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

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.

Download Full-text

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.

Download Full-text

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.

Download Full-text

Clonal relatedness and plasmid profiling of extensively drug-resistant New Delhi metallo-β-lactamase-producing Klebsiella pneumoniae clinical isolates

Future Microbiology ◽

10.2217/fmb-2020-0315 ◽

2021 ◽

Author(s):

Muhammad Usman Qamar ◽

Hasan Ejaz ◽

Timothy R Walsh ◽

Asad Ali Shah ◽

Dunia A Al Farraj ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Dna Hybridization ◽

Tertiary Care ◽

Health Concern ◽

New Delhi ◽

Care Hospital ◽

Carbapenem Resistant ◽

Extensively Drug Resistant ◽

Vitek 2 ◽

Plasmid Profiling

Aim: Carbapenem-resistant Klebsiella pneumoniae (CR-KP) particularly New Delhi metallo-β-lactamase (NDM) is a serious public health concern globally. The aim of the study to determine the molecular epidemiology of blaNDM-producing clinically isolated K. pneumoniae. Methods: Carbapenem-resistant K. pneumoniae isolates (n = 100) were collected from tertiary care hospital Lahore. Isolates were confirmed by VITEK® 2 system and MALDI-TOF. Minimum inhibitory concentration was performed by VITEK 2 and molecular characterization was done by PCR, PFGE, DNA hybridization and replicon typing. Results: Of 90 MBL-producing K. pneumoniae, 75 were NDM producers; 60 were NDM-1 and 11 NDM-5. A total of 27 K. pneumoniae belonged to ST11 and 14 to ST147. NDM positive isolates were 100% resistant to β-lactam antibiotics except for colistin. 13.3% isolates carried blaNDM on ∼140 kb plasmids. A total of 32 (52.4%) isolates were positive for IncA/C and 18 (29.5%) IncF/II. Conclusion: The extensively resistant lineage of NDM-producing K. pneumoniae is prevalent in the clinical setting.

Download Full-text

Antibiotic Susceptibility of NDM-Producing Enterobacterales Collected in the United States in 2017 and 2018

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00499-20 ◽

2020 ◽

Vol 64 (9) ◽

Cited By ~ 4

Author(s):

Joseph D. Lutgring ◽

Rocío Balbuena ◽

Natashia Reese ◽

Sarah E. Gilbert ◽

Uzma Ansari ◽

...

Keyword(s):

United States ◽

Antibiotic Susceptibility ◽

Treatment Options ◽

The United States ◽

Multidrug Resistant ◽

New Delhi ◽

Drug Resistant ◽

Carbapenem Resistant ◽

Extensively Drug Resistant

ABSTRACT The treatment of infections caused by carbapenem-resistant Enterobacterales, especially New Delhi metallo-β-lactamase (NDM)-producing bacteria, is challenging. Although less common in the United States than some other carbapenemase producers, NDM-producing bacteria are a public health threat due to the limited treatment options available. Here, we report on the antibiotic susceptibility of 275 contemporary NDM-producing Enterobacterales collected from 30 U.S. states through the Centers for Disease Control and Prevention’s Antibiotic Resistance Laboratory Network. The aims of the study were to determine the susceptibility of these isolates to 32 currently available antibiotics using reference broth microdilution and to explore the in vitro activity of 3 combination agents that are not yet available. Categorical interpretations were determined using Clinical and Laboratory Standards Institute (CLSI) interpretive criteria. For agents without CLSI criteria, Food and Drug Administration (FDA) interpretive criteria were used. The percentage of susceptible isolates did not exceed 90% for any of the FDA-approved antibiotics tested. The antibiotics with breakpoints that had the highest in vitro activity were tigecycline (86.5% susceptible), eravacycline (66.2% susceptible), and omadacycline (59.6% susceptible); 18.2% of isolates were susceptible to aztreonam. All NDM-producing isolates tested were multidrug resistant, and 116 isolates were extensively drug resistant (42.2%); 207 (75.3%) isolates displayed difficult-to-treat resistance. The difficulty in treating infections caused by NDM-producing Enterobacterales highlights the need for containment and prevention efforts to keep these infections from becoming more common.

Download Full-text

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-29704/v2 ◽

2020 ◽

Author(s):

Aalaa Mahgoub Albasha ◽

Esraa Hassan Osman ◽

Saga Abd Alhalim ◽

Elianz Alshaib ◽

Leena Al-Hassan ◽

...

