Capsular Type K1 Research Articles

Genomic characterization of the novel bacteriophage IME183, infecting Klebsiella pneumoniae of capsular type K2.

Klebsiella pneumoniae causes a wide range of serious and life-threatening infections. Klebsiella phage IME183, isolated from hospital sewage, exhibited lytic activity against K. pneumoniae of capsular type K2. Transmission electron microscopy revealed that phage IME183 has a head with a diameter of 50 nm and a short tail. Its genome is 41,384 bp in length with a GC content of 52.92%. It is predicted to contain 50 open reading frames (ORFs). The results of evolutionary analysis suggest that phage IME183 should be considered a member of a new species in the genus Przondovirus.

Identification of three capsule depolymerases in a bacteriophage infecting Klebsiella pneumoniae capsular types K7, K20, and K27 and therapeutic application

BackgroundKlebsiella pneumoniae capsular types K1, K2, K5, K20, K54, and K57 are prevalent hypervirulent types associated with community infections, and worrisomely, hypervirulent strains that acquired drug resistance have been found. In the search for alternative therapeutics, studies have been conducted on phages that infect K. pneumoniae K1, K2, K5, and K57-type strains and their phage-encoded depolymerases. However, phages targeting K. pneumoniae K20-type strains and capsule depolymerases capable of digesting K20-type capsules have rarely been reported. In this study, we characterized a phage that can infect K. pneumoniae K20-type strains, phage vB_KpnM‐20.MethodsA phage was isolated from sewage water in Taipei, Taiwan, its genome was analyzed, and its predicted capsule depolymerases were expressed and purified. The host specificity and capsule-digesting activity of the capsule depolymerases were determined. The therapeutic effect of the depolymerase targeting K. pneumoniae K20-type strains was analyzed in a mouse infection model.ResultsThe isolated Klebsiella phage, vB_KpnM‐20, infects K. pneumoniae K7, K20, and K27-type strains. Three capsule depolymerases, K7dep, K20dep, and K27dep, encoded by the phage were specific to K7, K20, and K27-type capsules, respectively. K20dep also recognized Escherichia coli K30-type capsule, which is highly similar to K. pneumoniae K20-type. The survival of K. pneumoniae K20-type-infected mice was increased following administration of K20dep.ConclusionsThe potential of capsule depolymerase K20dep for the treatment of K. pneumoniae infections was revealed using an in vivo infection model. In addition, K7dep, K20dep, and K27dep capsule depolymerases could be used for K. pneumoniae capsular typing.

Impact Assessment of vB_KpnP_K1-ULIP33 Bacteriophage on the Human Gut Microbiota Using a Dynamic In Vitro Model.

New control methods are needed to counter antimicrobial resistances and the use of bacteriophages as an alternative treatment seems promising. To that end, the effect of the phage vB_KpnP_K1-ULIP33, whose host is the hypervirulent Klebsiella pneumoniae SA12 (ST23 and capsular type K1), was assessed on intestinal microbiota, using an in vitro model: the SHIME® system (Simulator of the Human Intestinal Microbial Ecosystem). After stabilization of the system, the phage was inoculated for 7 days and its persistence in the different colons was studied until its disappearance from the system. The concentration of short chain fatty acids in the colons showed good colonization of the bioreactors by the microbiota and no significant effect related to the phage treatment. Diversity (α and β), the relative abundance of bacteria, and qPCR analysis targeting different genera of interest showed no significant variation following phage administration. Even if further in vitro studies are needed to assess the efficacy of this phage against its bacterial host within the human intestinal ecosystem, the phage ULIP33 exerted no significant change on the global colonic microbiota.

Isolation of new Klebsiella pneumoniae phage PSKP16.

