{"id":54683,"date":"2023-12-31T11:10:05","date_gmt":"2023-12-31T11:10:05","guid":{"rendered":"https:\/\/biomedpharmajournal.org\/?p=54683"},"modified":"2024-01-05T06:28:11","modified_gmt":"2024-01-05T06:28:11","slug":"whole-genome-sequence-for-klebsiella-pneumoniae-isolate-from-burn-skin","status":"publish","type":"post","link":"https:\/\/biomedpharmajournal.org\/staging\/vol16no4\/whole-genome-sequence-for-klebsiella-pneumoniae-isolate-from-burn-skin\/","title":{"rendered":"Whole Genome Sequence for Klebsiella pneumoniae isolate from Burn Skin"},"content":{"rendered":"\n

Introduction<\/strong><\/p>\n\n\n\n

Carl Friedlander isolated Klebsiella pneumoniae<\/em>, a gram-negative bacterium, in 1882. Klebsiella pneumoniae<\/em> causes a variety of nosocomial and community-acquired illnesses, including urinary tract infections (UTIs), pneumonia, surgical site infections, and bloodstream infections. Multiple investigations 1-3<\/sup> have found that it is the second main cause of gram-negative sepsis.<\/p>\n\n\n\n

Klebsiella pneumoniae<\/em> is gram negative bacteria first isolate in 1882 by Carl Friedlander. It is the second leading cause of gram-negative sepsis. Capsular polysaccharide (CPS) and a critical virulence component that is a substantial contributor in developing sepsis are both present in K. pneumoniae<\/em> 4<\/sup>. Two pathotypes, or clusters, of Klebsiella pneumoniae clinical isolates have been identified. Patients with compromised immune systems are the most common sources of classical strains (cKp), and these strains are often carbapenem-resistant (CR). On the other hand, carbapenem is effective against hypervirulent strains (hvKp), which are linked to invasive infections in the community 5,6<\/sup>. The HMV phenotype may be determined and hypervirulent K. pneumoniae<\/em> can be distinguished from classical K. pneumoniae<\/em> with the help of a simple microbiological test called the string test. Hyper-capsule generated by hypervirulent K. pneumoniae<\/em> (hvKP) 7<\/sup> confers the hyper-mucoviscous phenotype. Human defense mechanism expression and neutrophil and macrophage phagocytosis are both suppressed by CPS8<\/sup>. Additionally, the hyper-capsule enhances defenses against a wide variety of humoral defense mechanisms. This means that hvKP is protected against complement killing to a greater extent than cKP 9<\/sup>. Siderophores are low-molecular-weight secondary metabolites that can chelate iron. To transport ferric ions across the cell membrane, these compounds use small peptide molecules with side chains and functional groups that have high affinity ligands 10<\/sup>. Microbial siderophores are able to chelate iron and increase its uptake even at low concentrations thanks to the formation of a ferric-siderophore complex11<\/sup>. For K. pneumoniae<\/em> to cause disease, siderophores are also required 5<\/sup>. To thrive during an infection, K. pneumoniae<\/em> need a small amount of iron from the surrounding environment. As part of its nonspecific immune response, the host sequesters this metal during infection in an effort to curb the spread of multiple possible pathogens. Iron in the host plasma is usually bound to transferrin and other iron transport molecules, so there isn’t much free iron floating around 14<\/sup>. During a bacterial infection, mammals switch iron binding to lactoferrin, a naturally occurring defense protein found in bodily fluids 12,13<\/sup>. The creation of siderophores, molecules with a higher affinity for iron than host transport proteins, is the primary mechanism by which many infections, including K. pneumoniae<\/em>, acquire iron. Siderophores are able to scavenge iron from the environment or the host’s iron-chelating proteins 14<\/sup>. Enterobactin, yersiniabactin, salmochelin, and aerobactin are just few of the siderophores that Klebsiella pneumoniae<\/em> expresses 15<\/sup>. Only about 2\u20134% of nosocomial K. pneumoniae<\/em> strains contain the salmochelin siderophore, which is expressed by the iroB gene. Since there are very few evidence explain the mechanism for Klebsiella pneumoniae<\/em>, in current project try to study the mastery for multi antibiotics resistance by employ the NEXT GENERATION SEQUENCE NGS and bioinformatics tools to annotated the Klebsiella pneumoniae <\/em>genome.   <\/p>\n\n\n\n

