Molecular characterization of NDM-1-producing Klebsiella pneumoniae ST29, ST347, ST1224, and ST2558 causing sepsis in neonates in a tertiary care hospital of North-East India

Dramatic increase in antimicrobial resistance in ESKAPE clinical isolates over the 2010-2020 decade in India

RATIONALE AND OBJECTIVES

ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) constitute a threat to humans worldwide. India is now the most populous country. The goal was to investigate the evolution of the rates of antimicrobial resistance in ESKAPE pathogens across India over the 2010-20 decade.

METHODS

The data (89 studies) were retrieved from the Medline PubMed repository using specific keywords.

RESULTS

The study of 20 177 ESKAPE isolates showed that A. baumannii isolates were the most represented (35.9%, n = 7238), followed by P. aeruginosa (25.3%, n = 5113), K. pneumoniae (19.5%, n = 3934), S. aureus (16.3%, n = 3286), E. faecium (2.6%, n = 517) and Enterobacter spp. (0.4%, n = 89). A notable increase in the resistance rates to antimicrobial agents occurred over the 2010-20 decade. The most important levels of resistance were observed in 2016-20 for A. baumannii (90% of resistance to the amoxicillin-clavulanate combination) and K. pneumoniae (81.6% of resistance to gentamycin). The rise in β-lactamase activities was correlated with an increase in the positivity of Gram-negative isolates for β-lactamase genes.

CONCLUSIONS

This review highlighted that, in contrast to developed countries that kept resistance levels under control, a considerable increase in resistance to various classes of antibiotics occurred in ESKAPE pathogens in India over the 2010-2020 decade.

Use of ECT in Autism Spectrum Disorder and/or Intellectual Disability: A Single Site Retrospective Analysis

Autism spectrum disorder (ASD) and intellectual disability (ID) are heterogenous and prevalent conditions which may occur in isolation or as a co-morbidity. Psychiatric co-morbidity is common with limited treatment options. Preliminary research into electroconvulsive therapy (ECT) for these conditions has been encouraging. Thus, further research in this patient population is warranted. We conducted a 10-year retrospective review of the electronic medical record and identified intellectually capable individuals with ASD (IC-ASD), and those with ASD+ID or ID who received at least three ECT treatments. 32 patients were identified of which 30 (94%) experienced positive clinical response, defined as a clinical global impression-improvement (CGI-I) score of 3 or less. The average retrospective CGI-I score across all groups was 1.97, and results of a t-test performed on CGI-I scores indicated improvement across all groups [t = - 16.54, df = 31, p < 0.001, 95% CI = (1.72, 2.22)]. No significant adverse events were identified based on clinical documentation. Our findings further support previous ECT research in this patient population.

Treatment Response of Transcranial Magnetic Stimulation in Intellectually Capable Youth and Young Adults with Autism Spectrum Disorder: A Systematic Review and Meta-Analysis

To examine current clinical research on the use of transcranial magnetic stimulation (TMS) in the treatment of pediatric and young adult autism spectrum disorder in intellectually capable persons (IC-ASD). We searched peer-reviewed international literature to identify clinical trials investigating TMS as a treatment for behavioral and cognitive symptoms of IC-ASD. We identified sixteen studies and were able to conduct a meta-analysis on twelve of these studies. Seven were open-label or used neurotypical controls for baseline cognitive data, and nine were controlled trials. In the latter, waitlist control groups were often used over sham TMS. Only one study conducted a randomized, parallel, double-blind, and sham controlled trial. Favorable safety data was reported in low frequency repetitive TMS, high frequency repetitive TMS, and intermittent theta burst studies. Compared to TMS research of other neuropsychiatric conditions, significantly lower total TMS pulses were delivered in treatment and neuronavigation was not regularly utilized. Quantitatively, our multivariate meta-analysis results report improvement in cognitive outcomes (pooled Hedges' g = 0.735, 95% CI = 0.242, 1.228; p = 0.009) and primarily Criterion B symptomology of IC-ASD (pooled Hedges' g = 0.435, 95% CI = 0.359, 0.511; p < 0.001) with low frequency repetitive TMS to the dorsolateral prefrontal cortex. The results of our systematic review and meta-analysis data indicate that TMS may offer a promising and safe treatment option for pediatric and young adult patients with IC-ASD. However, future work should include use of neuronavigation software, theta burst protocols, targeting of various brain regions, and robust study design before clinical recommendations can be made.

Prevalence and clonal diversity of carbapenem-resistant Klebsiella pneumoniae causing neonatal infections: A systematic review of 128 articles across 30 countries

BACKGROUND

Klebsiella pneumoniae is the most common pathogen causing neonatal infections, leading to high mortality worldwide. Along with increasing antimicrobial use in neonates, carbapenem-resistant K. pneumoniae (CRKP) has emerged as a severe challenge for infection control and treatment. However, no comprehensive systematic review is available to describe the global epidemiology of neonatal CRKP infections. We therefore performed a systematic review of available data worldwide and combined a genome-based analysis to address the prevalence, clonal diversity, and carbapenem resistance genes of CRKP causing neonatal infections.