Klebsiella pneumoniae is a clinically relevant opportunistic pathogen belonging to the Enterobacteriaceae family. It is in the top three bacteria associated with antimicrobial resistance deaths globally, and one of the most dangerous bacteria causing nosocomial infections. Phage therapy offers a potential option for the treatment of drug-resistant bacterial infections. Phage PSKP16 was isolated against K. pneumoniae, capsular type K2 (isolated from a wound infection). PSKP16 is a new lytic phage with a Siphovirus-like morphology. PSKP16 is a linear double stranded DNA phage with a GC content of 50% and genome size of 46,712 bp, for which we predicted 67 ORFs. PSKP16 belongs to the genus Webervirus and shows high evolutionary proximity to Klebsiella phages JY917, Sushi, and B1. Phage isolation is fast, cheap and efficient, but it requires time and characterization (which adds expense) to ensure that the isolated phages do not pose a health risk, which is essential to safely use phage therapy to treat life-threatening bacterial infections.

Comparison of the therapeutic potential of bacteriophage KpV74 and phage-derived depolymerase (β-glucosidase) against Klebsiella pneumoniae capsular type K2

Bacteriophages and phage polysaccharide-degrading enzymes (depolymerases) are garnering attention as possible alternatives to antibiotics. Here, we describe the antimicrobial properties of bacteriophage KpV74 and phage depolymerase Dep_kpv74 specific to the hypervirulent Klebsiella pneumoniae of the K2 capsular type. The depolymerase Dep_kpv74 was identified as a specific glucosidase that cleaved the K2 type capsular polysaccharides of the K. pneumoniae by a hydrolytic mechanism. This depolymerase was effective against thigh soft tissue K. pneumoniae infection in mice without inducing adverse behavioral effects or toxicity. The depolymerase efficiency was similar to or greater than the bacteriophage efficiency. The phage KpV74 had a therapeutic effect only for treating the infection caused by the phage-propagating K. pneumoniae strain and was completely inactive against the infection caused by the K. pneumoniae strain that did not support phage multiplication. The depolymerase was effective in both cases. A mutant resistant to phage and depolymerase was isolated during the treatment of mice with bacteriophage. A confirmed one-base deletion in the flippase-coding wzx gene of this mutant is assumed to affect the polysaccharide capsule, abolishing the KpV74 phage adsorption and reducing the K. pneumoniae virulence.

Characterisation of clinical carbapenem-resistant K1 Klebsiella quasipneumoniae subsp. similipneumoniae strains harbouring a virulence plasmid

The continuous emergence of carbapenem-resistant and hypervirulent Klebsiella pneumoniae (CR-hvKP) poses a great challenge to human health owing to the associated extremely high morbidity and mortality. Klebsiella quasipneumoniae is a newly described bacterial species that is often misidentified as K. pneumoniae. Clinical K. quasipneumoniae strains have been reported worldwide, among which multidrug-resistant lineages have become a severe health problem, while less has been understood on this important pathogen. In this study, we characterised three clinical carbapenem-resistant K. quasipneumoniae subsp. similipneumoniae isolates belonging to sequence type 367 (ST367) and capsular type K1 and containing several virulence genes, including salmochelin (iroBCDN), aerobactin (iucABCDiutA) and regulator of mucoid phenotype (rmpA/A2), as well as some resistance genes, including blaKPC-2, blaTEM-1, blaOKP-B-9 and oqxAB. These carbapenem-resistant K. quasipneumoniae subsp. similipneumoniae strains containing virulence genes exhibited a higher level of virulence and serum resistance than a classical K. pneumoniae strain, while their virulence levels were slightly lower compared with typical ST11 CR-hvKP and ST23 K1 hvKP strains. This study reports for the first time the genetic and virulence characterisation of clinical K. quasipneumoniae subsp. similipneumoniae strains that simultaneously contained blaKPC-2 and virulence genes, contributing to a better understanding of their resistance and pathogenicity as well as for epidemic surveillance worldwide.

