,236-bp genome harbored 23 resistance determinants and 12 virulence factors that are of cardinal importance to infections.

scholarly journals Dissemination of High-Risk Clones of Extensively Drug-Resistant Pseudomonas aeruginosa in Colombia

2015 ◽  
Vol 59 (4) ◽  
pp. 2421-2425 ◽  
Author(s):  
Adriana Correa ◽  
Rosa del Campo ◽  
Marcela Perenguez ◽  
Victor M. Blanco ◽  
Mercedes Rodríguez-Baños ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
High Risk ◽  
Sequence Type ◽  
Single Locus ◽  
Drug Resistant ◽  
Class 1 Integron ◽  
Content Type ◽  
Extensively Drug Resistant ◽  
Single Locus Variant ◽  
Class 1

ABSTRACTThe ability ofPseudomonas aeruginosato develop resistance to most antimicrobials represents an important clinical threat worldwide. We report the dissemination in several Colombian hospitals of two predominant lineages of extensively drug-resistant (XDR) carbapenemase-producingP. aeruginosastrains. These lineages belong to the high-risk clones sequence type 111 (ST111) and ST235 and harborblaVIM-2on a class 1 integron andblaKPC-2on a Tn4401transposon, respectively. Additionally,P. aeruginosaST1492, a novel single-locus variant of ST111, was identified. Clonal dissemination and the presence of mobile genetic elements likely explain the successful spread of XDRP. aeruginosastrains in Colombia.

scholarly journals Characterization of Extensively Drug-Resistant or Pandrug-Resistant Sequence Type 147 and 101 OXA-48-Producing Klebsiella pneumoniae Causing Bloodstream Infections in Patients in an Intensive Care Unit

2018 ◽  
Vol 62 (7) ◽  
pp. e02457-17 ◽  
Author(s):  
Kalliope Avgoulea ◽  
Vincenzo Di Pilato ◽  
Olympia Zarkotou ◽  
Samanta Sennati ◽  
Leda Politi ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Intensive Care ◽  
Klebsiella Pneumoniae ◽  
Sequence Type ◽  
Snp Analysis ◽  
Drug Resistant ◽  
Pfge Profile ◽  
Content Type ◽  
Extensively Drug Resistant ◽  
Insertional Inactivation

ABSTRACT Carbapenem-resistant Klebsiella pneumoniae causes important health care-associated infections worldwide. An outbreak of sequence type 11 (ST11) OXA-48-producing K. pneumoniae (OXA-48-Kp) isolates occurred in Tzaneio Hospital in 2012 and was contained until 2014, when OXA-48-Kp reemerged. The present study involved 19 bloodstream infection (BSI) OXA-48-Kp isolates recovered from 19 intensive care unit (ICU) patients hospitalized between August 2014 and July 2016. MICs were determined by broth microdilution. Beta-lactamase genes were detected by PCR. All isolates were typed by pulsed-field gel electrophoresis/multilocus sequence typing (PFGE/MLST), and 10 representative isolates were typed by next-generation sequencing (NGS). Of the 19 study patients, 9 had previous hospitalizations, and 10 carried OXA-48-Kp prior to BSI isolation; median time from ICU admission to BSI was 29 days. Four OXA-48-Kp isolates belonged to PFGE profile A (ST147) and were pandrug resistant (PDR), while 15 isolates exhibited PFGE profile B (ST101) and were extensively drug resistant. Genes detected via NGS resistome analysis accounted for most of the resistance phenotypes, except for tigecycline and fosfomycin. Insertional inactivation of mgrB (distinct per clone) conferred colistin resistance in all 19 isolates. NGS single nucleotide polymorphism (SNP) analysis validated the clonal relatedness of the ST147 and ST101 strains and revealed the possible presence of two index ST147 strains and the microevolution of ST101 strains. Distinct, but highly related, IncL OXA-48-encoding plasmid lineages were identified; plasmids of the ST147 strains were identical with the plasmid of ST11 OXA-48-Kp which caused the 2012 outbreak. In conclusion, biclonal circulation of OXA-48-Kp and, alarmingly, emergence of a PDR clone are reported. These observations, along with the challenging phenotypic detection of OXA-48 producers and the high reported transmissibility of blaOXA-48, necessitate intensive efforts to prevent their further spread.

scholarly journals Spread of Plasmid-Encoded NDM-1 and GES-5 Carbapenemases among Extensively Drug-Resistant and Pandrug-Resistant Clinical Enterobacteriaceae in Durban, South Africa

2018 ◽  
Vol 62 (5) ◽  
Author(s):  
Torunn Pedersen ◽  
John Osei Sekyere ◽  
Usha Govinden ◽  
Krishnee Moodley ◽  
Audun Sivertsen ◽  
...  
Keyword(s):  
South Africa ◽  
South African ◽  
Molecular Mechanisms ◽  
Whole Genome Sequence ◽  
Drug Resistant ◽  
Content Type ◽  
Carbapenem Resistant ◽  
Extensively Drug Resistant ◽  
Horizontal Spread ◽  
Genome Assemblies

