Capsular Type Research Articles

Outbreak of group B Streptococcus in a neonatal care unit confirmed by whole-genome sequencing.

Clusters of group B Streptococcus (GBS) infections in neonatal intensive care units (NICU) are poorly documented. We aimed to assess GBS cross-transmission during an outbreak of GBS sepsis. The study was carried out between October and November 2021 in a French University Hospital. Neonatal intensive care unit (NICU) patients with GBS sepsis were included. Clinical data were retrieved from electronic patient records. Group B Streptococcus isolates were characterized at the molecular level using capsular genotyping and whole-genome sequencing (WGS). The outbreak of GBS sepsis affected three very preterm neonates with a gestational age of less than 26 weeks, including one recurrent male index case aged 26 days, and two female secondary cases aged 5 and 17 days. The microbiological investigation identified a GBS isolate of capsular type III and Sequence Type 17 as responsible for the four infectious episodes. Whole-genome sequencing confirmed the identity between the isolates. The outbreak and the results of the microbiological investigations led to an immediate reinforcement of hygiene measures. Clustered cases of GBS infections in NICU and horizontal transmission of the hypervirulent GBS Sequence Type 17 are likely underestimated. Prospective investigation of all nosocomial cases using WGS should contribute to improving vigilance regarding GBS cross-transmission and infection prevention.

Characterization of a novel bacteriophage endolysin (LysAB1245) with extended lytic activity against distinct capsular types associated with Acinetobacter baumannii resistance.

Capsular polysaccharides are considered as major virulence factors associated with the ability of multidrug-resistant (MDR) Acinetobacter baumannii to cause severe infections. In this study, LysAB1245, a novel bacteriophage-encoded endolysin consisting of a lysozyme-like domain from phage T1245 was successfully expressed, purified, and evaluated for its antibacterial activity against distinct capsular types associated with A. baumannii resistance. The results revealed a broad spectrum activity of LysAB1245 against all clinical MDR A. baumannii isolates belonging to capsular type (KL) 2, 3, 6, 10, 47, 49, and 52 and A. baumannii ATCC 19606. At 2 h following the treatment with 1.7 unit/reaction of LysAB1245, more than 3 log reduction in the numbers of bacterial survival was observed. In addition, LysAB1245 displayed rapid bactericidal activity within 30 min (nearly 3 log CFU/mL of bacterial reduction). Thermostability assay indicated that LysAB1245 was stable over a broad range of temperature from 4 to 70°C, while pH sensitivity assay demonstrated a wide range of pH from 4.5 to 10.5. Furthermore, both minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) of LysAB1245 against all MDR A. baumannii isolates and A. baumannii ATCC 19606 were 4.21 μg/mL (0.1 unit/reaction). Conclusively, these results suggest that LysAB1245 possesses potential application for the treatment of nosocomial MDR A. baumannii infections.

Genomic Characteristics of a Carbapenem-Resistant Klebsiella pneumoniae Co-Carrying bla NDM-5 and bla KPC-2 Capsular Type KL25 Recovered from a County Level Hospital in China.