Genetics and pathology associated with Klebsiella pneumoniae and Klebsiella spp. isolates from North American Pacific coastal marine mammals

Southern sea otters (SSO: Enhydra lutris nereis) are a federally-listed threatened subspecies found almost exclusively in California, USA. Despite their zoonotic potential and lack of host specificity, K. pneumoniae and Klebsiella spp. have largely unknown epizootiology in SSOs. Klebsiella pneumoniae is occasionally isolated at necropsy, but not from live SSOs. Hypermucoviscous (HMV) K. pneumoniae strains are confirmed pathogens of Pacific Basin pinnipeds, but have not been previously isolated from SSOs. We characterized the virulence profiles of K. pneumoniae isolates from necropsied SSOs, evaluated killing of marine mammal K. pneumoniae following in vitro exposure to California sea lion (CSL: Zalophanus californianus) whole blood and serum, and characterized lesion patterns associated with Klebsiella spp. infection in SSOs. Four of 15 SSO K. pneumoniae isolates were HMV and all were recovered from SSOs that stranded during 2005. Many K. pneumoniae infections were associated with moderate to severe pathology as a cause of death or sequela. All HMV infections were assessed as a primary cause of death or as a direct result of the primary cause of death. Klebsiella-infected SSOs exhibited bronchopneumonia, tracheobronchitis and/or pleuritis, enteritis, Profilicollis sp. acanthocephalan peritonitis, septic peritonitis, and septicemia. All SSO HMV isolates were capsular type K2, the serotype most associated with HMV infections in CSLs. Multiplex PCR revealed two distinct virulence gene profiles within HMV isolates and two within non-HMV isolates. In vitro experiments investigating CSL whole blood and serum killing of K. pneumoniae suggest that HMV isolates are more resistant to serum killing than non-HMV isolates.

The emergence of the\xa0hypervirulent Klebsiella pneumoniae (hvKp) strains among circulating clonal complex 147 (CC147) harbouring blaNDM/OXA-48 carbapenemases in a tertiary care center of Iran

BackgroundKlebsiella pneumoniae is a public health concern because of its ability to develop multidrug resistance and hypervirulent genotypes, of those capsular types K1 and K2 cause community and nosocomial life-threatening infections. This study aimed to determine the antibiotic susceptibility patterns and genotypic traits of a collection of Klebsiella spp. isolates. Furthermore, the clonal relatedness of blaNDM producing strains was investigated.MethodsDuring a 19-months surveillance study, 122 Klebsiella spp. isolates were cultured from extraintestinal specimens of patients admitted to the tertiary referral hospital in Semnan, Iran. Isolates were identified using biochemical tests and subjected to determination of phylogroups, capsular types and virulence/resistance genes content. Hypervirulent K. pneumoniae (hvKp) strains were detected genotypically, and Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR fingerprinting was used to determine the clonality of blaNDM producing strains.ResultsMultidrug resistant phenotype was detected in 75 (61.5%) isolates and amikacin was found as the most potent antibiotic with the susceptibility rate of 85.2%. The carbapenemase genes were detected in 45 (36.8%) strains, including 21 (17.2%) blaOXA-48, 7 (5.6%) blaNDM-1, 14 (11.4%) blaNDM-1/OXA-48 and 3 (2.4%) blaIMP- carrying strains, while 55 (45.08%) isolates showed carbapenem resistant phenotype. The first blaNDM-1 carrying strain was cultured from a sputum specimen on March 2015, while the last positive one was recovered from blood culture on September 2016. Most of the isolates (80.3%) belonged to phylogroup I, and blaNDM-1 was identified among all three phylogroups. The ERIC-PCR clustered the 101 blaNDM negative and 21 blaNDM-1 positive isolates into 25 and five clusters, respectively, and the latter group belonged to clonal complex 147 (CC147). One K1 and 15 K2 blaNDM-1 negative isolates were detected, of those three strains were identified as hvKp. Five K2 positive strains, including four blaOXA-48 producer and one hvKp sequence type 86 (ST86) were carbapenem resistant. Among carbapenem resistant isolates, CC147 strains harboured higher rates of siderophores iutA and ybtS.ConclusionThe present findings showed a hospital circulation of CC147 blaNDM-1 or blaNDM-1/OXA-48 producing strains, disseminated in different wards. The hvKp/ST86 strain expressing K2 capsular type and carbapenem resistant phenotype wasn’t reported from Iran so far. So, it seems that we must be aware of the emergence and spread of new K. pneumoniae clones associated with resistant and hypermucoviscous phenotypes.