METHODS AND FINDINGS

We performed a systematic review of studies reporting population-based neonatal infections caused by CRKP in combination with a genome-based analysis of all publicly available CRKP genomes with neonatal origins. We searched multiple databases (PubMed, Web of Science, Embase, Ovid MEDLINE, Cochrane, bioRxiv, and medRxiv) to identify studies that have reported data of neonatal CRKP infections up to June 30, 2022. We included studies addressing the prevalence of CRKP infections and colonization in neonates but excluded studies lacking the numbers of neonates, the geographical location, or independent data on Klebsiella or CRKP isolates. We used narrative synthesis for pooling data with JMP statistical software. We identified 8,558 articles and excluding those that did not meet inclusion criteria. We included 128 studies, none of which were preprints, comprising 127,583 neonates in 30 countries including 21 low- and middle-income countries (LMICs) for analysis. We found that bloodstream infection is the most common infection type in reported data. We estimated that the pooled global prevalence of CRKP infections in hospitalized neonates was 0.3% (95% confidence interval [CI], 0.2% to 0.3%). Based on 21 studies reporting patient outcomes, we found that the pooled mortality of neonatal CRKP infections was 22.9% (95% CI, 13.0% to 32.9%). A total of 535 neonatal CRKP genomes were identified from GenBank including Sequence Read Archive, of which 204 were not linked to any publications. We incorporated the 204 genomes with a literature review for understanding the species distribution, clonal diversity, and carbapenemase types. We identified 146 sequence types (STs) for neonatal CRKP strains and found that ST17, ST11, and ST15 were the 3 most common lineages. In particular, ST17 CRKP has been seen in neonates in 8 countries across 4 continents. The vast majority (75.3%) of the 1,592 neonatal CRKP strains available for analyzing carbapenemase have genes encoding metallo-β-lactamases and NDM (New Delhi metallo-β-lactamase) appeared to be the most common carbapenemase (64.3%). The main limitation of this study is the absence or scarcity of data from North America, South America, and Oceania.

CONCLUSIONS

CRKP contributes to a considerable number of neonatal infections and leads to significant neonatal mortality. Neonatal CRKP strains are highly diverse, while ST17 is globally prevalent and merits early detection for treatment and prevention. The dominance of blaNDM carbapenemase genes imposes challenges on therapeutic options in neonates and supports the continued inhibitor-related drug discovery.

Hypervirulent Klebsiella pneumoniae Causing Neonatal Bloodstream Infections: Emergence of NDM-1-Producing Hypervirulent ST11-K2 and ST15-K54 Strains Possessing pLVPK-Associated Markers

Klebsiella pneumoniae is a major cause of neonatal sepsis. Hypervirulent Klebsiella pneumoniae (hvKP) that cause invasive infections and/or carbapenem-resistant hvKP (CR-hvKP) limit therapeutic options. Such strains causing neonatal sepsis have rarely been studied. Characterization of neonatal septicemic hvKP/CR-hvKP strains in terms of resistance and virulence was carried out. Antibiotic susceptibility, molecular characterization, evaluation of clonality, in vitro virulence, and transmissibility of carbapenemase genes were evaluated. Whole-genome sequencing (WGS) and mouse lethality assays were performed on strains harboring pLVPK-associated markers. About one-fourth (26%, 28/107) of the studied strains, leading to mortality in 39% (11/28) of the infected neonates, were categorized as hvKP. hvKP-K2 was the prevalent pathotype (64.2%, 18/28), but K54 and K57 were also identified. Most strains were clonally diverse belonging to 12 sequence types, of which ST14 was most common. Majority of hvKPs possessed virulence determinants, strong biofilm-forming, and high serum resistance ability. Nine hvKPs were carbapenem-resistant, harboring blaNDM-1/blaNDM-5 on conjugative plasmids of different replicon types. Two NDM-1-producing high-risk clones, ST11 and ST15, had pLVPK-associated markers (rmpA, rmpA2, iroBCDEN, iucABCDiutA, and peg-344), of which one co-transferred the markers along with blaNDM-1. The 2 strains revealed high inter-genomic resemblance with the other hvKP reference genomes, and were lethal in mouse model. To the best of our knowledge, this study is the first to report on the NDM-1-producing hvKP ST11-K2 and ST15-K54 strains causing fatal neonatal sepsis. The presence of pLVPK-associated markers and blaNDM-1 in high-risk clones, and the co-transmission of these genes via conjugation calls for surveillance of these strains. IMPORTANCE Klebsiella pneumoniae is a leading cause of sepsis in newborns and adults. Among the 2 major pathotypes of K. pneumoniae, classical (cKP) and hypervirulent (hvKP), hvKP causes community-acquired severe fatal invasive infections in even healthy individuals, as it possesses several virulence factors. The lack of comprehensive studies on neonatal septicemic hvKPs prompted this work. Nearly 26% diverse hvKP strains were recovered possessing several resistance and virulence determinants. The majority of them exhibited strong biofilm-forming and high serum resistance ability. Nine of these strains were also carbapenem (last-resort antibiotic)-resistant, of which 2 high-risk clones (ST11-K2 and ST15-K54) harbored markers (pLVPK) noted for their virulence, and were lethal in the mouse model. Genome-level characterization of the high-risk clones showed resemblance with the other hvKP reference genomes. The presence of transmissible carbapenem-resistant gene, blaNDM, along with pLVPK-markers calls for vigilance, as most clinical microbiology laboratories do not test for them.