ABSTRACT Whole-genome sequence analyses revealed the presence of bla NDM-1 ( n = 31), bla GES-5 ( n = 8), bla OXA-232 ( n = 1), or bla NDM-5 ( n = 1) in extensively drug-resistant and pandrug-resistant Enterobacteriaceae organisms isolated from in-patients in 10 private hospitals (2012 to 2013) in Durban, South Africa. Two novel NDM-1-encoding plasmids from Klebsiella pneumoniae were circularized by PacBio sequencing. In p19-10_01 [IncFIB(K); 223.434 bp], bla NDM-1 was part of a Tn 1548 -like structure (16.276 bp) delineated by IS 26 . The multireplicon plasmid p18-43_01 [IncR_1/IncFIB(pB171)/IncFII(Yp); 212.326 bp] shared an 80-kb region with p19-10_01, not including the bla NDM-1 -containing region. The two plasmids were used as references for tracing NDM-1-encoding plasmids in the other genome assemblies. The p19-10_01 sequence was detected in K. pneumoniae ( n = 7) only, whereas p18-43_01 was tracked to K. pneumoniae ( n = 4), Klebsiella michiganensis ( n = 1), Serratia marcescens ( n = 11), Enterobacter spp. ( n = 7), and Citrobacter freundii ( n = 1), revealing horizontal spread of this bla NDM-1 -bearing plasmid structure. Global phylogeny showed clustering of the K. pneumoniae (18/20) isolates together with closely related carbapenemase-negative ST101 isolates from other geographical origins. The South African isolates were divided into three phylogenetic subbranches, where each group had distinct resistance and replicon profiles, carrying either p19-10_01, p18-10_01, or pCHE-A1 (8,201 bp). The latter plasmid carried bla GES-5 and aacA4 within an integron mobilization unit. Our findings imply independent plasmid acquisition followed by local dissemination. Additionally, we detected bla OXA-232 carried by pPKPN4 in K. pneumoniae (ST14) and bla NDM-5 contained by a pNDM-MGR194-like genetic structure in Escherichia coli (ST167), adding even more complexity to the multilayer molecular mechanisms behind nosocomial spread of carbapenem-resistant Enterobacteriaceae in Durban, South Africa.

Candida auris and Nosocomial Infection

2020 ◽  
Vol 21 (4) ◽  
pp. 365-373 ◽  
Author(s):  
Sweety Dahiya ◽  
Anil K. Chhillar ◽  
Namita Sharma ◽  
Pooja Choudhary ◽  
Aruna Punia ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Pathogenic Fungus ◽  
Control Measures ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Drug Resistant ◽  
Candida Auris ◽  
Preventive Control ◽  
Identification Techniques ◽  
Sensitivity Profile

The existence of the multi-drug resistant (MDR) pathogenic fungus, Candida auris came to light in 2009. This particular organism is capable of causing nosocomial infections in immunecompromised persons. This pathogen is associated with consistent candidemia with high mortality rate and presents a serious global health threat. Whole genome sequence (WGS) investigation detected powerful phylogeographic Candida auris genotypes which are specialized to particular geological areas indicating dissemination of particular genotype among provinces. Furthermore, this organism frequently exhibits multidrug-resistance and displays an unusual sensitivity profile. Identification techniques that are commercialized to test Candida auris often show inconsistent results and this misidentification leads to treatment failure which complicates the management of candidiasis. Till date, Candida auris has been progressively recorded from several countries and therefore its preventive control measures are paramount to interrupt its transmission. In this review, we discussed prevalence, biology, drug-resistance phenomena, virulence factors and management of Candida auris infections.

scholarly journals Genomic insights into multi-drug and extensively drug resistant Klebsiella pneumoniae from India

2020 ◽  
Vol 101 ◽  
pp. 12-13
Author(s):  
C. Shankar ◽  
P. Mathur ◽  
J.J. Jacob ◽  
C. Rodrigues ◽  
K. Walia ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Drug Resistant ◽  
Extensively Drug Resistant

scholarly journals Complete Genome Sequences of Four Extensively Drug-Resistant Acinetobacter baumannii Isolates from Thailand

2020 ◽  
Vol 9 (40) ◽  
Author(s):  
Peechanika Chopjitt ◽  
Thidathip Wongsurawat ◽  
Piroon Jenjaroenpun ◽  
Parichart Boueroy ◽  
Rujirat Hatrongjit ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Complete Genome ◽  
Sequence Type ◽  
Clinical Isolates ◽  
Drug Resistant ◽  
Genome Sequences ◽  
Content Type ◽  
Type Isolate ◽  
Resistant Genes ◽  
Extensively Drug Resistant

ABSTRACT Here, we report the complete genome sequences of four clinical isolates of extensively drug-resistant Acinetobacter baumannii (XDRAB), isolated in Thailand. These results revealed multiple antimicrobial-resistant genes, each involving two sequence type 16 (ST16) isolates, ST2, and a novel sequence type isolate, ST1479.

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