Draft Genome Sequences of Clinical K1-Type Klebsiella pneumoniae Strains Isolated in Russia.

Klebsiella pneumoniae of capsular type K1 is the most common causative agent of both health care-associated and community-acquired infections. Here, we report the draft genome sequences of 10 K1-type K. pneumoniae strains isolated from patients in an infectious disease hospital and neurosurgical intensive care unit in Russia.

1495. Fluoroquinolone as an Alternative Regimen for Klebsiella pneumoniae Liver Abscess

Background Klebsiella pneumoniae liver abscess (KPLA) is an endemic disease in East Asia. KPLA is usually caused by hypervirulent strains that are susceptible to all kinds of antibiotics except ampicillin. Patients with KPLA are commonly treated with β-lactams and need prolonged duration of intravenous therapy. Fluoroquinolone has high oral bioavailability and has the potential to shorten the duration of intravenous therapy, but studies regarding fluoroquinolone use in KPLA are limited. We aimed to compare the outcomes of patients with KPLA treated with β-lactams and fluoroquinolone.MethodsConsecutive patients with KPLA in a tertiary medical center of Taiwan between 2011 and 2018 were enrolled retrospectively. Clinical characteristics and treatment outcomes were compared between cases treated with β-lactams and fluoroquinolones. Logistic regression was performed to identify risk factors of prolonged hospitalization (defined as > 30 days). Capsular genotypes and presence of rmpA or rmpA2 genes were analyzed among K. pneumoniae strains collected after July 2012. Hypervirulent strains were defined as those had rmpA or rmpA2 genes.ResultsA total of 330 KPLA patients identified, and the in-hospital mortality was 0.9% (n = 3). Nearly all K. pneumoniae strains were hypervirulent strains (97.1%). Capsular type K1 (n = 176) and K2 (n = 63) were the most common capsular types. Most patients received β-lactams (n = 296, 89.7%), and only 34 (10.3%) patients received fluoroquinolones as the main antibiotics (levofloxacin = 17; moxifloxacin = 10; ciprofloxacin = 7). The duration of intravenous antibiotics use in fluoroquinolones group was shorter than β-lactams group (20.12 ± 9.21 vs. 26.81 ± 16.10, P = 0.001). Prolonged hospitalization was more common in β-lactams group than fluoroquinolones group (32.1% vs. 11.8%, P = 0.014). The in-hospital mortality, duration of antibiotic use, and recurrence rate were similar between the two groups. Fluoroquinolones was independent protective factor for prolonged hospitalization (hazard ratio, 0.28; P = 0.026).ConclusionFluoroquinolone is able to shorten the duration of intravenous antibiotic use and beneficial in prolonged hospitalization in patients with KPLA.Disclosures All authors: No reported disclosures.

K2 Capsule Depolymerase Is Highly Stable, Is Refractory to Resistance, and Protects Larvae and Mice from Acinetobacter baumannii Sepsis.