The crisis of carbapenemase-mediated carbapenem resistance across the human-animal-environmental interface in India

Carbapenems are the decision-making antimicrobials used to combat severe Gram-negative bacterial infections in humans. Carbapenem resistance poses a potential public health emergency, especially in developing countries such as India, accounting for high morbidity, mortality, and healthcare cost. Emergence and transmission of plasmid-mediated "big five" carbapenemase genes including KPC, NDM, IMP, VIM and OXA-48-type among Gram-negative bacteria is spiralling the issue. Carbapenemase-producing carbapenem-resistant organisms (CP-CRO) cause multi- or pan-drug resistance by co-harboring several antibiotic resistance determinants. In addition of human origin, animals and even environmental sites are also the reservoir of CROs. Spillage in food-chains compromises food safety and security and increases the chance of cross-border transmission of these superbugs. Metallo-β-lactamases, mainly NDM-1 producing CROs, are commonly shared between human, animal and environmental interfaces worldwide, including in India. Antimicrobial resistance (AMR) surveillance using the One Health approach has been implemented in Europe, the United-Kingdom and the United-States to mitigate the crisis. This concept is still not implemented in most developing countries, including India, where the burden of antibiotic-resistant bacteria is high. Lack of AMR surveillance in animal and environmental sectors underestimates the cumulative burden of carbapenem resistance resulting in the silent spread of these superbugs. In-depth indiscriminate AMR surveillance focusing on carbapenem resistance is urgently required to develop and deploy effective national policies for preserving the efficacy of carbapenems as last-resort antibiotics in India. Tracking and mapping of international high-risk clones are pivotal for containing the global spread of CP-CRO.

Resistance Phenotype and Molecular Epidemiology of Carbapenem-Resistant Klebsiella pneumoniae Isolated from Nanjing Children's Hospital in Jiangsu Province, China

Objective

The drug resistance phenotype and molecular epidemiological characteristics of carbapenem-resistant Klebsiella pneumoniae (CRKP) were identified among children in Jiangsu Province, China.

Methods

CRKP strains were collected from the Children’s Hospital of Nanjing Medical University from December 2020 to March 2022. CRKP strains were characterized for further study: antimicrobial susceptibility testing, carbapenem resistance genes and homology analysis.

Results

Among 86 strains of CRKP, 85 carried carbapenemase genes; the dominant gene was bla_KPC-2 (88.2%, 75/85), followed by bla_NDM-1 (4.7%, 4/85), bla_NDM-5 (4.7%, 4/85), bla_IMP-8 (2.3%, 2/85), and bla_OXA-181 (1.2%, 1/85). Among the 86 strains of CRKP, one isolate contained both the bla_NDM-5 and bla_OXA-181 genes, which is the first time that Klebsiella pneumoniae has been shown to jointly carry these genes in China. Another CRKP strain did not carry any carbapenemase gene. MLST analysis identified a total of 10 different sequence types, among which sequence type (ST) 11 was the most common. PFGE analysis identified 75 bla_KPC-2-producing CRKP ST11 strains, of which 68 were dominant clusters distributed among 11 different wards, mainly the neonatal medical centre (18 strains), neonatal surgery (17 strains) and cardiac care unit (CCU) (8 strains) wards.

Conclusion

Clonal dissemination of KPC-2-producing CRKP ST11 was observed in multiple departments. Additionally, non-ST11 strains showed high polymorphism based on molecular typing, indicating increasing diversity in CRKP strains. To our knowledge, this is the first report of NDM-5 and OXA-181-coproducing Klebsiella pneumoniae causing infection in children in China, which poses a significant health risk for paediatric patients. Active surveillance and effective control measures are urgently needed to prevent further transmission of these strains among children.

Causative agents of bloodstream infections in two Croatian hospitals and their resistance mechanisms

Blood samples were collected alongside with routine blood cultures (BC) from patients with suspected sepsis, to evaluate the prevalence of different causative agents in patients with bacteraemia. Among 667 blood samples, there were 122 positive BC (18%). Haemoglobin content, platelet number, and systolic blood pressure values were significantly lower in patients with positive BC, whereas serum lactate levels, CRP, creatinine and urea content were significantly higher in patients with positive BC. The rate of multidrug (MDR) or extensively drug resistant (XDR) bacteria was 24% (n = 29): Klebsiella pneumoniae (9), Pseudomonas aeruginosa (9), Acinetobacter baumannii (4), Escherichia coli (1), vancomycin resistant Enterococcus spp (VRE) (3), and methicillin-resistant Staphylococcus aureus MRSA (3). The dominant resistance mechanisms were the production of extended-spectrum β-lactamases, OXA-48 carbapenemase, and colistin resistance in K. pneumoniae, VIM metallo-β-lactamases in P. aeruginosa and OXA-23-like oxacillinases in A. baumannii. The study revealed high rate of MDR strains among positive BCs in Zagreb, Croatia.

Genomic Epidemiology of Carbapenemase-Producing and Colistin-Resistant Enterobacteriaceae among Sepsis Patients in Ethiopia: a Whole-Genome Analysis

