Detection of Several Carbapenems Resistant and Virulence Genes in Classical and Hyper-virulent Strains of Klebsiella Pneumoniae Isolated From Hospitalized Neonates and Adults in Khartoum

Abstract Objective Klebsiella pneumoniae (K. pneumoniae) involves both community-acquired and nosocomial infections. It is responsible for a wide variety of infections, including infections of the urinary tract, pneumonia, bacteremia, meningitis, wound infection and purulent abscesses. We constructed this study to detect several carbapenems resistant and virulence genes in classical and hyper-virulent strains of K. pneumoniae isolated from hospitalized neonates and adults in Khartoum state. Results Seventy percent of the isolates were resistant to ceftazidime, 18(30%) to ciprofloxacin, 23(38.3%) to chloramphenicol, 24(40%) to gentamicin and 8% to imipenem, 35% were multidrug-resistant, and 7% extensively drug-resistant, all blood isolates (n=14) were resistant to ceftazidime. entB was the most predominant virulence gene (93.3%), followed by mrkD (78.3%), kfu (60%), K2 (51.7%), magA (18.3%) and rmpA (5%). blaOXA-48 was the most predominant carbapenem-resistant gene (68.3%), followed by blaNDM (10%), blaKPC (8.3%), and blaIMP (3.3%). Eight hyper-virulent strains were positive for blaOXA-48 and two for blaNDM genes.

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Detection of Several Carbapenems Resistant and Virulence Genes in Classical and Hyper-virulent Strains of Klebsiella pneumoniae Isolated from Hospitalized Neonates and Adults in Khartoum

10.21203/rs.3.rs-26141/v1 ◽

2020 ◽

Author(s):

Aalaa Mahgoub Albasha ◽

Esraa Hassan Osman ◽

Saga Abd Alhalim ◽

Elianz Alshaib ◽

Leena Al-Hassan ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Virulence Genes ◽

Age Groups ◽

Hospitalized Patients ◽

High Rate ◽

Drug Resistant ◽

Carbapenem Resistant ◽

Resistant Genes ◽

Virulent Strains ◽

Wide Range

Abstract Background Carbapenems resistant hypervirulent strains of Klebsiella pneumoniae are one of the most critical organisms that cause fatal nosocomial infections. This study aimed to detect and characterize K. pneumoniae virulence genes (mrkD, entB, rmpA, K2, kfu, and magA) and carbapenem resistant (blaNDM, blaIMP, blaOXA−48, and blaKPC) genes Methods Sixty K. pneumoniae strains were isolated from urine, blood, wound swab, and sputum samples, in two age groups: neonates and adults. String test was used to detect hypervirulent strains. Susceptibility testing for a wide range of antibiotics was performed on all isolates. DNA was extracted by the guanidine chloride method, then multiplex PCR was used for the detection of carbapenem-resistance and virulence genes. Results Seventy percent of the isolates were resistant to ceftazidime and 8% to imipenem, 35% were multi-drug resistant, and 7% extensively drug-resistant, all neonatal blood isolates (n = 15) were resistant to ceftazidime. entB was the most predominant virulence gene (93.3%), followed by mrkD (78.3%), kfu (60%), K2 (51.7%), magA (18.3%) and rmpA (5%). blaOXA−48 was the most predominant carbapenem-resistant gene (68.3%), followed by blaNDM (10%), blaKPC (8.3%), and blaIMP (3.3%). Eight hyper-virulent strains were positive for blaOXA−48 and two for blaNDM genes. The study concluded that there is a high rate of carbapenems resistant genes in hyper-virulent strains of K. pneumoniae isolated from hospitalized patients. Conclusion The study reported for the first time in Sudan presence of carbapenems resistant genes in hyper-virulent strains of K. pneumoniae isolated from hospitalized patients. Presence of MDR and XDR strains of K. pneumoniae in neonatal ward in some Sudanese hospitals.

