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Genome Analysis of Klebsiella pneumoniae Reveals International High-Risk Pandemic MDR Clones Emerging in Tertiary Healthcare Settings in Uganda.

ABSTRACT: Klebsiella pneumoniae is a threat to public health due to its continued evolution. In this study, we investigated the evolution, convergence, and transmission of hypervirulent and multi-drug resistant (MDR) clones of K. pneumoniae within healthcare facilities in Uganda. There was high resistance to piperacillin (90.91%), cefuroxime (86.96%), ceftazidime (84.62%), cefotaxime (84.00%), amoxicillin/clavulanate (75%), nalidixic acid (73.68%), and nitrofurantoin (71.43%) antibiotics among K. pneumoniae isolates. The isolates were genetically diverse, consisting of 20 different sequence types (STs) and 34 K-serotype groups. Chromosomal fosA (for fosfomycin) and oqxAB efflux pump genes were detected in all isolates. Two carbapenem resistance genes, blaNDM-5 and blaOXA-181 plus extended-spectrum beta-lactamase (bla_CTX-M-15) gene (68.12%), quinolone-resistant genes qnrS1 (28.99%), qnrB1 (13.04%), and qnrB6 (13.04%) and others were found. All, except three of the isolates, harbored plasmids. While the isolates carried a repertoire of virulence genes, only two isolates carried hypervirulent genes demonstrating a low prevalence (2.90%) of hypervirulent strains. Our study demonstrated genetically diverse populations of K. pneumoniae, low levels of carbapenem resistance among the isolates, and no convergence of MDR and hypervirulence. Emerging high-risk international pandemic clones (ST11, ST14, ST147, ST 86 and ST307) were detected in these healthcare settings which are difficult to treat.

SUBMITTER: Byarugaba DK

PROVIDER: S-EPMC10674604 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature

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Genome Analysis of Klebsiella pneumoniae Reveals International High-Risk Pandemic MDR Clones Emerging in Tertiary Healthcare Settings in Uganda.

Byarugaba Denis K DK Erima Bernard B Wokorach Godfrey G Alafi Stephen S Kibuuka Hannah H Mworozi Edison E Najjuka Florence F Kiyengo James J Musinguzi Ambrose K AK Wabwire-Mangen Fred F

Pathogens (Basel, Switzerland) 20231109 11

Klebsiella pneumoniae is a threat to public health due to its continued evolution. In this study, we investigated the evolution, convergence, and transmission of hypervirulent and multi-drug resistant (MDR) clones of K. pneumoniae within healthcare facilities in Uganda. There was high resistance to piperacillin (90.91%), cefuroxime (86.96%), ceftazidime (84.62%), cefotaxime (84.00%), amoxicillin/clavulanate (75%), nalidixic acid (73.68%), and nitrofurantoin (71.43%) antibiotics amo ...[more]

PMID: 38003798

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Project description:BackgroundOngoing studies have revealed the global prevalence of severe infections caused by the hypervirulent strains of Klebsiella pneumoniae (K. pneumoniae). Meanwhile, the World Health Organization and the Centers for Disease Control declared carbapenem-resistant K. pneumoniae as an urgent public health threat, requiring swift and effective action to mitigate its spread. Low- and middle-income countries are severely impacted by such devastating infectious diseases owing to the ill implementation of antimicrobial practices and infection control policies. Having both hypervirulence and carbapenemase gene determinants, the emergence of convergent hypervirulent carbapenem-resistant K. pneumoniae is now being reported worldwide.MethodsIn this study, we sequenced 19 carbapenemase-producing K. pneumoniae strains recovered from various clinical specimens. Additionally, we evaluated the phenotypic antimicrobial susceptibility to multiple antimicrobial classes using the VITEK2 automated system. Utilizing the sequencing data, we characterized the sequence types, serotypes, pangenome, resistance profiles, virulence profiles, and mobile genetic elements of the examined isolates. We highlighted the emergence of high-risk clones carrying hypervirulence genetic determinants among the screened isolates.ResultsOur findings revealed that all carbapenem-resistant isolates exhibited either extensive- or pan-drug resistance and harbored multiple variants of resistance genes spanning nearly all the antimicrobial classes. The most prevalent carbapenemase genes detected within the isolates were blaNDM-5 and blaOXA-48. We identified high-risk clones, such as ST383-K30, ST147-K64, ST11-K15, and ST14-K2, which may have evolved into putative convergent strains by acquiring the full set of hypervirulence-associated genetic determinants (iucABCD, rmpA and/ or rmpA2, putative transporter peg-344). Additionally, this study identified ST709-K9 as a high-risk clone for the first time and uncovered that capsule types K15 and K9 carried hypervirulence genetic determinants. The most frequent Inc types found in these isolates were Col440I, IncHI1B, and Inc FII(K).ConclusionThis study highlights the emergence of high-risk, extensively carbapenem-resistant K. pneumoniae strains co-carrying hypervirulence determinants in Egyptian clinical settings. This poses an imminent threat not only to Egypt but also to the global community, underscoring the urgent need for enhanced surveillance and control strategies to combat this pathogen.