Sepsis due to carbapenemase-producing and colistin-resistant Enterobacteriaceae is a global health threat. A multicenter study was conducted between October 2019 and September 2020 at four hospitals located in different parts of Ethiopia. From a total of 1,416 sepsis patients, blood culture was performed. Enterobacteriaceae were confirmed using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS). Carbapenem and colistin susceptibility testing was performed using disk diffusion, broth microdilution, and Etest strip. Enterobacteriaceae isolates (n = 301) were subjected to whole-genome sequencing using Illumina HiSeq 2500. SPAdes version 3.9 was used for genome assembly. Carbapenem and colistin resistance genes, chromosomal point mutations, sequence types, and plasmid replicons were identified using tools at the Center for Genomic Epidemiology. Phylogeny structure was constructed using CSI Phylogeny 1.4. Visualization of trees and metadata was done using iTOL v6.5.2. Among 301 Enterobacteriaceae, 22 Klebsiella pneumoniae, 2 Klebsiella variicola, and 3 Enterobacter cloacae isolates showed reduced susceptibility to meropenem (7% of tested isolates). bla_NDM-1, bla_NDM-5, and bla_OXA-181 were variants of carbapenemase genes detected. Co-occurrence of bla_NDM-5 and bla_OXA-181 was detected with 4 K. pneumoniae strains. K. pneumoniae and K. variicola showed chromosomal alterations of ompK36 and ompk37. Plasmid incompatibility (Inc) groups Col, IncC, IncHI, IncF, IncFII, IncR, and IncX3 were identified among carbapenem-resistant K. pneumoniae and E. cloacae isolates. Two mcr-9 genes were detected from Salmonella species and K. pneumoniae. The dissemination of carbapenemase-producing Enterobacteriaceae in all hospitals is worrying. Multiple carbapenemase genes were detected, with bla_NDM variants the most frequent. The occurrence of colistin-resistant Enterobacteriaceae among sepsis patients is critical. Implementation of effective antimicrobial stewardship is urgently needed.

The Emergence of Carbapenem-Resistant Gram-Negative Bacteria in Mizoram, Northeast India

(Background) Numerous reports on carbapenem resistance in different parts of India have been published, yet there are insufficient studies on the prevalence of antibiotic resistance in the northeast region of the country. This study evaluated the emergence of carbapenem resistance in the clinical isolates collected in Mizoram. (Results) A total of 141 Gram-negative clinical isolates were collected from the two hospitals, including the Civil Hospital in Lunglei and the Synod Hospital in Aizawl. The isolates include Escherichia coli (n = 62, 43.9%), Klebsiella spp. (n = 43, 30.4%), Pseudomonas aeruginosa (n = 9, 6.3%), Serratia marcescens (n = 3, 2.1%), Proteus mirabilis (n = 2, 1.4%), Shigella spp. (n = 4, 2.8%), Enterobacter spp. (n = 6, 4.2%) and Acinetobacter spp. (n = 12, 8.5%). The isolates were found to be resistant to meropenem (11%), colistin (48%), tigecycline (25%) and cefotaxime (50%). A total of four E. coli and one Shigella sonnei encoded the blaOXA-48-like gene. The blaCTX-M-1 gene was detected in 13 isolates, of which eight were E. coli, two Shigella flexneri, and one isolates each of K. pneumoniae, K. oxytoca and Shigella sonnei, respectively. (Conclusion) Carbapenem-resistant Enterobacteriaceae are common among other parts of India, despite limited access to antibiotics, the emergence of resistance in the northeastern region is worrying.

A new and effective genes-based method for phylogenetic analysis of Klebsiella pneumoniae

The exponential increase in the number of genomes deposited in public databases can help us gain a more holistic understanding of the phylogeny and epidemiology of Klebsiella pneumoniae. However, inferring the evolutionary relationships of K. pneumoniae based on big genomic data is challenging for existing methods. In this study, core genes of K. pneumoniae were determined and analysed in terms of differences in GC content, mutation rate, size, and potential functions. We then developed a stable genes-based method for big data analysis and compared it with existing methods. Our new method achieved a higher resolution phylogenetic analysis of K. pneumoniae. Using this genes-based method, we explored global phylogenetic relationships based on a public database of nearly 953 genomes. The results provide useful information to facilitate the phylogenetic and epidemiological analysis of K. pneumoniae, and the findings are relevant for security applications.

Early-Onset Neonatal Sepsis in Low- and Middle-Income Countries: Current Challenges and Future Opportunities

Neonatal sepsis is defined as a systemic infection within the first 28 days of life, with early-onset sepsis (EOS) occurring within the first 72h, although the definition of EOS varies in literature. Whilst the global incidence has dramatically reduced over the last decade, neonatal sepsis remains an important cause of neonatal mortality, highest in low- and middle-income countries (LMICs). Symptoms at the onset of neonatal sepsis can be subtle, and therefore EOS is often difficult to diagnose from clinical presentation and laboratory testing and blood cultures are not always conclusive or accessible, especially in resource limited countries. Although the World Health Organisation (WHO) currently advocates a ß-lactam, and gentamicin for first line treatment, availability and cost influence the empirical antibiotic therapy administered. Antibiotic treatment of neonatal sepsis in LMICs is highly variable, partially caused by factors such as cost of antibiotics (and who pays for them) and access to certain antibiotics. Antimicrobial resistance (AMR) has increased considerably over the past decade and this review discusses current microbiology data available in the context of the diagnosis, and treatment for EOS. Importantly, this review highlights a large variability in data availability, methodology, availability of diagnostics, and aetiology of sepsis pathogens.

Gram-negative neonatal sepsis in low- and lower-middle-income countries and WHO empirical antibiotic recommendations: A systematic review and meta-analysis

BACKGROUND

Neonatal sepsis is a significant global health issue associated with marked regional disparities in mortality. Antimicrobial resistance (AMR) is a growing concern in Gram-negative organisms, which increasingly predominate in neonatal sepsis, and existing WHO empirical antibiotic recommendations may no longer be appropriate. Previous systematic reviews have been limited to specific low- and middle-income countries. We therefore completed a systematic review and meta-analysis of available data from all low- and lower-middle-income countries (LLMICs) since 2010, with a focus on regional differences in Gram-negative infections and AMR.