Acinetobacter baumannii is emerging as a major nosocomial pathogen in intensive care units. The bacterial capsules are considered major virulence factors, and the particular A. baumannii capsular type K2 has been associated with high antibiotic resistance. In this study, we identified a K2 capsule-specific depolymerase in a bacteriophage tail spike C terminus, a fragment that was heterologously expressed, and its antivirulence properties were assessed by in vivo experiments. The K2 depolymerase is active under a broad range of environmental conditions and is highly thermostable, with a melting point (Tm ) at 67°C. In the caterpillar larva model, the K2 depolymerase protects larvae from bacterial infections, using either pretreatments or with single-enzyme injection after bacterial challenge, in a dose-dependent manner. In a mouse sepsis model, a single K2 depolymerase intraperitoneal injection of 50 μg is able to protect 60% of mice from an otherwise deadly infection, with a significant reduction in the proinflammatory cytokine profile. We showed that the enzyme makes bacterial cells fully susceptible to the host complement system killing effect. Moreover, the K2 depolymerase is highly refractory to resistance development, which makes these bacteriophage-derived capsular depolymerases useful antivirulence agents against multidrug-resistant A. baumannii infections.IMPORTANCEAcinetobacter baumannii is an important nosocomial pathogen resistant to many, and sometimes all, antibiotics. The A. baumannii K2 capsular type has been associated with elevated antibiotic resistance. The capsular depolymerase characterized here fits the new trend of alternative antibacterial agents needed against multidrug-resistant pathogens. They are highly specific, stable, and refractory to resistance, as they do not kill bacteria per se; instead, they remove bacterial surface polysaccharides, which diminish the bacterial virulence and expose them to the host immune system.

New Bacteriophages against Emerging Lineages ST23 and ST258 of Klebsiella pneumoniae and Efficacy Assessment in Galleria mellonella Larvae.

Klebsiella pneumoniae is a bacterial pathogen of high public health importance. Its polysaccharide capsule is highly variable but only a few capsular types are associated with emerging pathogenic sublineages. The aim of this work is to isolate and characterize new lytic bacteriophages and assess their potential to control infections by the ST23 and ST258 K. pneumoniae sublineages using a Galleria mellonella larvae model. Three selected bacteriophages, targeting lineages ST258 (bacteriophages vB_KpnP_KL106-ULIP47 and vB_KpnP_KL106-ULIP54) and ST23 (bacteriophage vB_KpnP_K1-ULIP33), display specificity for capsular types KL106 and K1, respectively. These podoviruses belong to the Autographivirinae subfamily and their genomes are devoid of lysogeny or toxin-associated genes. In a G. mellonella larvae model, a mortality rate of 70% was observed upon infection by K. pneumoniae ST258 and ST23. This number was reduced to 20% upon treatment with bacteriophages at a multiplicity of infection of 10. This work increases the number of characterized bacteriophages infecting K. pneumoniae and provides information regarding genome sequence and efficacy during preclinical phage therapy against two prominent sublineages of this bacterial species.

Molecular Characterization of Carbapenem Resistant Klebsiella pneumoniae and Klebsiella quasipneumoniae Isolated from Lebanon

Klebsiella pneumoniae is a Gram-negative organism and a major public health threat. In this study, we used whole-genome sequences to characterize 32 carbapenem-resistant K. pneumoniae (CRKP) and two carbapenem-resistant K. quasipneumoniae (CRKQ). Antimicrobial resistance was assessed using disk diffusion and E-test, while virulence was assessed in silico. The capsule type was determined by sequencing the wzi gene. The plasmid diversity was assessed by PCR-based replicon typing to detect the plasmid incompatibility (Inc) groups. The genetic relatedness was determined by multilocus sequence typing, pan-genome, and recombination analysis. All of the isolates were resistant to ertapenem together with imipenem and/or meropenem. Phenotypic resistance was due to blaOXA-48,blaNDM-1, blaNDM-7, or the coupling of ESBLs and outer membrane porin modifications. This is the first comprehensive study reporting on the WGS of CRKP and the first detection of CRKQ in the region. The presence and dissemination of CRKP and CRKQ, with some additionally having characteristics of hypervirulent clones such as the hypermucoviscous phenotype and the capsular type K2, are particularly concerning. Additionally, mining the completely sequenced K. pneumoniae genomes revealed the key roles of mobile genetic elements in the spread of antibiotic resistance and in understanding the epidemiology of these clinically significant pathogens.