Materials\nand methods: <\/strong><\/p>\n\n\n\n

Bacterial isolate<\/strong><\/p>\n\n\n\n

Standard microbiological techniques were used\nfor isolation and identification. The bacteria grow on\nnutritive and selective medium after being taken from swab samples taken from\nindividuals who suffer from burned skin. After that, the colony that displayed\nmultidrug resistance was isolated, and DNA was extracted from this solitary colony\nby utilizing a GENEAID,\nbacterial DNA extraction kit\/Korea, extracted genomic DNA the included\ninstructions, which were followed very strictly, albeit with minor adjustments\nmade to cut down on the amount of contamination and boost the amount of pure DNA\nobtained.  This research aimed to get\ninsight into the whole genome of multidrug-resistant microorganisms because so\nlittle attention has been paid to doing so in the past. <\/p>\n\n\n\n

Genome sequence <\/strong><\/p>\n\n\n\n

Illumina genome sequencing was performed on the DNA samples (Psomagen\/USA, reference order number HN00194138). After quality control (QC), samples’ DNA was randomly fragmented before 5′ and 3′ adapter ligation for library creation. Create and sequence the library with NGS. After sequencing, raw results were evaluated for GC (percentage), total bases, and total reads. Quality filtering and Fast QC (https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/) reduced analytical biases. We assessed data quality at the end of each cycle using the phred quality score (Q20(%) and Q30(%)). De novo contigs were built from raw readings using SPAdes v.3.5 8<\/sup>.  <\/p>\n\n\n\n

Genome analysis:<\/strong><\/p>\n\n\n\n

The assembled genome of K. pneumoniae<\/em> was obtained by the PATRS comprehensive genome analysis facility 9<\/sup>. The sequencing data were mapped using the reference genome of Klebsiella pneumoniae<\/em>. The genome was fully annotated to identify functional genes within subsystem categories. Comparative mapping was conducted to analyze the findings, highlighting conserved and distinctive sequencing properties. Additionally, high-quality maps were constructed to validate and visually represent the annotated features. The removal of duplicates, identification of variations, and mapping of filtered data reads to the reference genome were accomplished by the utilization of several bioinformatics tools 10,11,12,13,14<\/sup>. <\/p>\n\n\n\n

Results<\/strong><\/p>\n\n\n\n

Genome\nquality<\/strong><\/p>\n\n\n\n

The genome quality\nwas good and the coarse consistency was 96.5 and fine consistency was 55.3. as\nit displays in figure (1).<\/p>\n\n\n\n

Table 1: and give the table legend should be Genome quality of Klebsiella pneumoniae<\/em><\/strong><\/p>\n\n\n\n\n\n\n\n\n
\n

Genome Quality<\/strong><\/p>\n<\/td>\n

\n

Percentage<\/strong><\/p>\n<\/td>\n<\/tr>\n

\n

coarse consistency<\/p>\n<\/td>\n

\n

96.5%<\/p>\n<\/td>\n<\/tr>\n

\n

fine consistency<\/p>\n<\/td>\n

\n

55.3%<\/p>\n<\/td>\n<\/tr>\n

\n

genome quality<\/p>\n<\/td>\n

\n

Good<\/p>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

 <\/p>\n\n\n

Antibiotics resistance profile<\/strong><\/p>\n\n\n\n

Antibiotic resistance was observed in the isolate. Furthermore, as shown in table 2, the isolate showed sensitivity to just nine antibiotics: ertapenem, ciprofloxacin, meropenem, imipenem, aztreonam, levofloxacin, cefoxitin, and piperacillin-tazobactam.<\/p>\n\n\n\n

Table 2: showing the resistance and sensitivity for Klebsiella pneumoniae<\/em> isolate. <\/strong><\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
\n