METHODS AND FINDINGS

All studies published from 1 January 2010 to 21 April 2021 about microbiologically confirmed bloodstream infections or meningitis in neonates and AMR in LLMICs were assessed for eligibility. Small case series, studies with a small number of Gram-negative isolates (<10), and studies with a majority of isolates prior to 2010 were excluded. Main outcomes were pooled proportions of Escherichia coli, Klebsiella, Enterobacter, Pseudomonas, Acinetobacter and AMR. We included 88 studies (4 cohort studies, 3 randomised controlled studies, and 81 cross-sectional studies) comprising 10,458 Gram-negative isolates from 19 LLMICs. No studies were identified outside of Africa and Asia. The estimated pooled proportion of neonatal sepsis caused by Gram-negative organisms was 60% (95% CI 55% to 65%). Klebsiella spp. was the most common, with a pooled proportion of 38% of Gram-negative sepsis (95% CI 33% to 43%). Regional differences were observed, with higher proportions of Acinetobacter spp. in Asia and Klebsiella spp. in Africa. Resistance to aminoglycosides and third-generation cephalosporins ranged from 42% to 69% and from 59% to 84%, respectively. Study limitations include significant heterogeneity among included studies, exclusion of upper-middle-income countries, and potential sampling bias, with the majority of studies from tertiary hospital settings, which may overestimate the burden caused by Gram-negative bacteria.

CONCLUSIONS

Gram-negative bacteria are an important cause of neonatal sepsis in LLMICs and are associated with significant rates of resistance to WHO-recommended first- and second-line empirical antibiotics. AMR surveillance should underpin region-specific empirical treatment recommendations. Meanwhile, a significant global commitment to accessible and effective antimicrobials for neonates is required.

Antibiotic resistance, virulence-associated genes analysis and molecular typing of Klebsiella pneumoniae strains recovered from clinical samples

Klebsiella pneumoniae is a multidrug-resistant (MDR) opportunistic pathogen that causes nosocomial infections. Virulence analysis and molecular typing as powerful approaches can provide relevant information on K. pneumoniae infection. In the current study, antibiotic resistance, virulence-associated genes analysis, as well as molecular typing of K. pneumoniae strains were investigated. Out of 505 clinical samples collected from hospitalized patients, 100 K. pneumoniae strains were isolated by standard microbiological methods and subjected to the phenotypic and genotyping analysis. The highest prevalence of resistance was observed against ciprofloxacin (75%), trimethoprim-sulfamethoxazole (73%) and nitrofurantoin (68%). Virulence associated genes including entB, traT, ybts, magA, iucC, htrA and rmpA were found in 80%, 62%, 75%, 5%, 30%, 72% and 48%, of the isolates, respectively. The prevalence of biofilm-associated genes including mrkA, fimH, and mrkD were equally 88% for all tested isolates. Moreover, the efflux pump genes including AcrAB, TolC and mdtK were observed in 41 (41%), 33 (33%) and 26 (26%) of the strains respectively. A significant statistical association was observed between MDR strains and high expression of efflux pump and biofilm genes. The K. pneumoniae strains were differentiated into 11 different genetic patterns using the repetitive element sequence-based PCR (rep-PCR) technique. High prevalence of resistance, presence of various virulence factors, high level of efflux pump, and biofilm gene expression in diverse clones of K. pneumoniae strains pose an important health issue in clinical settings.

Neonatal Sepsis: The Impact of Carbapenem-Resistant and Hypervirulent Klebsiella pneumoniae

The convergence of a vulnerable population and a notorious pathogen is devastating, as seen in the case of sepsis occurring during the first 28 days of life (neonatal period). Sepsis leads to mortality, particularly in low-income countries (LICs) and lower-middle-income countries (LMICs). Klebsiella pneumoniae, an opportunistic pathogen is a leading cause of neonatal sepsis. The success of K. pneumoniae as a pathogen can be attributed to its multidrug-resistance and hypervirulent-pathotype. Though the WHO still recommends ampicillin and gentamicin for the treatment of neonatal sepsis, K. pneumoniae is rapidly becoming untreatable in this susceptible population. With escalating rates of cephalosporin use in health-care settings, the increasing dependency on carbapenems, a "last resort antibiotic," has led to the emergence of carbapenem-resistant K. pneumoniae (CRKP). CRKP is reported from around the world causing outbreaks of neonatal infections. Carbapenem resistance in CRKP is largely mediated by highly transmissible plasmid-encoded carbapenemase enzymes, including KPC, NDM, and OXA-48-like enzymes. Further, the emergence of a more invasive and highly pathogenic hypervirulent K. pneumoniae (hvKP) pathotype in the clinical context poses an additional challenge to the clinicians. The deadly package of resistance and virulence has already limited therapeutic options in neonates with a compromised defense system. Although there are reports of CRKP infections, a review on neonatal sepsis due to CRKP/ hvKP is scarce. Here, we discuss the current understanding of neonatal sepsis with a focus on the global impact of the CRKP, provide a perspective regarding the possible acquisition and transmission of the CRKP and/or hvKP in neonates, and present strategies to effectively identify and combat these organisms.