Hypervirulent carbapenem-resistant K. pneumoniae (hv-CRKP) has been spreading rapidly worldwide. Here, we investigated the genomic characteristics of ST11 K. pneumoniae isolate SM117 with capsular serotype KL25, co-carrying bla NDM-5, two copies of bla KPC-2 and multiple plasmid-borne virulence genes from a county level hospital in China. Antimicrobial susceptibility of K. pneumoniae SM117 was evaluated. The Illumina NovaSeq 6000 and Oxford Nanopore MinION platforms were applied to sequence the genome and then de novo assembled. The genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline and further subjected to identify the sequence type (ST), capsular type, antibiotic resistance genes, plasmid replicon types and virulence genes. The phylogenetic analysis was performed based on the core genome single nucleotide polymorphisms (cgSNPs) using CSI Phylogeny 1.4, and further visualized by Interactive Tree of Life (iTOL) V5 web server. The whole-genome sequence of K. pneumoniae SM117 is made up of eight contigs totaling 6,104,486 bp, contain a 5,612,620 bp single chromosome and seven plasmids. The isolate was assigned to ST11 with capsular serotype KL25, co-carrying including bla NDM-5, bla KPC-2 and multiple plasmid-borne virulence genes including rmpA2 and aerobactin genes iucABCD-iutA. The coexistence of bla KPC and bla NDM in K. pneumoniae strains exhibit a high degree of resistance to β-lactam antibiotics. The strain SM117 also carries multiple antibiotic resistance genes, making it resistant to all antibiotics except polymyxin. The closest relative of K. pneumoniae C793 was identified in 2023 from a hospital surface sample in Zhejiang, China, with just 52 SNPs difference. This study reported the genomic characteristics of a multidrug-resistant ST11 K. pneumoniae with capsular serotype KL25, co-carrying bla NDM-5, two copies of bla KPC-2 genes and multiple plasmid-borne virulence genes in China. These findings will provide important knowledge of the antibiotic resistance mechanisms, genomic epidemiological characteristics and transmission dynamics of multidrug-resistant K. pneumoniae.

Multidrug-resistant clinical K. pneumoniae ST16, ST218, and ST283 and emergence of pandrug-resistant KPC-positive ST6434/K2 lineage in Iraq.

The increasing incidence of Klebsiella pneumoniae infections, both in the community and in hospitals, is a huge health problem. This is due to the increasing resistance of the bacteria to antibiotics and biofilm formation, as well as the presence of a capsule. This study focuses on two main objectives: to survey the most common capsular types in local isolates for the first time in Anbar, Iraq, on molecular level and to distinguish between infectious pathogen strains using multilocus sequence typing (MLST) for more efficient epidemiological and surveillance analysis, in order to determine the source of these strains (invasive or purebred). Multidrug-resistant (MDR) isolates adapted to genomic extraction and molecular screening of capsular type and MLST, and then to data processing by Pasteur Institut. For the first time, one isolate was registered as a new strain in the world with ST 6434; the other strains demonstrated as preregistered with ST16, ST218, and ST283. 33% of MDR isolates belonged to the capsular K2 type. The study's findings were not aligned with the global knowledge base about the distribution of capsular type in Asia. To prevent the spread of highly resistant strains, careful monitoring of virulence determinants is necessary in addition to the observation of antibiotic resistance.

Depolymerisation of the Klebsiella pneumoniae Capsular Polysaccharide K21 by Klebsiella Phage K5.

Klebsiella pneumoniae is a pathogen associated with various infection types, which often exhibits multiple antibiotic resistance. Phages, or bacterial viruses, have an ability to specifically target and destroy K. pneumoniae, offering a potential means of combatting multidrug-resistant infections. Phage enzymes are another promising therapeutic agent that can break down bacterial capsular polysaccharide, which shields K. pneumoniae from the immune response and external factors. In this study, Klebsiella phage K5 was isolated; this phage is active against Klebsiella pneumoniae with the capsular type K21. It was demonstrated that the phage can effectively lyse the host culture. The adsorption apparatus of the phage has revealed two receptor-binding proteins (RBPs) with predicted polysaccharide depolymerising activity. A recombinant form of both RBPs was obtained and experiments showed that one of them depolymerised the capsular polysaccharide K21. The structure of this polysaccharide and its degradation fragments were analysed. The second receptor-binding protein showed no activity on capsular polysaccharide of any of the 31 capsule types tested, so the substrate for this enzyme remains to be determined in the future. Klebsiella phage K5 may be considered a useful agent against Klebsiella infections.

Streptococcus pneumoniae serotype 33G: genetic, serological, and structural analysis of a new capsule type.