1175. Clinical and Microbiological Features of Klebsiella pneumoniae Liver Abscess Caused by Multidrug-Resistant Strains

BackgroundThe endemic Klebsiella pneumoniae liver abscess (KPLA) in East Asian countries are usually caused by hypervirulent strains. These hypervirulent strains are usually susceptible to commonly used antibiotics, aside from their intrinsic resistance to ampicillin. However, hypervirulent K. pneumonaie strains with multidrug-resistant (MDR) phenotype has been reported recently. We aim to investigate clinical and microbiological features of KPLA caused by MDR-resistant strains, and the evolution of drug-resistance in the resistant strain causing recurrent KPLA.MethodsPatients with KPLA were retrospectively identified at Taipei Veterans General Hospital during January 2013 to February 2018. Capsular genotypes were analyzed in all K. pneumoniae isolates. Antimicrobial-resistant mechanisms were determined for MDR isolates. Pulse-field gel electrophoresis (PFGE), conjugation experiment, and in vivo mice lethality were determined on the strains from a patient with recurrent infection.ResultsDuring the study period, a total of 211 patients with KPLA, and five patients with recurrence were identified. Most of K. pneumoniae isolates (n = 175, 83.3%) belonged to capsular type K1/K2/K5/K20/K54/K57. Nineteen MDR strains were identified and 15 of them had virulent capsular types (K1 = 7, K2 = 5, K5 = 2, K54 = 1). The major resistance mechanisms of these MDR strains involved the presence of β-lactamases and the overexpression of efflux pumps. The in-hospital mortality of KPLA caused by MDR strains was not significantly higher than wild-type stains (10.53% vs. 4.69%, P = 0.275). In a case with recurrent KPLA, the recurrent capsular type K1 strain (TVGHKP2611) with blaSHV-12 was genetically identical to the primary wild-type resistance strain (TVGHKP2329) by PFGE. The SHV-12-carrying plasmid from TVGHKP2611 was successfully conjugated to Eschericia coli J53. TVGHKP2611 retained high virulence similar to TVGHKP2329 in mice lethality study (median lethal dose < 500 CFU) despite carrying the resistance determinant.ConclusionMDR K. pneumoniae strains belonging to virulent capsular types have emerged in KPLA. One SHV-12 producing capsular K1 strain causing recurrent KPLA retained its high virulence, which signals this highly pathogenic and resistant strain could be a major concern in the future.Disclosures All authors: No reported disclosures.

Draft Genome Sequences of 10 Clinical K2-Type Klebsiella pneumoniae Strains Isolated in Russia.

We report here the genome sequences of 10 Klebsiella pneumoniae strains of capsular type K2 isolated in Russia from patients in an infectious clinical hospital and neurosurgical intensive care unit. The draft genome sizes range from 5.34 to 5.87 Mb and include 5,448 to 6,137 protein-coding sequences.

High mortality among patients infected with hypervirulent antimicrobial-resistant capsular type K1 Klebsiella pneumoniae strains in Taiwan

Capsular type K1 Klebsiella pneumoniae, highly virulent strains which are common in Asian countries, can cause pyogenic infections. These hypervirulent strains are usually susceptible to most antimicrobials, except for ampicillin. Little is known regarding the clinical and molecular characteristics of antimicrobial-resistant K1 K. pneumoniae strains. This retrospective study evaluated patients infected with capsular type K1 K. pneumoniae strains in a Taiwanese medical centre between April 2013 and March 2016. Antimicrobial-resistant strains were defined based on non-susceptibility to antimicrobial agents except ampicillin. We compared the clinical outcome of patients infected with and without antimicrobial-resistant strains. The in vivo virulence, genetic relatedness, and resistance mechanisms of these hypervirulent antimicrobial-resistant strains were also investigated. A total of 182 capsular type K1 K. pneumoniae strains were identified, including 18 antimicrobial-resistant strains. The 28-day mortality rate among the 18 cases caused by antimicrobial-resistant strains was significantly higher than that among 164 cases caused by antimicrobial-sensitive strains (50% vs. 10.4%, P < 0.001). Infection with antimicrobial-resistant strain independently increased the 28-day mortality risk. Most antimicrobial-resistant strains were not clonally related, and they exhibited high in vivo virulence in a mouse lethality experiment. The major resistance mechanisms involved the presence of β-lactamases and the overexpression of efflux pumps. In conclusion, hypervirulent antimicrobial-resistant capsular type K1 K. pneumoniae strains can predispose to a fatal outcome. These strains may represent an emerging threat to public health in Taiwan.