Clinical evolution of ST11 carbapenem resistant and hypervirulent Klebsiella pneumoniae

Carbapenem-resistant and hypervirulent K. pneumoniae (CR-HvKP) strains that have emerged recently have caused infections of extremely high mortality in various countries. In this study, we discovered a conjugative plasmid that encodes carbapenem resistance and hypervirulence in a clinical ST86 K2 CR-HvKP, namely 17ZR-91. The conjugative plasmid (p17ZR-91-Vir-KPC) was formed by fusion of a non-conjugative pLVPK-like plasmid and a conjugative bla_KPC-2-bearing plasmid and is present dynamically with two other non-fusion plasmids. Conjugation of p17ZR-91-Vir-KPC to other K. pneumoniae enabled them to rapidly express the carbapenem resistance and hypervirulence phenotypes. More importantly, genome analysis provided direct evidence that p17ZR-91-Vir-KPC could be directly transmitted from K2 CR-HvKP strain, 17ZR-91, to ST11 clinical K. pneumoniae strains to convert them into ST11 CR-HvKP strains, which explains the evolutionary mechanisms of recently emerged ST11 CR-HvKP strains.

Carbapenem-resistant and hypervirulent Klebsiella pneumoniae strains are emerging. Here Xie et al. show that these phenotypes are carried on a plasmid formed from the fusion of a virulence plasmid with a conjugative plasmid.

The present danger of New Delhi metallo-β-lactamase: a threat to public health

The evolution of antimicrobial-resistant Gram-negative pathogens is a substantial menace to public health sectors, notably in developing countries because of the scarcity of healthcare facilities. New Delhi metallo-β-lactamase (NDM) is a potent β-lactam enzyme able to hydrolyze several available antibiotics. NDM was identified from the clinical isolates of Klebsiella pneumoniae and Escherichia coli from a Swedish patient in New Delhi, India. This enzyme horizontally passed on to various Gram-negative bacteria developing resistance against a variety of antibiotics which cause treatment crucial. These bacteria increase fatality rates and play an integral role in the economic burden. The efficient management of NDM-producing isolates requires the coordination between each healthcare setting in a region. In this review, we present the prevalence of NDM in children, fatality and the economic burden of resistant bacteria, the clonal spread of NDM harboring bacteria and modern techniques for the detection of NDM producing pathogens.

Molecular Epidemiology of Carbapenemases in Enterobacteriales from Humans, Animals, Food and the Environment

The Enterobacteriales order consists of seven families including Enterobacteriaceae, Erwiniaceae, Pectobacteriaceae, Yersiniaceae, Hafniaceae, Morganellaceae, and Budviciaceae and 60 genera encompassing over 250 species. The Enterobacteriaceae is currently considered as the most taxonomically diverse among all seven recognized families. The emergence of carbapenem resistance (CR) in Enterobacteriaceae caused by hydrolytic enzymes called carbapenemases has become a major concern worldwide. Carbapenem-resistant Enterobacteriaceae (CRE) isolates have been reported not only in nosocomial and community-acquired pathogens but also in food-producing animals, companion animals, and the environment. The reported carbapenemases in Enterobacteriaceae from different sources belong to the Ambler class A (bla_KPC), class B (bla_IMP, bla_VIM, bla_NDM), and class D (bla_OXA-48) β-lactamases. The carbapenem encoding genes are often located on plasmids or associated with various mobile genetic elements (MGEs) like transposons and integrons, which contribute significantly to their spread. These genes are most of the time associated with other antimicrobial resistance genes such as other β-lactamases, as well as aminoglycosides and fluoroquinolones resistance genes leading to multidrug resistance phenotypes. Control strategies to prevent infections due to CRE and their dissemination in human, animal and food have become necessary. Several factors involved in the emergence of CRE have been described. This review mainly focuses on the molecular epidemiology of carbapenemases in members of Enterobacteriaceae family from humans, animals, food and the environment.

Emergence of NDM-5-Producing Carbapenem-Resistant Klebsiella pneumoniae and SIM-Producing Hypervirulent Klebsiella pneumoniae Isolated from Aseptic Body Fluid in a Large Tertiary Hospital, 2017-2018: Genetic Traits of blaNDM-Like and blaSIM-Like Genes as Determined by NGS

Purpose

To characterize the clinical, resistance, and virulence features of carbapenem-resistant Klebsiella pneumonaie (CRKP) and hypervirulent Klebsiella pneumoniae (hvKP) and also provide an effective selection of drug in CRKP and hvKP treatment.

Materials and Methods

Twelve strains were collected and investigated these isolates for their antimicrobial susceptibility and molecular features. Resistance mechanisms, virulence-associated genes, multilocus sequence typing (MLST), and serotypes were detected by PCR and sequencing. Next general sequencing (NGS) was carried out to determine the features of carbapenem resistance and virulence. The synergistic activity of tigecycline–imipenem (TGC+IPM), tigecycline–meropenem (TGC+MEM), and tigecycline–aztreonam (TGC+ATM) combinations were performed by microdilution checkerboard method.

Results

Eleven CRKP and one hvKP strains were collected. All strains showed highly sensitive rates to tigecycline (TGC) and amikacin (AMK). NDM (33.3%, 4/12) was the main resistance mechanism and MLST assigned 3 of them to ST11. CTX-M-producing (n = 1) and KPC-2-producing (n = 1) isolates belonged to ST147 and ST11, respectively. The MICs of ATM and quinolones in NDM-1 CRKP and NDM-5 CRKP strains were different. The serotype of the majority strains was KL22KL137 (58.3%, 7/12), hvKP stain belonged to K64. CRKP strains harbored plasmid-mediated quinolone resistance genes (oqxA, oqxB, qnrS, qnrB), β-lactams (bla_CTX-M-3), aminoglycosides, type I and type III fimbriae genes, siderophore genes, and transporter and pumps. SIM-producing ST1764 K64 showed typical features of hvKP, showing hypermucoviscosity phenotype. The virulence genes, including rmpA2, alls and aerobactin genes, linked to hvKP, were found in ST1764 hvKP. hvKP was sensitive to quinolone; also, oqxA gene was detected. All TGC combinations showed highly synergistic effects and TGC+IPM was more effective treatment.