Streptococcus pneumoniae (the pneumococcus) is a bacterial pathogen with the greatest burden of disease in Asia and Africa. The pneumococcal capsular polysaccharide has biological relevance as a major virulence factor as well as public health importance as it is the target for currently licensed vaccines. These vaccines have limited valency, covering up to 23 of the >100 known capsular types (serotypes) with higher valency vaccines in development. Here, we have characterized a new pneumococcal serotype, which we have named 33G. We detected serotype 33G in nasopharyngeal swabs (n = 20) from children and adults hospitalized with pneumonia, as well as healthy children in Mongolia. We show that the genetic, serological, and biochemical properties of 33G differ from existing serotypes, satisfying the criteria to be designated as a new serotype. Future studies should focus on the geographical distribution of 33G and any changes in prevalence following vaccine introduction.

Выделение и характеристика вирулентных бактериофагов против Klebsiella pneumoniae значимых капсульных типов

The growing proportion of antibiotic-resistant Klebsiella pneumoniae strains raises challenges to the healthcare system and requires the development of alternative treatment options. Bacteriophage therapy is one of such options. The study was aimed to isolate and describe bacteriophages effective against K. pneumoniae strains of clinically significant capsular types. The bacteriophages were isolated from the sewage and river water samples using the enrichment culture technique. The spectrum of lytic activity of the phages was tested on the collection of K. pneumoniae clinical isolates (n = 279). The studied bacteriophages lysed 52.8–100% of K. pneumoniae strains of respective capsular types: phage VKV295 lysed 100% of strains with the capsular type KL1, SAA231 — 52.8 of strains with KL2, NNK-G4 — 100% of strains with KL39, VSG32 — 66.7% of strains with KL41, NKA196 — 87.5% of strains with KL47, Rappa3 — 87.5% of strains with KL57, PEA128 — 95.5% of strains with KL64, and ChM-G5 — 69.6% of strains with KL102. Whole-genome sequencing and subsequent bioinformatic analysis revealed that the phages belong to the Autographiviridae family and are classified into three genera.The lytic spectrum of phages was limited to specific capsular types due to the presence of specific receptor-binding proteins, polysaccharide depolymerases. The isolated bacteriophages were strictly virulent, did not carry harmful genetic determinants, and had a specific host range, making them applicable in therapeutic practice for combating antibiotic-resistant infections caused by K. pneumoniae.

Brazilian Clinical Strains of Actinobacillus pleuropneumoniae and Pasteurella multocida: Capsular Diversity, Antimicrobial Susceptibility (In Vitro) and Proof of Concept for Prevention of Natural Colonization by Multi-Doses Protocol of Tildipirosin.

One hundred Actinobacillus pleuropneumoniae (App) and sixty Pasteurella multocida subsp. multocida serogroup A (PmA) isolates were recovered from porcine pneumonic lungs collected from eight central or southern states of Brazil between 2014 and 2018 (App) or between 2017 and 2021 (PmA). A. pleuropneumoniae clinical isolates were typed by multiplex PCR and the most prevalent serovars were 8, 7 and 5 (43, 25% and 18%, respectively). In addition, three virulence genes were assessed in P. multocida isolates, all being positive to capA (PmA) and kmt1 genes, all negative to capD and toxA, and most of them (85%) negative to pfhA gene. The susceptibility of both pathogens to tildipirosin was investigated using a broth microdilution assay. The percentage of isolates susceptible to tildipirosin was 95% for App and 73.3% for PmA. The MIC50 values were 0.25 and 1 μg/mL and the MIC90 values were 4 and >64 μg/mL for App and PmA, respectively. Finally, a multiple-dose protocol of tildipirosin was tested in suckling piglets on a farm endemic for both pathogens. Tildipirosin was able to prevent the natural colonization of the tonsils by App and PmA and significantly (p < 0.0001) reduced the burden of Glaesserella parasuis in this tissue. In summary, our results demonstrate that: (i) tildipirosin can be included in the list of antibiotics to control outbreaks of lung disease caused by App regardless of the capsular type, and (ii) in the case of clinical strains of App and PmA that are sensitive to tildipirosin based on susceptibility testing, the use of this antibiotic in eradication programs for A. pleuropneumoniae and P. multocida can be strongly recommended.