Evaluation of Virulence Factors and Antibiotic Resistance Patterns in Clinical Urine Isolates of Klebsiella pneumoniae in Semnan, Iran

Background: Klebsiella pneumoniae as an opportunistic pathogen can be the cause of a range of nosocomial and community - acquired infections. Many virulence factors help these bacteria overcome an immune system and cause various diseases. K1 and K2 capsular antigens, also magA, wcaG, and rmpA are well - known K. pneumoniae virulence factors. Klebsiella pneumoniae has been revealed to have the ability to acquire resistance to many antibiotics, which cause treatment failure. Objectives: This study aimed at determining the prevalence of magA, wcaG, rmpA, Capsular type K1, Capsular type K2, TEM, and SHV in K. pneumoniae isolates. Methods: A total of 173 non - duplicate K. pneumoniae isolates were collected from two different hospitals in Semnan, Iran, from urine specimens. Klebsiella pneumoniae was identified by conventional bacteriological tests. Disk diffusion test was performed according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI). Detection of virulence factors, TEM, and SHV gene was performed by specific primers. Results: Frequency of virulence factors was as follow: capsular type K2: 32.9%, rmpA: 20.2%, capsular type K1: 6.9%, and wcaG: 16.2%. Also, the SHV and TEM were observed in 46.8% and 33.5%, respectively. Antibiotics resistance rates were as follow, imipenem: 7.5%, ciprofloxacin: 16.1%, levofloxacin: 17.3%, amoxicillin - clavulanic acid: 30%, trimethoprim - sulfamethoxazole: 32.9%, cefepime: 34.1%, nitrofurantoin: 35.8%, amikacin: 36.4%, aztreonam: 39.3%, ceftazidime: 42.7%. Conclusions: Frequency of some virulence factors including capsular type K2, rmpA, wcaG, and also resistant rate to imipenem, amikacin, and ceftazidime were significantly higher than similar studies. Presence of virulence factors accompanied by drug resistance should make bacteria an infectious agent and lead to treatment failure.

Comparative analysis of Klebsiella pneumoniae strains isolated in 2012–2016 that differ by antibiotic resistance genes and virulence genes profiles

The antibacterial resistance and virulence genotypes and phenotypes of 148 non-duplicate Klebsiella pneumoniae strains collected from 112 patients in Moscow hospitals in 2012–2016 including isolates from the respiratory system (57%), urine (30%), wounds (5%), cerebrospinal fluid (4%), blood (3%), and rectal swab (1%) were determined. The majority (98%) were multidrug resistant (MDR) strains carrying blaSHV (91%), blaCTX-M (74%), blaTEM (51%), blaOXA (38%), and blaNDM (1%) beta-lactamase genes, class 1 integrons (38%), and the porin protein gene ompK36 (96%). The beta-lactamase genes blaTEM-1, blaSHV-1, blaSHV-11, blaSHV-110, blaSHV-190, blaCTX-M-15, blaCTX-M-3, blaCTX-M-55, blaOXA-48, blaOXA-244, and blaNDM-1 were detected; class 1 integron gene cassette arrays (aadA1), (dfrA7), (dfrA1-orfC), (aadB-aadA1), (dfrA17-aadA5), and (dfrA12-orfF-aadA2) were identified. Twenty-two (15%) of clinical K. pneumoniae strains had hypermucoviscous (HV) phenotype defined as string test positive. The rmpA gene associated with HV phenotype was detected in 24% of strains. The intrapersonal mutation of rmpA gene (deletion of one nucleotide at the polyG tract) was a reason for negative hypermucoviscosity phenotype and low virulence of rmpA-positive K. pneumoniae strain KPB584. Eighteen virulent for mice strains with LD50 ≤ 104 CFU were attributed to sequence types ST23, ST86, ST218, ST65, ST2174, and ST2280 and to capsular types K1, K2, and K57. This study is the first report about hypervirulent K. pneumoniae strain KPB2580-14 of ST23K1 harboring extended-spectrum beta-lactamase CTX-M-15 and carbapenemase OXA-48 genes located on pCTX-M-15-like and pOXA-48-like plasmids correspondingly.