Project description:Hypervirulent Klebsiella pneumoniae (hvKp) is a hypermucoviscous phenotype of classical Klebsiella pneumoniae (cKp) that causes serious infections in the community. The recent emergence of multidrug-resistant hvKp isolates (producing extended-spectrum beta-lactamases and carbapenemases) along with other virulence factors in health care settings has become a clinical crisis. Here, we aimed to compare the distribution of virulence determinants and antimicrobial resistance (AMR) genes in relation to various sequence types (STs) among the clinical hvKp isolates from both settings, to reinforce our understanding of their epidemiology and pathogenic potential. A total of 120 K. pneumoniae isolates confirmed by matrix-assisted laser desorption ionization-time of flight mass spectrometry were selected. hvKp was phenotypically identified by string test and genotypically confirmed by the presence of the iucA gene using PCR. Molecular characterization of hvKp isolates was done by whole-genome sequencing (WGS). Of the K. pneumoniae isolates, 11.6% (14/120) isolates were confirmed as hvKp by PCR (9.1% [11/120] string positive and 3.3% [4/120] positive by both methods); these were predominantly isolated from bloodstream infection (50%, 7/14), urinary tract infection (29%, 4/14), and respiratory tract infection (21%, 3/14). For all 14 hvKp infections, for 14.2% the source was in the community and for 85.7% the source was a health care setting. Two virulent plasmids were identified by WGS among the hvKp isolates from both settings. K64 was found to be the commonest capsular serotype (28.5%, 4/14), and ST2096 was the most common ST (28.5%, 4/14) by WGS. Two new STs were revealed: ST231 (reported to cause outbreaks) and ST43. The genome of one isolate was determined to be carrying AMR genes (blaCTX-M-15, blaNDM-1, blaNDM-5, blaOXA-181, blaOXA-232, etc.) in addition to virulence genes, highlighting the clonal spread of hvKp in both community and health care settings. IMPORTANCE To date, studies comparing the genomic characteristics of hospital- and community-acquired hvKp were very few in India. In this study, we analyzed the clinical and genomic characteristics of hvKp isolates from hospital and community settings. ST2096 was found as the most common ST along with novel STs ST231 and ST43. Our study also revealed the genome is simultaneously carrying AMR as well as virulence genes in isolates from both settings, highlighting the emergence of MDR hvKp STs integrated with virulence genes in both community and health care settings. Thus, hvKp may present a serious global threat, and essential steps are needed to prevent its further dissemination.

Project description:BACKGROUND:Endemic presence of Klebsiella pneumoniae resistant to carbapenem in Italy has been due principally to the clonal expansion of CC258 isolates; however, recent studies suggest an ongoing epidemiological change in this geographical area. METHODS:50 K. pneumoniae strains, 25 carbapenem-resistant (CR-Kp) and 25 susceptible (CS-Kp), collected from march 2014 to march 2016 at the Laboratory of Bacteriology of the Paolo Giaccone Polyclinic University hospital of Palermo, Italy, were characterized for antibiotic susceptibility and fully sequenced by next generation sequencing (NGS) for the in silico analysis of resistome, virulome, multi-locus sequence typing (MLST) and core single nucleotide polymorphism (SNP) genotypes RESULTS: MLST in silico analysis of CR-Kp showed that 52% of isolates belonged to CC258, followed by ST395 (12%), ST307 (12%), ST392 (8%), ST348 (8%), ST405 (4%) and ST101 (4%). In the CS-Kp group, the most represented isolate was ST405 (20%), followed by ST392 and ST15 (12%), ST395, ST307 and ST1727 (8%). The in silico β-lactamase analysis of the CR-Kp group showed that the most detected gene was blaSHV (100%), followed by blaTEM (92%), blaKPC (88%), blaOXA (88%) and blaCTX-M (32%). The virulome analysis detected mrk operon in all studied isolates, and wzi-2 was found in three CR-Kp isolates (12%). Furthermore, the distribution of virulence genes encoding for the yersiniabactin system, its receptor fyuA and the aerobactin system did not show significant distribution differences between CR-Kp and CS-Kp, whereas the Klebsiella ferrous iron uptake system (kfuA, kfuB and kfuC genes), the two-component system kvgAS and the microcin E495 were significantly (p < 0.05) prevalent in the CS-Kp group compared to the CR-Kp group. Core SNP genotyping, correlating with the MLST data, allowed greater strain tracking and discrimination than MLST analysis. CONCLUSIONS:Our data support the idea that an epidemiological change is ongoing in the Palermo area (Sicily, Italy). In addition, our analysis revealed the co-existence of antibiotic resistance and virulence factors in CR-Kp isolates; this characteristic should be considered for future genomic surveillance studies.

Dataset Information

Genome Analysis of Klebsiella pneumoniae Reveals International High-Risk Pandemic MDR Clones Emerging in Tertiary Healthcare Settings in Uganda.

Publications

Genome Analysis of <i>Klebsiella pneumoniae</i> Reveals International High-Risk Pandemic MDR Clones Emerging in Tertiary Healthcare Settings in Uganda.

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