Comparison of next generation technologies and bioinformatics pipelines for capsular typing of Streptococcus pneumoniae.

Whole genome sequencing (WGS)-based approaches for pneumococcal capsular typing have become an alternative to serological methods. In silico serotyping from WGS has not yet been applied to long-read sequences produced by third-generation technologies. The objective of the study was to determine the capsular types of pneumococci causing invasive disease in Catalonia (Spain) using serological typing and WGS and to compare the performance of different bioinformatics pipelines using short- and long-read data from WGS. All invasive pneumococcal pediatric isolates collected in Hospital Sant Joan de Déu (Barcelona) from 2013 to 2019 were included. Isolates were assigned a capsular type by serological testing based on anticapsular antisera and by different WGS-based pipelines: Illumina sequencing followed by serotyping with PneumoCaT, SeroBA, and Pathogenwatch vs MinION-ONT sequencing coupled with serotyping by Pathogenwatch from pneumococcal assembled genomes. A total of 119 out of 121 pneumococcal isolates were available for sequencing. Twenty-nine different serotypes were identified by serological typing, with 24F (n = 17; 14.3%), 14 (n = 10; 8.4%), and 15B/C (n = 8; 6.7%) being the most common serotypes. WGS-based pipelines showed initial concordance with serological typing (>91% of accuracy). The main discrepant results were found at the serotype level within a serogroup: 6A/B, 6C/D, 9A/V, 11A/D, and 18B/C. Only one discrepancy at the serogroup level was observed: serotype 29 by serological testing and serotype 35B/D by all WGS-based pipelines. Thus, bioinformatics WGS-based pipelines, including those using third-generation sequencing, are useful for pneumococcal capsular assignment. Possible discrepancies between serological typing and WGS-based approaches should be considered in pneumococcal capsular-type surveillance studies.

Characteristics of Haemophilus influenzae carriage among healthy children in China: A meta-analysis.

Haemophilus influenzae (Hi) commonly causes invasive and noninvasive bacterial infections. Nationwide investigation on the carriage characteristics of H influenzae in healthy children in China is lacking. We reviewed the prevalence of H influenzae infections in this population. PubMed, CNKI, Wanfang, VIP, and CBM databases were electronically searched to collect cross-sectional studies on the prevalence of Hi among healthy children in China from inception to November 2021. Two reviewers independently screened the literature, extracted the data, and assessed the risk of bias in the included studies. Meta-analysis was performed using Stata 14.0. A total of 28 studies involving 14,301 children were included, among whom there were 2878 children with Hi. The pooled carriage rate of Hi was 0.21 (95% CI: 0.17-0.25). Subgroup analysis indicated no significant sex- or age-related differences. The proportion of Hi in winter (29%) was higher than that in other seasons. Results indicated significant differences among the provinces, with carriage proportions ranging from 0.11 to 0.60. The proportion of nontypeable H influenzae (NTHi) was higher than that of the capsular type. The proportion of Hib in the capsular type (2%) was higher than that in other serotypes. The carriage rate of Hi in healthy children in China was 21% with no sex-related age differences. The proportion of Hi in winter was high, and the proportions of Hi in different regions were significantly different. NTHi was the predominant serotype detected in children.

Exploring Streptococcus pneumoniae capsular typing through MALDI-TOF mass spectrometry and machine-learning algorithms in Argentina: Identifying prevalent NON PCV13 serotypes alongside PCV13 serotypes