Virulence genes in isolates of Klebsiella pneumoniae from the UK during 2016, including among carbapenemase gene-positive hypervirulent K1-ST23 and 'non-hypervirulent' types ST147, ST15 and ST383.

Klebsiella pneumoniae is a concern because of its multidrug resistance and the ability of hypervirulent types, especially capsular type K1-clonal complex 23 (K1-CC23), to cause community-acquired, life-threatening infections. Hypervirulent types carry an array of virulence genes including rmpA/rmpA2, coding for capsule up-regulation. We sought to identify isolates carrying these elements among submissions to the UK national reference laboratory during 2016. Virulence elements and carbapenemase genes were sought by PCR or from whole genome sequences. Isolates were typed by variable number tandem repeat analysis or by multi locus sequence typing from whole genome sequences. Long read nanopore sequencing was carried out on two isolates.Results/Key findings. Twelve of 1090 isolates (1.1 %) belonged to hypervirulent K1-CC23, with one carrying blaOXA-48 (KpvST23L_OXA-48). A further 24 rmpA/rmpA2-positive isolates were detected: eight belonged to hypervirulent types of capsular types K2 and K54; and 14 belonged to 'non-hypervirulent' ST147, ST15 and ST383 and also carried carbapenemase gene(s). Virulence, heavy metal and antibiotic resistance gene contents were compared from whole genome sequences of KpvST23L_OXA-48 and one of the ST147 isolates carrying blaNDM-1. They carried 94/96 and 26/96 of the virulence genes sought, and 23/23 and 9/23 of the heavy metal resistance genes, respectively. In the ST147 isolate, rmpA/rmpA2 and the aerobactin siderophore cluster were on a large virulence plasmid together with resistance genes. The yersiniabactin cluster was widely present among carbapenemase gene-positive isolates, including among those that were rmpA/rmpA2-negative. Our results highlight a combination of virulence and resistance genes, which could lead to untreatable invasive infections.

Comparative genome analysis of novel Podoviruses lytic for hypermucoviscous Klebsiella pneumoniae of K1, K2, and K57 capsular types

Hypermucoviscous (HV) strains of capsular types K1, K2 and K57 are the most virulent representatives of the Klebsiella pneumoniae species. Eight novel bacteriophages lytic for HV K. pneumoniae were isolated and characterized. Three bacteriophages, KpV41, KpV475, and KpV71 were found to have a lytic activity against mainly K. pneumoniae of capsular type K1. Two phages, KpV74, and KpV763 were lytic for K2 capsular type K. pneumoniae, and the phage KpV767 was specific to K57-type K. pneumoniae only. Two more phages, KpV766, and KpV48 had no capsular specificity. The phage genomes consist of a linear double-stranded DNA of 40,395–44,623bp including direct terminal repeats of 180–246 bp. The G + C contents are 52.3–54.2 % that is slightly lower than that of genomes of K. pneumoniae strains being used for phage propagation. According to the genome structures, sequence similarity and phylogenetic data, the phages are classified within the genus Kp32virus and Kp34virus of subfamily Autographivirinae, family Podoviridae. In the phage genomes, genes encoding proteins with putative motifs of polysaccharide depolymerase were identified. Depolymerase genes of phages KpV71 and KpV74 lytic for hypermucoviscous K. pneumoniae of K1 and K2 capsular type, respectively, were cloned and expressed in Escherichia coli, and the recombinant gene products were purified. The specificity and polysaccharide-degrading activity of the recombinant depolymerases were demonstrated.