Taxon ID<\/strong><\/p>\n<\/td>\n

\n

Genome ID<\/strong><\/p>\n<\/td>\n

\n

Genome Name<\/strong><\/p>\n<\/td>\n

\n

Antibiotic<\/strong><\/p>\n<\/td>\n

\n

Resistant Phenotype<\/strong><\/p>\n<\/td>\n<\/tr>\n

\n

573<\/p>\n<\/td>\n

\n

573.37830<\/p>\n<\/td>\n

\n

Klebsiella pneumoniae<\/p>\n<\/td>\n

\n

tetracycline<\/p>\n<\/td>\n

\n

Resistant<\/p>\n<\/td>\n<\/tr>\n

\n

573<\/p>\n<\/td>\n

\n

573.37830<\/p>\n<\/td>\n

\n

Klebsiella pneumoniae<\/p>\n<\/td>\n

\n

ertapenem<\/p>\n<\/td>\n

\n

Susceptible<\/p>\n<\/td>\n<\/tr>\n

\n

573<\/p>\n<\/td>\n

\n

573.37830<\/p>\n<\/td>\n

\n

Klebsiella pneumoniae<\/p>\n<\/td>\n

\n

tobramycin<\/p>\n<\/td>\n

\n

Resistant<\/p>\n<\/td>\n<\/tr>\n

\n

573<\/p>\n<\/td>\n

\n

573.37830<\/p>\n<\/td>\n

\n

Klebsiella pneumoniae<\/p>\n<\/td>\n

\n

amikacin<\/p>\n<\/td>\n

\n

Resistant<\/p>\n<\/td>\n<\/tr>\n

\n

573<\/p>\n<\/td>\n

\n

573.37830<\/p>\n<\/td>\n

\n

Klebsiella pneumoniae<\/p>\n<\/td>\n

\n

ciprofloxacin<\/p>\n<\/td>\n

\n

Susceptible<\/p>\n<\/td>\n<\/tr>\n

\n

573<\/p>\n<\/td>\n

\n

573.37830<\/p>\n<\/td>\n

\n

Klebsiella pneumoniae<\/p>\n<\/td>\n

\n

meropenem<\/p>\n<\/td>\n

\n

Susceptible<\/p>\n<\/td>\n<\/tr>\n

\n

573<\/p>\n<\/td>\n

\n

573.37830<\/p>\n<\/td>\n

\n

Klebsiella pneumoniae<\/p>\n<\/td>\n

\n

imipenem<\/p>\n<\/td>\n

\n

Susceptible<\/p>\n<\/td>\n<\/tr>\n

\n

573<\/p>\n<\/td>\n

\n

573.37830<\/p>\n<\/td>\n

\n

Klebsiella pneumoniae<\/p>\n<\/td>\n

\n

aztreonam<\/p>\n<\/td>\n

\n

Susceptible<\/p>\n<\/td>\n<\/tr>\n

\n

573<\/p>\n<\/td>\n

\n

573.37830<\/p>\n<\/td>\n

\n

Klebsiella pneumoniae<\/p>\n<\/td>\n

\n

cefepime<\/p>\n<\/td>\n

\n

Susceptible<\/p>\n<\/td>\n<\/tr>\n

\n

573<\/p>\n<\/td>\n

\n

573.37830<\/p>\n<\/td>\n

\n

Klebsiella pneumoniae<\/p>\n<\/td>\n

\n

levofloxacin<\/p>\n<\/td>\n

\n

Susceptible<\/p>\n<\/td>\n<\/tr>\n

\n

573<\/p>\n<\/td>\n

\n

573.37830<\/p>\n<\/td>\n

\n

Klebsiella pneumoniae<\/p>\n<\/td>\n

\n

trimethoprim sulfamethoxazole<\/p>\n<\/td>\n

\n

Resistant<\/p>\n<\/td>\n<\/tr>\n

\n

573<\/p>\n<\/td>\n

\n

573.37830<\/p>\n<\/td>\n

\n

Klebsiella pneumoniae<\/p>\n<\/td>\n

\n

gentamicin<\/p>\n<\/td>\n

\n

Resistant<\/p>\n<\/td>\n<\/tr>\n

\n

573<\/p>\n<\/td>\n

\n

573.37830<\/p>\n<\/td>\n

\n

Klebsiella pneumoniae<\/p>\n<\/td>\n

\n

cefoxitin<\/p>\n<\/td>\n

\n

Susceptible<\/p>\n<\/td>\n<\/tr>\n

\n

573<\/p>\n<\/td>\n

\n

573.37830<\/p>\n<\/td>\n

\n

Klebsiella pneumoniae<\/p>\n<\/td>\n

\n

piperacillin tazobactam<\/p>\n<\/td>\n

\n

Susceptible<\/p>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

 <\/p>\n\n\n

Based on annotation statistics and PATRIC genomes of the same species, this genome looks to be high-quality. After readings filtering, phred quality scores of bases above Q20 and Q30 were 97.8% and 94.0 %. The Comprehensive Genome Analysis revealed 167 contigs, 11,068,038 bp, and 2,454 coding proteins in this assembled genome (Table-4). GC averages 55.90%. Figure-1 shows GC content and GC skew analysis schematically. A protein subsystem implements a biological activity or structural complex. 278 genome-specific subsystems were identified during annotation. Figure-2 provides a genome subsystem overview.<\/p>\n\n\n\n