IntroductionLaboratory surveillance of Streptococcus pneumoniae serotypes plays a crucial role in effectively implementing vaccines to prevent invasive pneumococcal diseases. The conventional method of serotyping, known as the Quellung reaction, is both time-consuming and expensive. However, the emergence of MALDI-TOF MS technology has revolutionized microbiology laboratories by enabling rapid and cost-effective serotyping based on protein profiles. ObjectivesIn this study, we aimed to investigate the viability of utilizing MALDI-TOF MS technology as an adjunctive and screening method for capsular typing of Streptococcus pneumoniae. Our approach involved developing classification models based on MALDI-TOF MS to discern between Streptococcus pneumoniae strains originating from PCV13 (13-valent pneumococcal conjugate vaccine) and NON PCV13 isolates. MethodsFirstly, we established a comprehensive spectral database comprising isolates of serotypes present in the PCV13 vaccine, along with the top 10 most prevalent NON PCV13 serotypes based on local epidemiological data. This database served as a foundation for developing unsupervised models utilizing MALDI-TOF MS spectra, which enabled us to identify inherent patterns and relationships within the data. Our analysis involved a dataset comprising 215 new isolates collected from nationwide surveillance in Argentina. Our approach involved developing classification models based on MALDI-TOF MS to discern between Streptococcus pneumoniae strains originating from PCV13 (13-valent pneumococcal conjugate vaccine) and NON PCV13 isolates. ResultsAlthough our findings revealed suboptimal performance in serotype classification, they provide valuable insights into the potential of machine learning algorithms in this context. The sensitivity of the models ranged from 0.41 to 0.46, indicating their ability to detect certain serotypes. The observed specificity consistently remained at 0.60, suggesting a moderate level of accuracy in identifying non-vaccine serotypes. These results highlight the need for further refinement and optimization of the algorithms to enhance their discriminative power and predictive accuracy in serotype identification.By addressing the limitations identified in this study, such as exploring alternative feature selection techniques or optimizing algorithm parameters, we can unlock the full potential of machine learning in robust and reliable serotype classification of S. pneumoniae. Our work not only provides a comprehensive evaluation of multiple machine learning models but also emphasizes the importance of considering their strengths and limitations. ConclusionOverall, our study contributes to the growing body of research on utilizing MALDI-TOF MS and machine learning algorithms for serotype identification purposes.

Analysis of the capsular bend in posterior capsular opacification using anterior segment optical coherence tomography

PurposeTo investigate the link between the capsular bend and the morphological types and characteristics of posterior capsular opacification (PCO) using anterior segment optical coherence tomography.MethodsThirty eyes with PCO were examined, and three types of PCO were identified: pearl, fibrosis, and mixed. We assessed anterior capsular overlap, intraocular lens-capsule adhesion, and capsular bending. In addition to measuring the intraocular lens-posterior capsule distance and capsule bending angle (CBA), the PCO parameters (area, density, and score at 6-, 5-, and 3-mm intraocular lens optic regions) were recorded. The associations between capsular bend and PCO type and characteristics were investigated. A control group of 12 eyes without PCO was used to compare the study variables.ResultsWith p values greater than 0.001, there was a statistically significant difference in the mean PCO area and score at the 6-, 5-, and 3-mm optic zones in different PCO types, with the pearl type having the highest value, followed by the mixed type, and finally the fibrosis type. The PCO group had a significantly higher mean CBA than the control group (P = 0.001). CBA was positively related to intraocular lens-posterior capsule distance, PCO area, and PCO score at the 6-, 5-, and 3-mm zones (P = 0.001). The receiver operating characteristic curve's cut-off point for CBA was 96.85° when comparing PCO cases to controls. Partial overlap and incomplete adhesion were statistically more common in the PCO eyes than in the control (P = 0.001, 0.003, respectively).ConclusionPCO types and CBA have a strong relationship with PCO score and intraocular lens-posterior capsule space. In PCO's eyes, CBA has a cut-off value of 96.85°.

Broad-range capsule-dependent lytic Sugarlandvirus against Klebsiella sp.