Keyword(s):

Urinary Tract ◽

Klebsiella Pneumoniae ◽

Nosocomial Infections ◽

Virulence Genes ◽

Virulence Gene ◽

Multidrug Resistant ◽

Drug Resistant ◽

Carbapenem Resistant ◽

Extensively Drug Resistant ◽

Virulent Strains

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.

Download Full-text

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-29704/v1 ◽

2020 ◽

Author(s):

Aalaa Mahgoub Albasha ◽

Esraa Hassan Osman ◽

Saga Abd Alhalim ◽

Elianz Alshaib ◽

Leena Al-Hassan ◽

...

Keyword(s):

Urinary Tract ◽

Klebsiella Pneumoniae ◽

Nosocomial Infections ◽

Virulence Genes ◽

Virulence Gene ◽

Drug Resistant ◽

Carbapenem Resistant ◽

Extensively Drug Resistant ◽

Virulent Strains ◽

Neonatal Blood

Abstract ObjectiveKlebsiella pneumoniae (K. pneumoniae) involves both community-acquired infections 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. ResultsSeventy 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.

Download Full-text

First Report on a Hyperepidemic Clone of KPC-3-Producing Klebsiella pneumoniae in Israel Genetically Related to a Strain Causing Outbreaks in the United States

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00987-08 ◽

2008 ◽

Vol 53 (2) ◽

pp. 818-820 ◽

Cited By ~ 126

Author(s):

Shiri Navon-Venezia ◽

Azita Leavitt ◽

Mitchell J. Schwaber ◽

J. Kamile Rasheed ◽

Arjun Srinivasan ◽

...

Keyword(s):

United States ◽

Klebsiella Pneumoniae ◽

The United States ◽

Drug Resistant ◽

Resistant Clone ◽

Bacterial Strains ◽

First Report ◽

Carbapenem Resistant ◽

Extensively Drug Resistant ◽

Global Spread

ABSTRACT A highly epidemic carbapenem-resistant clone of KPC-3-producing Klebsiella pneumoniae emerged in Israel in 2006, causing a nationwide outbreak. This clone was genetically related to outbreak strains from the United States isolated in 2000 but differed in KPC-carrying plasmids. The threat of the global spread of hyperepidemic, extensively drug-resistant bacterial strains should be recognized and confronted.

Download Full-text

Decreased carO gene expression and OXA-type carbapenemases among extensively drug-resistant Acinetobacter baumannii strains isolated from burn patients in Tehran, Iran

Acta Microbiologica et Immunologica Hungarica ◽

10.1556/030.2020.01138 ◽

2020 ◽

Cited By ~ 1

Author(s):

Elham Abbasi ◽

Hossein Goudarzi ◽

Ali Hashemi ◽

Alireza Salimi Chirani ◽

Abdollah Ardebili ◽

...

Keyword(s):

Gene Expression ◽

Acinetobacter Baumannii ◽

High Rate ◽

Burn Patients ◽

Drug Resistant ◽

Disc Diffusion ◽

Carbapenem Resistant ◽

Extensively Drug Resistant ◽

Sds Page ◽

Extensively Drug Resistance

AbstractA major challenge in the treatment of infections has been the rise of extensively drug resistance (XDR) and multidrug resistance (MDR) in Acinetobacter baumannii. The goals of this study were to determine the pattern of antimicrobial susceptibility, blaOXA and carO genes among burn-isolated A. baumannii strains. In this study, 100 A. baumannii strains were isolated from burn patients and their susceptibilities to different antibiotics were determined using disc diffusion testing and broth microdilution. Presence of carO gene and OXA-type carbapenemase genes was tested by PCR and sequencing. SDS-PAGE was done to survey CarO porin and the expression level of carO gene was evaluated by Real-Time PCR. A high rate of resistance to meropenem (98%), imipenem (98%) and doripenem (98%) was detected. All tested A. baumannii strains were susceptible to colistin. The results indicated that 84.9% were XDR and 97.9% of strains were MDR. In addition, all strains bore blaOXA-51 like and blaOXA-23 like and carO genes. Nonetheless, blaOXA-58 like and blaOXA-24 like genes were harbored by 0 percent and 76 percent of strains, respectively. The relative expression levels of the carO gene ranged from 0.06 to 35.01 fold lower than that of carbapenem-susceptible A. baumannii ATCC19606 and SDS – PAGE analysis of the outer membrane protein showed that all 100 isolates produced CarO. The results of current study revealed prevalence of blaOXA genes and changes in carO gene expression in carbapenem resistant A.baumannii.

Download Full-text