Conclusion

We first identified the NDM-5-producing ST690 CRKP and SIM-producing ST1764 hvKP strains in Shanxi province. Tigecycline-carbapenem combinations were available treatments for CRKP.

Epidemic Characteristics of Carbapenem-Resistant Klebsiella pneumoniae in the Pediatric Intensive Care Unit of Yanbian University Hospital, China

Introduction

Carbapenem-resistant Enterobacteriaceae (CRE) pose a serious threat to clinical patient management and public health, as they are generally resistant to most antibiotics and cause infections with high mortality rates. Klebsiella pneumoniae ranks second among Enterobacteriaceae species that cause nosocomial infections. In this study, we investigated the epidemic characteristics of carbapenem-resistant K. pneumoniae (CRKP) in the pediatric intensive care unit (PICU) of Yanbian University Hospital.

Materials and Methods

A total of 14 non-duplicate CRKP strains, collected from March 2015 to November 2019, were subjected to automated microbial identification and antimicrobial susceptibility tests using the Phoenix-100 ID/AST system. The strains were also subjected to genotypic resistance testing, polymerase chain reaction assays to detect genes encoding carbapenemases and other β-lactamases, multi-locus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE)-based homology analysis.

Results

Two carbapenemase genes, KPC-2 and NDM-1 (in eight and six strains, respectively), were detected. MLST enabled the division of the strains into two sequence types, ST11 and ST1224 (containing eight and six strains, respectively). PFGE results classified the 14 strains into clonotypes A–D, of which clonotypes A and B belonged to ST11, while clonotypes C and D belonged to ST1224.

Conclusion

Our study reveals that epidemics of the KPC-2-ST11 and NDM-1-ST1224 strains occurred in the PICU of Yanbian University Hospital. Surveillance and strict implementation of prevention and control measures are crucial to prevent the occurrence and rapid spread of nosocomial infections.

KPC-2-producing Klebsiella pneumoniae ST147 in a neonatal unit: Clonal isolates with differences in colistin susceptibility attributed to AcrAB-TolC pump

This study characterizes four KPC-2-producing Klebsiella pneumoniae isolates from neonates belonging to a single sequence type 147 (ST147) in relation to carbapenem resistance and explores probable mechanisms of differential colistin resistance among the clonal cluster. Whole genome sequencing (WGS) revealed that the isolates were nearly 100% identical and harbored resistance genes (bla_KPC-2,_OXA-9,_CTX-M-15,_SHV-11,_OXA-1,_TEM-1B, oqxA, oqxB, qnrB1, fosA, arr-2, sul1, aacA4, aac(6')Ib-cr, aac(6')Ib), and several virulence genes. bla_KPC-2 was the only carbapenem-resistant gene found, bracketed between ISKpn7 and ISKpn6 of Tn4401b on a non-conjugative IncFII plasmid. Remarkably, one of the clonal isolates was resistant to colistin, the mechanistic basis of which was not apparent from comparative genomics. The transmissible colistin resistance gene, mcr, was absent. Efflux pump inhibitor, carbonyl cyanide 3-chlorophenylhydrazone (CCCP) rendered a 32-fold decrease in the minimum inhibitory concentration (MIC) of colistin in the resistant isolate only. acrB, tolC, ramA, and soxS genes of the AcrAB-TolC pump system overexpressed exclusively in the colistin-resistant isolate, although the corresponding homologs of the AcrAB-TolC pump, regulators and promoters were mutually identical. No change was observed in the expression of other efflux genes (kpnE/F and kpnG/H) or two-component system (TCS) genes (phoP/phoQ, pmrA/pmrB). Colistin resistance in one of the clonal KPC-2-producing isolates is postulated to be due to overexpression of the AcrAB-TolC pump. This study is probably the first to report clinical clonal K. pneumoniae isolates with differences in colistin susceptibility. The presence of carbapenem-resistant isolates with differential behavior in the expression of a genomically identical pump system indicates the nuances of the resistance mechanisms and the difficulty of treatment thereof.

Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia

BACKGROUND

Klebsiella pneumoniae is a leading cause of bloodstream infection (BSI). Strains producing extended-spectrum beta-lactamases (ESBLs) or carbapenemases are considered global priority pathogens for which new treatment and prevention strategies are urgently required, due to severely limited therapeutic options. South and Southeast Asia are major hubs for antimicrobial-resistant (AMR) K. pneumoniae and also for the characteristically antimicrobial-sensitive, community-acquired "hypervirulent" strains. The emergence of hypervirulent AMR strains and lack of data on exopolysaccharide diversity pose a challenge for K. pneumoniae BSI control strategies worldwide.

METHODS

We conducted a retrospective genomic epidemiology study of 365 BSI K. pneumoniae from seven major healthcare facilities across South and Southeast Asia, extracting clinically relevant information (AMR, virulence, K and O antigen loci) using Kleborate, a K. pneumoniae-specific genomic typing tool.