The emergence of antibiotic-resistant bacteria has become a serious global health threat requiring the development of novel treatments. Klebsiella pneumoniae is an encapsulated bacterium considered a major concern due to its high resistance, prevalence, and mortality rates. Phage therapy has been proposed as a very promising alternative to combat infections by Klebsiella sp. infections. However, most of the Klebsiella phages described so far present a high specificity, infecting one or a few capsular types due to the presence of depolymerases in their genomes, which limits their therapeutic potential. Here, we present three new Klebsiella phages isolated from the environment, vB_Kpn_K7PH164C4, vB_Kpn_K30λ2.2, and vB_Kpl_K32PH164C1, belonging to the family Demerecviridae and the genus Sugarlandvirus. The most important feature of these new Klebsiella phages is their broad host range, especially vB_Kpn_K7PH164C4 and vB_Kpn_K30λ2.2, which infects strains of more than 20 different capsular types, representing the broadest infection range observed for Klebsiella phages. Genomic analysis revealed the presence of three receptor-binding proteins lacking depolymerase domains. Nevertheless, capsule expression is suggested to be a determining factor in phage infectivity, despite the absence of depolymerase activity against capsular components. Our findings hold potential for the development of promising phage-based therapeutics directed against K. pneumoniae.IMPORTANCEThe emergence of multi-drug resistant bacteria is a global health problem. Among them, Klebsiella pneumoniae is considered a high-priority pathogen, making it necessary to develop new therapeutic tools to reduce the bacterial burden in an effective and sustainable manner. Phages, bacterial viruses, are very promising tools. However, phages are highy specific, rendering large-scale therapeutics costly to implement. This is especially certain in Klebsiella, a capsular bacterium in which phages have been shown to be capsular type dependent, infecting one or a few capsular types through specific enzymes called depolymerases. In this study, we have isolated and characterized novel phages with lytic ability against bacteria from a wide variety of capsular types, representing the Klebsiella phages with the widest range of infection described. Remarkably, these broad-range phages showed capsule dependency, despite the absence of depolymerases in their genomes, implying that infectivity could be governed by alternative mechanisms yet to be uncovered.

Pathology, virulence associated gene profiling, antimicrobial susceptibility and pathogenicity of untypeable capsular serotypes of Pasteurella multocida isolated from slaughtered pigs of India.

Pasteurella multocida is widely distributed in all pig-rearing countries, affecting the economic viability and profitability of pig production. The present research highlights the molecular characterization and pathology of untypeable capsular serotypes of P. multocida in slaughtered pigs from prominent pig-rearing states of India. The prevalence of Pasteurellosis was 27.17% by PM-PCR assay, while isolation rate was 7.62%. The microscopic lesions of bronchopneumonia, tonsillitis, and the presence of bacterial antigens in IHC confirmed P. multocida with pathologies. In capsular typing, the majority of the isolates were untypeable with prevalence of 52.15% and 43.58% in molecular and microbiological methods respectively. All the isolates showed the uniform distribution of virulence genes such as exbB, nanB, sodC, plpB, and oma87 (100%), while the variations were observed in ptfA, hasR, ptfA, pfhA, hsf-1, and plpE genes. The untypeable isolates showed higher prevalence of hsf-1 gene as compared to others. The untypeable serotypes showed a higher degree of resistance to ampicillin, amoxicillin, and penicillin antibiotics. The mouse pathogenicity testing of untypeable capsular isolates confirmed its pathogenic potential. The higher frequency of pathogenic untypeable isolates with antibiotic resistance profile might pose a serious threat to the pigs, and therefore, preventive measures should be adopted for effective control.

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.

The enigmatical manipulators in the capsule synthesis of Pasteurella multocida: Iron acquisition proteins

Aim: Spontaneous capsular loss or capsular changes in Pasteurella multocida can result from repeated laboratory passages, positive or negative regulatory genes, or an unknown gene. This study, it was aimed to compare the properties of phenotypic, genotypic, and biotypic of each non-typical, and typical Pasteu-rella multocida strain, to determine the dominant genes on capsule synthesis. Materials and Methods: Fifty-six strains, which capsular type was determined, and thirty -six, which capsular type was not determined, were used in this study. Multiple linear regression analysis was used based on the presence of dominant genes (serogroup, serotype, toxin, adhesin, iron acquisition, and protectin) in the isolates. Results: When colony morphologies of strains were evaluated of these strains by culture methods, mucoid colony formation was commonly detected in typical strains (87.5%), in contrast to non-typical strains (27.7%). In typical strains, the highest percentages of ptfA, ompA, and tadD genes were 78.57%, 75%, and 69.64%, respectively. In non-typical strains, the highest rates of ompA, ptfA, and tadD genes were 61.1%, 52.78%, and 52.78%, respectively. According to multiple linear regression analysis results, the together hgbA with hgbB genes caused the increase of capsule synthesis in these strains. The presence of the ompA gene in these strains was secondly a induction on these strains. Other genes were not effective in capsule synthesis in these strains. Conclusion: It was determined that the most significant effect in the forming of non-typical P. multocida strains was related to not enough HgbA and HgbB genes. It was supposed that P. multocida may not be heavily encapsulated under iron-restricted conditions. Consequently, P. multocida may change its capsule or lose its capsule related to iron acquisition proteins.