Table 3: Summary for the genome assembly and annotated features details.<\/strong><\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
\n

Genome Annotation Pipeline (PGAP)<\/strong><\/p>\n<\/td>\n

\n

Results<\/strong><\/p>\n<\/td>\n<\/tr>\n

\n

Total length:<\/p>\n<\/td>\n

\n

11,068,038 bp<\/p>\n<\/td>\n<\/tr>\n

\n

GC Content %<\/p>\n<\/td>\n

\n

55.91<\/p>\n<\/td>\n<\/tr>\n

\n

Number of Contigs:<\/p>\n<\/td>\n

\n

167<\/p>\n<\/td>\n<\/tr>\n

\n

Number of Subsystems<\/p>\n<\/td>\n

\n

278<\/p>\n<\/td>\n<\/tr>\n

\n

Genes (total)<\/p>\n<\/td>\n

\n

 2,530<\/p>\n<\/td>\n<\/tr>\n

\n

CDSs (total)<\/p>\n<\/td>\n

\n

5,074<\/p>\n<\/td>\n<\/tr>\n

\n

Genes (coding) proteins<\/p>\n<\/td>\n

\n

11,132<\/p>\n<\/td>\n<\/tr>\n

\n

rRNA<\/p>\n<\/td>\n

\n

9<\/p>\n<\/td>\n<\/tr>\n

\n

tRNAs<\/p>\n<\/td>\n

\n

134<\/p>\n<\/td>\n<\/tr>\n

\n

Contig L50<\/p>\n<\/td>\n

\n

13<\/p>\n<\/td>\n<\/tr>\n

\n

Contig N50<\/p>\n<\/td>\n

\n

264,921<\/p>\n<\/td>\n<\/tr>\n

\n

Plasmids<\/p>\n<\/td>\n

\n

0<\/p>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n\n\n\n
\"\"<\/td>\nFigure 1: – <\/strong>K. pneumoniae<\/em> circular genome. The red ring indicates genomic backbone (contigs) while the innermost ring reflects chromosomal position. <\/strong>

<\/p>\n

Click here to view Figure<\/a><\/p>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n\n\n

This genome has too many\ncontigs to be rendered clearly. The circular display has been limited to the 90\nlongest contigs of the 352 contigs in the genome.<\/p>\n\n\n\n

Table 4: Summary proteins features details.<\/strong><\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n
\n

Proteins features <\/strong><\/p>\n<\/td>\n

\n

PATRICS<\/strong><\/p>\n<\/td>\n<\/tr>\n

\n

Hypothetical proteins<\/p>\n<\/td>\n

\n

3053<\/p>\n<\/td>\n<\/tr>\n

\n

Proteins with functional assignments<\/p>\n<\/td>\n

\n

8079<\/p>\n<\/td>\n<\/tr>\n

\n

Proteins with EC number assignments<\/p>\n<\/td>\n

\n

0<\/p>\n<\/td>\n<\/tr>\n

\n

Proteins with GO assignments<\/p>\n<\/td>\n

\n

1928<\/p>\n<\/td>\n<\/tr>\n

\n

Proteins with pathway assignments<\/p>\n<\/td>\n

\n

0<\/p>\n<\/td>\n<\/tr>\n

\n

Proteins with Subsystem assignments<\/p>\n<\/td>\n

\n

0<\/p>\n<\/td>\n<\/tr>\n

\n

Proteins with PATRIC genus-specific family (PLfam) assignments<\/p>\n<\/td>\n

\n

5374<\/p>\n<\/td>\n<\/tr>\n

\n

Proteins with PATRIC cross-genus family (PGfam) assignments<\/p>\n<\/td>\n

\n

10435<\/p>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

 <\/p>\n\n\n

Subsystem Analysis<\/strong><\/p>\n\n\n\n

A subsystem is a set of proteins\nthat together implement a specific biological process or structural complexand PATRIC annotation includes an analysis of the subsystems unique to\neach genome. An overview of the subsystems for this genome is provided\nin Figure 2.<\/p>\n\n\n\n\n\n
\"\"<\/td>\nFigure 2: Subsystem distribution of Serratia marcescens<\/em>. RAST annotated the genome. The pie chart and SEED viewer showed subsystem feature counts and coverage.<\/strong>

<\/p>\n

Click here to view Figure<\/a><\/p>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n\n\n