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Detection of Several Carbapenems Resistant and Virulence Genes in Classical and Hyper-virulent Strains of Klebsiella pneumoniae Isolated from Hospitalized Neonates and Adults in Khartoum

10.21203/rs.3.rs-22765/v1 ◽

2020 ◽

Author(s):

Aalaa Mahgoub Albasha ◽

Esraa Hassan Osman ◽

Saga Abd Alhalim ◽

Elianz Alshaib ◽

Leena Al-Hassan ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Virulence Genes ◽

Age Groups ◽

Hospitalized Patients ◽

High Rate ◽

Drug Resistant ◽

Carbapenem Resistant ◽

Resistant Genes ◽

Virulent Strains ◽

Wide Range

Abstract Background Carbapenems resistant hypervirulent strains of Klebsiella pneumoniae are one of the most critical organisms that cause fatal nosocomial infections. This study aimed to detect and characterize K. pneumoniae virulence genes (mrkD, entB, rmpA, K2, kfu, and magA) and carbapenem resistant (blaNDM, blaIMP, blaOXA−48, and blaKPC) genes Methods Sixty K. pneumoniae strains were isolated from urine, blood, wound swab, and sputum samples, in two age groups: neonates and adults. String test was used to detect hypervirulent strains. Susceptibility testing for a wide range of antibiotics was performed on all isolates. DNA was extracted by the guanidine chloride method, then multiplex PCR was used for the detection of carbapenem-resistance and virulence genes. Results Seventy percent of the isolates were resistant to ceftazidime and 8% to imipenem, 35% were multi-drug resistant, and 7% extensively drug-resistant, all neonatal blood isolates (n = 15) were resistant to ceftazidime. entB was the most predominant virulence gene (93.3%), followed by mrkD (78.3%), kfu (60%), K2 (51.7%), magA (18.3%) and rmpA (5%). blaOXA−48 was the most predominant carbapenem-resistant gene (68.3%), followed by blaNDM (10%), blaKPC (8.3%), and blaIMP (3.3%). Eight hyper-virulent strains were positive for blaOXA−48 and two for blaNDM genes. The study concluded that there is a high rate of carbapenems resistant genes in hyper-virulent strains of K. pneumoniae isolated from hospitalized patients. Conclusion The study reported for the first time in Sudan presence of carbapenems resistant genes in hyper-virulent strains of K. pneumoniae isolated from hospitalized patients. Presence of MDR and XDR strains of K. pneumoniae in neonatal ward in some Sudanese hospitals.

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Detection of extensively drug-resistant and hypervirulent Klebsiella pneumoniae ST15, ST147, ST377 and ST442 in Iran

Acta Microbiologica et Immunologica Hungarica ◽

10.1556/030.2021.01562 ◽

2021 ◽

Author(s):

Sara Davoudabadi ◽

Hossein Goudarzi ◽

Mehdi Goudarzi ◽

Abdollah Ardebili ◽

Ebrahim Faghihloo ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Pcr Amplification ◽

Multidrug Resistant ◽

Diffusion Method ◽

Drug Resistant ◽

Carbapenem Resistant ◽

Extensively Drug Resistant ◽

String Test ◽

Pcr Method ◽

Extensively Drug Resistance

Abstract In this study, we focused on the emergence of extensively drug-resistant (XDR), pandrug-resistant (PDR), and hypervirulent Klebsiella pneumoniae (hvKP) in Iran. During 2018 to 2020 a total of 52 K. pneumoniae isolates were collected from different clinical specimens. The hvKP isolates were identified by PCR amplification of virulence and capsular serotype-specific genes. Hypermucoviscous K. pneumoniae (hmKP) were identified by string test. Carbapenem-resistant hvKP (CR-hvKP), multidrug-resistant hvKP (MDR-hvKP), extensively drug-resistant hvKP (XDR-hvKP), and pandrug-resistant hvKP (PDR-hvKP) were determined by disc diffusion method, Carba-NP test and PCR method. XDR-hvKP isolates were typed by multilocus sequence typing (MLST). Among all K. pneumoniae isolates 14 (26.9%) were identified as hvKP and 78.6% (11/14) of them were hmKP however, none of the classic K. pneumoniae (cKP) isolates were hmKP. The predominant capsular serotype of hvKP was K2 (42.85%) followed by K1 (35.71%). The prevalence of MDR-hvKP, XDR-hvKP and PDR-hvKP isolates were 6 (42.9%), 5 (35.7%) and 1 (7.1%), respectively. ESBL production was found in 85.7% of hvKP isolates and most of them carried bla TEM gene (78.6%) and 6 isolates (42.9%) were CR-hvKP. Among hvKP isolates, 1 (7.1%), 2 (14.3%), 3 (21.4%), 8 (28.6%), and 11 (78.6%) carried bla NDM-6, bla OXA-48, bla CTX-M, bla SHV, and bla TEM genes, respectively. According to MLST analysis, 2, 1, 1, and 1 XDR-hvKP isolates belonged to ST15, ST377, ST442, and ST147, respectively. The occurrence of such isolates is deeply concerning due to the combination of hypervirulence and extensively drug-resistance or pandrug-resistance.