Investigation of carbapenem-resistant Klebsiella pneumoniae in Taiwan revealed strains co-harbouring blaNDM and blaOXA-48-like and a novel plasmid co-carrying blaNDM-1 and blaOXA-181

The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) is related to the transmission of carbapenemase genes. Strains carrying more than one carbapenemase with a broadened spectrum of antibiotic resistance have been detected, which is concerning. Although blaKPC-encoding ST11-KL47/KL64 strains are dominant, other clones are emerging. This study investigated 137 CRKP from patients' blood samples in Taiwan. Polymerase chain reaction (PCR) was used to identify carbapenemase genes and capsular (KL) types. Most strains (56%, 77/137) possessed blaKPC alone; however, 12% (17/137) carried blaNDM+blaOXA-48-like and these strains showed high resistance to imipenem and meropenem. Strains carrying blaNDM+blaOXA-48-like predominantly belonged to KL51 (n=15), followed by KL64 (n=1) and KL47 (n=1). Whole-genome sequencing of one KL51 strain indicated that blaNDM-4 and blaOXA-181 are carried on two different plasmids. PCR was performed using specific primers located in these plasmids, and all blaNDM+blaOXA-48-like-encoding strains except the KL64 strain were considered to carry the two abovementioned plasmids. Genome analysis for the KL64 strain revealed that blaNDM-1 and blaOXA-181 are encoded in one plasmid. Notably, the KL51 blaOXA-181 plasmid shared high sequence similarity with the KL64 blaNDM-1+blaOXA-181 plasmid, except the KL64 plasmid comprised a 15,040-bp insertion encoding blaNDM-1. The data revealed KL51 as a predominant KL type carrying blaNDM-4+blaOXA-181, and identified a novel plasmid carrying blaNDM-1+blaOXA-181, highlighting the spread of specific plasmids and clones of CRKP in Taiwan.

Multi-approach methods to predict cryptic carbapenem resistance mechanisms in Klebsiella pneumoniae detected in Central Italy.

The rapid emergence of carbapenem-resistant Klebsiella pneumoniae (Kp) strains in diverse environmental niches, even outside of the clinical setting, poses a challenge for the detection and the real-time monitoring of novel antimicrobial resistance trends using molecular and whole genome sequencing-based methods. The aim of our study was to understand cryptic resistance determinants responsible for the phenotypic carbapenem resistance observed in strains circulating in Italy by using a combined approach involving whole genome sequencing (WGS) and genome-wide association study (GWAS). In this study, we collected 303 Kp strains from inside and outside clinical settings between 2018-2022 in the Abruzzo region of Italy. The antimicrobial resistance profile of all isolates was assessed using both phenotypic and bioinformatic methods. We identified 11 strains resistant to carbapenems, which did not carry any known genetic determinants explaining their phenotype. The GWAS results showed that incongruent carbapenem-resistant phenotype was associated specifically with strains with two capsular types, KL13 and KL116 including genes involved in the capsule synthesis, encoding proteins involved in the assembly of the capsule biosynthesis apparatus, capsule-specific sugar synthesis, processing and export, polysaccharide pyruvyl transferase, and lipopolysaccharide biosynthesis protein. These preliminary results confirmed the potential of GWAS in identifying genetic variants present in KL13 and KL116 that could be associated with carbapenem resistance traits in Kp. The implementation of advanced methods, such as GWAS with increased antimicrobial resistance surveillance will potentially improve Kp infection treatment and patient outcomes.