Phylogenetic Analysis <\/strong><\/p>\n\n\n\n

PATRIC offered reference and representative genomes for phylogenetic\nresearch. Figure-3 shows the closest reference and typical genotypes.<\/p>\n\n\n\n\n\n
\"\"<\/td>\n\n

Figure 3: Phylogenic relationship representation of the K. pneumoniae<\/em><\/strong><\/p>\n

<\/p>\n

Click here to view Figure<\/a><\/p>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n\n\n

Discussion<\/strong><\/p>\n\n\n\n

Gram-negative bacilli infections are\nthe most dangerous and potentially fatal infectious illness causes in\nhospitalized patients[1, 2]. K. pneumoniae<\/em> is an opportunistic\npathogen that causes pneumonia, abscess, bacteremia, and urinary tract\ninfections in both community-acquired and nosocomial infections[3]. K. pneumoniae<\/em> has become a global\nproblem due to its propensity to rapidly acquire antibiotic resistance,\nrequiring action to avoid the spread of multidrug-resistant bacteria[4]. Whole-genome sequencing (WGS) has grown more\naccessible and economical in recent years, leading in increased application in\na variety of domains, including clinical microbiology[5-7]. One of the primary advantages of employing WGS\nis the ability to characterize the genetic content of clinically relevant\nbacteria and tie it to virulence-associated phenotypes, allowing for a better\nunderstanding of their transmission within the hospital and the use of timely\nmedicines. The current investigation intended to describe K. pneumoniae<\/em>\nisolates from burns skin patients hospitalized in Baghdad City. This study\nconsider as is the first study in Iraq to use WGS to characterize an\nopportunistic pathogen in depth. <\/p>\n\n\n\n

Conclusion<\/strong><\/p>\n\n\n\n

In conclusion, our study is the first in Iraq to analyze the genome of K. pneumoniae<\/em>. Furthermore,  the K. pneumoniae<\/em> genome was compared to those of clinical reference strains, and its display of antibiotic resistance and virulence genes was identified. More whole genome sequencing and comparative genomics research is needed to better understand the background and assessment of multidrug-resistant isolates from different hospital rooms with special attention on delivery room.<\/p>\n\n\n\n

Acknowledgments<\/strong><\/p>\n\n\n\n

The authors acknowledge Medical and science colleges\/Misan University and Science college\/ Kirkuk for their support.  <\/p>\n\n\n\n

Funding<\/strong> Sources<\/strong><\/p>\n\n\n\n

These authors declare that above-submitted work was not funded by any governmental or private funding source nor sup- ported by any financial projects. <\/p>\n\n\n\n

Conflict of Interest<\/strong><\/p>\n\n\n\n

The authors declare that they have no\nconflict of interest. <\/p>\n\n\n\n

References<\/strong><\/p>\n\n\n\n

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     CrossRef <\/a><\/li><\/ol>\n\n\n\n

    <\/p>\n","protected":false},"excerpt":{"rendered":"

    Introduction Carl Friedlander isolated Klebsiella pneumoniae, a gram-negative bacterium, in […]<\/p>\n","protected":false},"author":15,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[111],"tags":[],"class_list":["post-54683","post","type-post","status-publish","format-standard","hentry","category-vol16no4"],"_links":{"self":[{"href":"https:\/\/biomedpharmajournal.org\/staging\/wp-json\/wp\/v2\/posts\/54683","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/biomedpharmajournal.org\/staging\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/biomedpharmajournal.org\/staging\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/biomedpharmajournal.org\/staging\/wp-json\/wp\/v2\/users\/15"}],"replies":[{"embeddable":true,"href":"https:\/\/biomedpharmajournal.org\/staging\/wp-json\/wp\/v2\/comments?post=54683"}],"version-history":[{"count":5,"href":"https:\/\/biomedpharmajournal.org\/staging\/wp-json\/wp\/v2\/posts\/54683\/revisions"}],"predecessor-version":[{"id":55095,"href":"https:\/\/biomedpharmajournal.org\/staging\/wp-json\/wp\/v2\/posts\/54683\/revisions\/55095"}],"wp:attachment":[{"href":"https:\/\/biomedpharmajournal.org\/staging\/wp-json\/wp\/v2\/media?parent=54683"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/biomedpharmajournal.org\/staging\/wp-json\/wp\/v2\/categories?post=54683"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/biomedpharmajournal.org\/staging\/wp-json\/wp\/v2\/tags?post=54683"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}