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Anatomy of an extensively drug-resistant Klebsiella pneumoniae outbreak in Tuscany, Italy

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2110227118 ◽

2021 ◽

Vol 118 (48) ◽

pp. e2110227118

Author(s):

Melissa J. Martin ◽

Brendan W. Corey ◽

Filomena Sannio ◽

Lindsey R. Hall ◽

Ulrike MacDonald ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Genomic Analysis ◽

New Delhi ◽

Drug Resistant ◽

First Line ◽

Healthcare Facilities ◽

Carbapenem Resistant ◽

Extensively Drug Resistant ◽

Cd1 Mice ◽

Over Time

A protracted outbreak of New Delhi metallo-β-lactamase (NDM)–producing carbapenem-resistant Klebsiella pneumoniae started in Tuscany, Italy, in November 2018 and continued in 2020 and through 2021. To understand the regional emergence and transmission dynamics over time, we collected and sequenced the genomes of 117 extensively drug-resistant, NDM-producing K. pneumoniae isolates cultured over a 20-mo period from 76 patients at several healthcare facilities in southeast Tuscany. All isolates belonged to high-risk clone ST-147 and were typically nonsusceptible to all first-line antibiotics. Albeit sporadic, resistances to colistin, tigecycline, and fosfomycin were also observed as a result of repeated, independent mutations. Genomic analysis revealed that ST-147 isolates circulating in Tuscany were monophyletic and highly genetically related (including a network of 42 patients from the same hospital and sharing nearly identical isolates), and shared a recent ancestor with clinical isolates from the Middle East. While the blaNDM-1 gene was carried by an IncFIB-type plasmid, our investigations revealed that the ST-147 lineage from Italy also acquired a hybrid IncFIB/IncHIB–type plasmid carrying the 16S methyltransferase armA gene as well as key virulence biomarkers often found in hypervirulent isolates. This plasmid shared extensive homologies with mosaic plasmids circulating globally including from ST-11 and ST-307 convergent lineages. Phenotypically, the carriage of this hybrid plasmid resulted in increased siderophore production but did not confer virulence to the level of an archetypical, hypervirulent K. pneumoniae in a subcutaneous model of infection with immunocompetent CD1 mice. Our findings highlight the importance of performing genomic surveillance to identify emerging threats.

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Non-active antibiotic and bacteriophage synergism to successfully treat recurrent urinary tract infection caused by extensively drug-resistant Klebsiella pneumoniae

Emerging Microbes & Infections ◽

10.1080/22221751.2020.1747950 ◽

2020 ◽

Vol 9 (1) ◽

pp. 771-774 ◽

Cited By ~ 12

Author(s):

Juan Bao ◽

Nannan Wu ◽

Yigang Zeng ◽

Liguang Chen ◽

Linlin Li ◽

...