Dissemination of the high-risk cloneST147 carbapenem-resistant klebsiella pneumoniae from a local tertiary care hospital in the Republic of Korea

BackgroundThe emergence of carbapenem-resistant Enterobacterales (CRE) infections is rapidly increasing and represents a serious public threat. In 2020, a total of 16,883 carbapenemase-producing Enterobacterales strains were collected; among these isolates, 21 strains were repeatedly isolated in a local tertiary care hospital.MethodsAntimicrobial susceptibility testing was performed using the broth microdilution method. All 21 strains of CRKP were analyzed by PFGE after XbaI digestion. The 21 CRKP strains were sequenced on the Illumina Miseq and Oxford Nanopore GridION platforms.ResultsThese 21 CRKP isolates showed an identical antimicrobial resistance profile, including resistance to ampicillin, carbapenems, cephems, chloramphenicol, fluoroquinolone, macrolides and trimethoprim/sulfamethoxazole. Based on whole-genome analysis, these 21 CRKP isolates shared a common genetic structure (ISAba125-IS630-blaNDM−1-bleMBL) and harbored additional resistance determinants (blaOXA−1, blaCTX−M−15, blaSHV−11, blaSHV−67, aac(6’)-Ib-cr, qnrS1, OqxA, OqxB, catB3, mph(A), sul1, and dfrA12) and mutations in the quinolone resistance-determining regions of gyrA (S83I) and parC (S80I). These isolates belonged to the ST147 and KL64 capsular types, which were carried on IncFIB replicon plasmids. The 21 CRKP strains collected from one hospital were divided into five PFGE patterns, and they were closely related with a minimum similarity value of 95.2%. These isolates were found to be highly related based on the presence of between 2 and 27 SNPs.ConclusionsThese findings indicate that NDM-1-producing K. pneumoniae ST147 may have been introduced via a common source, implying nosocomial transmission; furthermore, continuous monitoring is necessary to prevent endemic transmission.

Multidrug-Resistant and Extensively Drug-Resistant Acinetobacter baumannii Causing Nosocomial Meningitis in the Neurological Intensive Care Unit.

Acinetobacter baumannii is one of the significant healthcare-associated meningitis agents characterized by multidrug resistance and a high mortality risk. Thirty-seven A. baumannii strains were isolated from thirty-seven patients of Moscow neuro-ICU with meningitis in 2013-2020. The death rate was 37.8%. Strain susceptibility to antimicrobials was determined on the Vitek-2 instrument. Whole-genome sequencing was conducted using Illumina technology; the sequence types (ST), capsular types (KL), lipooligosaccharide outer core locus (OCL), antimicrobial resistance genes, and virulence genes were identified. The prevalent ST was ST2, belonging to the international clone IC2, and rarer, ST1, ST19, ST45, ST78, ST106, and ST400, with prevalence of KL9 and OCL1. Twenty-nine strains belonged to multidrug-resistant (MDR) and eight extensively drug-resistant (XDR) categories. Genes conferring resistance to beta-lactams (blaPER, blaGES, blaADC, blaCARB, blaCTX-M, blaTEM, and blaOXA-types), aminoglycosides (aac, aad, ant, aph, and arm), tetracyclines (tet), macrolides (msr and mph), phenicols (cml, cat, and flo), sulfonamides (dfr and sul), rifampin (arr), and antiseptics (qac) were identified. Virulence genes of nine groups (Adherence, Biofilm formation, Enzymes, Immune evasion, Iron uptake, Regulation, Serum resistance, Stress adaptation, and Antiphagocytosis) were detected. The study highlights the heterogeneity in genetic clones, antimicrobial resistance, and virulence genes variability among the agents of A. baumannii meningitis, with the prevalence of the dominant international clone IC2.