RESULTS

K. pneumoniae BSI isolates were highly diverse, comprising 120 multi-locus sequence types (STs) and 63 K-loci. ESBL and carbapenemase gene frequencies were 47% and 17%, respectively. The aerobactin synthesis locus (iuc), associated with hypervirulence, was detected in 28% of isolates. Importantly, 7% of isolates harboured iuc plus ESBL and/or carbapenemase genes. The latter represent genotypic AMR-virulence convergence, which is generally considered a rare phenomenon but was particularly common among South Asian BSI (17%). Of greatest concern, we identified seven novel plasmids carrying both iuc and AMR genes, raising the prospect of co-transfer of these phenotypes among K. pneumoniae.

CONCLUSIONS

K. pneumoniae BSI in South and Southeast Asia are caused by different STs from those predominating in other regions, and with higher frequency of acquired virulence determinants. K. pneumoniae carrying both iuc and AMR genes were also detected at higher rates than have been reported elsewhere. The study demonstrates how genomics-based surveillance-reporting full molecular profiles including STs, AMR, virulence and serotype locus information-can help standardise comparisons between sites and identify regional differences in pathogen populations.

Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia

BACKGROUND

Klebsiella pneumoniae is a leading cause of bloodstream infection (BSI). Strains producing extended-spectrum beta-lactamases (ESBLs) or carbapenemases are considered global priority pathogens for which new treatment and prevention strategies are urgently required, due to severely limited therapeutic options. South and Southeast Asia are major hubs for antimicrobial-resistant (AMR) K. pneumoniae and also for the characteristically antimicrobial-sensitive, community-acquired "hypervirulent" strains. The emergence of hypervirulent AMR strains and lack of data on exopolysaccharide diversity pose a challenge for K. pneumoniae BSI control strategies worldwide.

METHODS

We conducted a retrospective genomic epidemiology study of 365 BSI K. pneumoniae from seven major healthcare facilities across South and Southeast Asia, extracting clinically relevant information (AMR, virulence, K and O antigen loci) using Kleborate, a K. pneumoniae-specific genomic typing tool.

RESULTS

K. pneumoniae BSI isolates were highly diverse, comprising 120 multi-locus sequence types (STs) and 63 K-loci. ESBL and carbapenemase gene frequencies were 47% and 17%, respectively. The aerobactin synthesis locus (iuc), associated with hypervirulence, was detected in 28% of isolates. Importantly, 7% of isolates harboured iuc plus ESBL and/or carbapenemase genes. The latter represent genotypic AMR-virulence convergence, which is generally considered a rare phenomenon but was particularly common among South Asian BSI (17%). Of greatest concern, we identified seven novel plasmids carrying both iuc and AMR genes, raising the prospect of co-transfer of these phenotypes among K. pneumoniae.

CONCLUSIONS

K. pneumoniae BSI in South and Southeast Asia are caused by different STs from those predominating in other regions, and with higher frequency of acquired virulence determinants. K. pneumoniae carrying both iuc and AMR genes were also detected at higher rates than have been reported elsewhere. The study demonstrates how genomics-based surveillance-reporting full molecular profiles including STs, AMR, virulence and serotype locus information-can help standardise comparisons between sites and identify regional differences in pathogen populations.

Molecular epidemiology of carbapenem-resistance plasmids using publicly available sequences

Carbapenem-resistant bacteria have quickly become a worldwide concern in nosocomial infections. Of the seven known carbapenemases, four have been shown to be particularly problematic: KPC, NDM, IMP, and VIM. To date, many local and species- or carbapenemase-specific epidemiological studies have been performed, which often focus on the organism itself. This report attempts to perform an inclusive (encompass both species and carbapenemase) epidemiologic study using publicly available plasmid sequences from NCBI. In this report, the gene content of these various plasmids has been characterized, replicon types of the plasmids identified, and the global spread and species promiscuity of the plasmids analyzed. Additionally, support to several groups targeting plasmid maintenance and transfer mechanisms to slow the spread of resistance plasmids is given.

Plasmid evolution in carbapenemase-producing Enterobacteriaceae: a review

Carbapenem-resistant Enterobacteriaceae (CRE) have been listed by the WHO as high-priority pathogens owing to their high association with mortalities and morbidities. Resistance to multiple β-lactams complicates effective clinical management of CRE infections. Using plasmid typing methods, a wide distribution of plasmid replicon groups has been reported in CREs around the world, including IncF, N, X, A/C, L/M, R, P, H, I, and W. We performed a literature search for English research papers, published between 2013 and 2018, reporting on plasmid-mediated carbapenem resistance. A rise in both carbapenemase types and associated plasmid replicon groups was seen, with China, Canada, and the United States recording a higher increase than other countries. bla_KPC was the most prevalent, except in Angola and the Czech Republic, where OXA-181 (n = 50, 88%) and OXA-48-like (n = 24, 44%) carbapenemases were most prevalent, respectively; bla_KPC-2/3 accounted for 70% (n = 956) of all reported carbapenemases. IncF plasmids were found to be responsible for disseminating different antibiotic resistance genes worldwide, accounting for almost 40% (n = 254) of plasmid-borne carbapenemases. bla_CTX-M , bla_TEM , bla_SHV , bla_OXA-1/9 , qnr, and aac-(6')-lb were mostly detected concurrently with carbapenemases. Most reported plasmids were conjugative but not present in multiple countries or species, suggesting limited interspecies and interboundary transmission of a common plasmid. A major limitation to effective characterization of plasmid evolution was the use of PCR-based instead of whole-plasmid sequencing-based plasmid typing.