Keyword(s):

Urinary Tract Infection ◽

Urinary Tract ◽

Tract Infection ◽

Klebsiella Pneumoniae ◽

Recurrent Urinary Tract Infection ◽

Drug Resistant ◽

Extensively Drug Resistant

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Virulence-associated characteristics of carbapenem-resistant Klebsiella pneumoniae in hospital-acquired infections: results from a hospital in central China

10.21203/rs.2.15544/v1 ◽

2019 ◽

Author(s):

OUYANG Pengwen ◽

Bin JIANG ◽

Juan WANG ◽

Na PENG ◽

Jianrong YE ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Virulence Genes ◽

Virulence Gene ◽

Central China ◽

Capsular Antigen ◽

Hospital Acquired Infections ◽

Carbapenem Resistant ◽

Positive Strain ◽

Significant Difference ◽

Hospital Acquired

Abstract Background Carbapenem-resistant Klebsiella pneumoniae (CRKP) have been a clinically significant pathogen worldwide, but related reports about their virulence features in hospital-acquired infections (HAI) are pretty lacking.Methods CRKP causing HAI were continuously collected in 2018 from a hospital in central China. Isolates identification and antimicrobial susceptibility test were done using VITEK-2 compact system or MALDI-TOF MS. String test, multilocus sequence typing, carbapenemase genes, virulence genes and capsular antigen genes detection were conducted to understand their phenotype and genetic background. As well as case datas were collected and compared to assess their virulence characteristics.Results A total of 62 isolates of CRKP from 62 patients with HAI were collected. 41 carbapenemase genestic-confirmed hypervirulent Klebsiella pneumoniae (CR-hvKP) and 21 carbapenem resistant non-hypervirulent Klebsiella pneumoniae (CR-NhvKP) were screened out. Most CRKP causing HAI were ST11 KPC-2 producing strains and maily causing pneumonia. Only for blaKPC-2 there was a significant difference between CR-hvKP and CR-NhvKP (p<0.001). No significant difference of the two group strains in resistance against amikacin, trimethoprim-sulfamethoxazoleare, cefepime, ceftazidime, imipenem, piperacillin-tazobactam, colistin and tigecycline were found except levofloxacin (p<0.001), and all strains showed sensitive to tigecycline and colistin. In the CR-hvKP group, IucA (64.5%) were the most commonly detected virulence gene, followed by iroN (48.4%), prmpA2 (30.6%) and prmpA (4.8%), only 1 (2.4%) capsular serotype positive strain and 2 (4.9%) hypermucoviscosity phenotype strains were detected, while no hypermucoviscosity phenotype or capsular antigen gene positive strain was detected in the CR-NhvKP group. And there was no significant difference between the two groups in age, types of infection, departmental distribution, survival time or the final outcome of infection.Conclusion ST11 KPC-2-producing Klebsiella pneumoniae are most prevalent CRKP in HAI. Virulence gene espacially iucA has a high proportion and worth paying attention to. Hypermucoviscous phenotype and virulence-associated capsular serotype in CRKP both have a low prevalence. CRKP harboring virulence genes have a higher expression of KPC-2 and less sensitive to levofloxacin than those harboring no virulence gene, and there is no significant difference for virulence manifestations between the two groups.

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Relationship between Escherichia coli strains causing urinary tract infection in women and the dominant faecal flora of the same hosts

Epidemiology and Infection ◽

10.1017/s0950268806005917 ◽

2006 ◽

Vol 134 (5) ◽

pp. 1015-1023 ◽

Cited By ~ 48

Author(s):

E. MORENO ◽

A. ANDREU ◽

T. PÉREZ ◽

M. SABATÉ ◽

J. R. JOHNSON ◽

...

Keyword(s):

Escherichia Coli ◽

Urinary Tract Infection ◽

Urinary Tract ◽

Tract Infection ◽

Virulence Genes ◽

Virulence Gene ◽

Faecal Flora ◽

E Coli ◽

Virulent Strains ◽

Faecal Samples

To clarify whether prevalence or special pathogenicity is more important in determining urinary tract infection (UTI) causation, we compared the biotype, phylogenetic group, and virulence genes of Escherichia coli urine strains from 11 women with acute lower UTI with those of the host's dominant intestinal E. coli strain(s). Twenty-one unique E. coli clones were identified. For three women, the single faecal clone identified was also the host's urine clone, whereas for eight women faecal samples yielded 1 or 2 distinct non-urine clones (total, n=10), either with (n=3) or without (n=5) the concurrent urine clone. The eight urine clones from the latter eight women exhibited significantly greater inferred virulence, according to virulence gene content and phylogenetic background, than did the hosts' 10 corresponding ‘faecal only’ clones. In contrast, the three urine clones that were detected as the host's sole faecal clone exhibited significantly lower inferred virulence than the other eight urine clones, and were statistically indistinguishable from the 10 ‘faecal only’ clones. In conclusion, special pathogenicity is an important determinant of UTI pathogenesis in women, although prevalence may occasionally allow less virulent strains to cause UTI.

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Extensively Drug-resistant Acinetobacter baumannii Belonging to International Clone II from A Pet Cat with Urinary Tract Infection; The First Report from Pakistan

Polish Journal of Microbiology ◽

10.33073/pjm-2020-017 ◽

2020 ◽

Vol 69 (2) ◽

pp. 231-234 ◽

Cited By ~ 1

Author(s):

ZEESHAN TAJ ◽

MUHAMMAD HIDAYAT RASOOL ◽

AHMAD ALMATROUDI ◽

MUHAMMAD SAQALEIN ◽

MOHSIN KHURSHID

Keyword(s):

Urinary Tract Infection ◽

Urinary Tract ◽

Tract Infection ◽

Acinetobacter Baumannii ◽

Drug Resistant ◽

Nosocomial Pathogen ◽

Resistance Determinants ◽

Carbapenem Resistant ◽

Extensively Drug Resistant ◽

Human Infections

The carbapenem-resistant Acinetobacter baumannii (CRAB) has got global attention as a notorious nosocomial pathogen. This study describes a case of urinary tract infection in a 2-years old pet female cat infected with A. baumannii. The susceptibility profiling, screening for the resistance determinants, and the multilocus sequence typing was performed. The A. baumannii isolate was found to harbor the blaOXA23-like gene and corresponded to International clone II that has been widely reported to be involved in human infections. The study proposes that the pets may contribute towards the spread of clinically relevant antimicrobial-resistant pathogens.

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Anatomy of an Extensively Drug Resistant Klebsiella pneumoniae Outbreak in Tuscany, Italy

10.1101/2021.06.02.446696 ◽

2021 ◽

Author(s):

Melissa J Martin ◽

Brendan W Corey ◽

Filomena Sannio ◽

Lindsey R Hall ◽

Ulrike MacDonald ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Genomic Analysis ◽

Health Care Facilities ◽

New Delhi ◽

Drug Resistant ◽

First Line ◽

Carbapenem Resistant ◽

Extensively Drug Resistant ◽

Care Facilities ◽

Cd1 Mice

A protracted outbreak of New Delhi metallo–β–lactamase (NDM)–producing carbapenem–resistant Klebsiella pneumoniae, started in Tuscany, Italy, in November 2018 and has continued in 2020 and through 2021. To understand the regional emergence and transmission dynamics over time, we collected and sequenced the genomes of 117 extensively drug–resistant, NDM–producing K. pneumoniae isolates cultured over a 20–month period from 76 patients at several health care facilities in South–East Tuscany. All isolates belonged to high–risk clone ST–147 and were typically non–susceptible to all first line antibiotics. Albeit sporadic, resistances to colistin, tigecycline and fosfomycin were also observed as a result of repeated, independent mutations. Genomic analysis revealed that ST–147 isolates circulating in Tuscany were monophyletic, highly genetically related (including a network of 42 patients from the same hospital and sharing nearly identical isolates) and shared a recent ancestor with isolates collected from the Middle East. While the blaNDM–1 gene was carried by an IncFIB–type plasmid, our investigations revealed that the ST–147 lineage from Italy also acquired a hybrid IncH–type plasmid carrying the 16S methyltransferase armA gene as well as key virulence biomarkers often found in hypervirulent isolates. This plasmid shared extensive homologies with mosaic plasmids circulating globally including from ST–11 and ST–307 convergent lineages. Phenotypically, the carriage of this hybrid plasmid resulted in increased siderophore production but did not confer virulence to the level of archetypical, hypervirulent K. pneumoniae in a subcutaneous model of infection with immunocompetent CD1 mice. Our findings highlight the importance of performing genomic surveillance to identify emerging threats.

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