Genomic Investigation Reveals Contaminated Detergent as the Source of an Extended-Spectrum-β-Lactamase-Producing Klebsiella michiganensis Outbreak in a Neonatal Unit

An adapted method for Cas9-mediated editing reveals the species-specific role of β-glucoside utilization driving competition between Klebsiella species

Cas9-based gene editing tools have revolutionized genetics, enabling the fast and precise manipulation of diverse bacterial species. However, widely applicable genetic tools for non-model gut bacteria are unavailable. Here, we present a two-plasmid Cas9-based system designed for gene deletion and knock-in complementation in three members of the Klebsiella oxytoca species complex (KoSC), which we applied to study the genetic factors underlying the role of these bacteria in competition against Klebsiella pneumoniae. Firstly, the system allowed efficient and precise full-length gene deletion via enhanced lambda Red expression. Furthermore, we tested the efficiency of two independent, functionally validated complementation strategies. Ultimately, the insertion of universal "bookmark" targets during gene deletion subsequently allows the most optimal genetic complementation in K. oxytoca, Klebsiella michiganensis, and Klebsiella grimontii. This approach offers a significant advantage by enabling the use of a single high-efficiency "bookmark" for complementing other loci or strains, eliminating the need for site-specific design. We revealed that the carbohydrate permease CasA is critical in ex vivo assays for K. pneumoniae inhibition by K. oxytoca but is neither sufficient nor required for K. michiganensis and K. grimontii. Thus, the adaptation of state-of-the-art genetic tools to KoSC allows the identification of species-specific functions in microbial competition.

IMPORTANCE

Cas9-based gene editing tools have revolutionized bacterial genetics, yet, their application to non-model gut bacteria is frequently hampered by various limitations. We utilized a two-plasmid Cas9-based system designed for gene deletion in Klebsiella pneumoniae and demonstrate after optimization its utility for gene editing in three members of the Klebsiella oxytoca species complex (KoSC) namely K. oxytoca, Klebsiella michiganensis, and Klebsiella grimontii. We then adapted a recently developed protocol for functional complementation based on universal "bookmark" targets applicable to all tested species. In summary, species-specific adaptation of state-of-the-art genetic tools allows efficient gene deletion and complementation in type strains as well as natural isolates of KoSC members to study microbial interactions.

Growth of Gram-Negative Bacteria in Antiseptics, Disinfectants and Hand Hygiene Products in Two Tertiary Care Hospitals in West Africa-A Cross-Sectional Survey

Antiseptics, disinfectants, and hand hygiene products can act as reservoirs of Gram-negative bacteria causing healthcare-associated infections. This problem is rarely documented in low- and middle-income countries, particularly in sub-Saharan Africa. In a cross-sectional survey, we assessed the bacterial contamination of antiseptics, disinfectants, and hand hygiene products in two university hospitals in Burkina Faso and Benin. During ward visits and staff interviews, in-use products were cultured for the presence of Gram-negative bacteria. The growth of Gram-negative bacteria was absent or rare in alcohol-based products, povidone iodine, and Dakin solution. Contamination was highest (73.9% (51/69)) for liquid soap products (versus antiseptic/disinfectants (4.5%, 7/157) (p < 0.0001)), mostly used in high-risk areas and associated with high total bacterial counts (>10,000 colony-forming units/mL). Contaminating flora (105 isolates) included Enterobacterales and the Vibrio non-cholerae/Aeromonas group (17.1%) and non-fermentative Gram-negative rods (82.8%). Multidrug resistance was present among 9/16 Enterobacterales (Klebsiella and Enterobacter spp.) and 3/12 Acinetobacter spp., including carbapenem resistance (Acinetobacter baumannii: NDM, Pseudomonas stutzeri: VIM). The risk factors for contamination included the type of product (cleaning grade and in-house prepared liquid soap), use of recycled disposable containers and soft drink bottles, absence of labeling, topping-up of containers, dilution with tap water (pharmacy and ward), and poor-quality management (procurement, stock management, expiry dates, and period after opening).

GraphSNP: an interactive distance viewer for investigating outbreaks and transmission networks using a graph approach

BACKGROUND

Cluster and transmission analysis utilising pairwise SNP distance are increasingly used in genomic epidemiological studies. However, current methods are often challenging to install and use, and lack interactive functionalities for easy data exploration.

RESULTS

GraphSNP is an interactive visualisation tool running in a web browser that allows users to rapidly generate pairwise SNP distance networks, investigate SNP distance distributions, identify clusters of related organisms, and reconstruct transmission routes. The functionality of GraphSNP is demonstrated using examples from recent multi-drug resistant bacterial outbreaks in healthcare settings.

CONCLUSIONS

GraphSNP is freely available at https://github.com/nalarbp/graphsnp . An online version of GraphSNP, including demonstration datasets, input templates, and quick start guide is available for use at https://graphsnp.fordelab.com .

Genomic and functional analysis of high-level tigecycline resistant Klebsiella michiganensis co-carrying tet(X4) and tmexCD2-toprJ2 from pork

Tigecycline plays an important role in the clinical treatment of infections caused by multidrug-resistant pathogens. The emergence of plasmid-mediated tigecycline resistance genes tet(X) and tmexCD1-tmexJ1 has been reported in a variety of animal and animal-derived foods, and have the potential spread to humans, seriously limiting the choice of clinical medication. Herein, three ST92 Klebsiella michiganensis isolates co-harboring tet(X4) and tmexCD2-toprJ2 were collected from pork samples in Jiangsu Province, China. These K. michiganensis isolates were all multidrug-resistant isolates. Genome analysis showed that tmexCD2-toprJ2 and tet(X4) were located on IncFIB(K) and IncX1 plasmids, respectively. The IncFIB(K) plasmid pMX581-77k is a novel tmexCD2-toprJ2-bearing plasmid. Worryingly, there were only a small number of SNPs between K. michiganensis isolated from pork in this study and K. michiganensis from human sources, with the possibility of clonal transmission. In addition, tet(X4) and tmexCD2-toprJ2 in K. michiganensis were able to stabilize in the absence of antibiotics. The growth curve indicated that the tmexCD2-toprJ2-positive plasmid imposed a burden on the growth of host bacteria. Interestingly, we found that the high-level resistance phenotype to tigecycline in these K. michiganensis isolates was mainly mediated by tet(X4). However, both tet(X4) and tmexCD2-toprJ2 expression were significantly elevated when host bacteria were exposed to tigecycline. This study systematically investigated K. michiganensis co-carrying tet(X4) and tmexCD2-toprJ2, emphasizing the importance for continuous surveillance of tigecycline-resistant K. michiganensis in animal-derived foods.

Evaluation of Phenotypic Tests to Detect Extended-Spectrum β-Lactamase (ESBL)-Producing Klebsiella oxytoca Complex Strains

Klebsiella oxytoca complex (KoC) species may overproduce their chromosomal class A OXY β-lactamases, conferring reduced susceptibility to piperacillin-tazobactam, expanded-spectrum cephalosporins and aztreonam. Moreover, since clavulanate maintains its ability to inhibit these enzymes, the resulting resistance phenotype may falsely resemble the production of acquired extended-spectrum β-lactamases (ESBLs). In this work, a collection of 44 KoC strains of human and animal origin was characterized with whole-genome sequencing (WGS) and broth microdilution (BMD) susceptibility testing. Comparison of ESBL producers (n = 11; including CTX-M-15 [n = 6] and CTX-M-1 [n = 5] producers) and hyperproducers of OXYs (n = 21) showed certain phenotypic differences: piperacillin-tazobactam (MIC_90s: 16 versus >64 μg/mL), cefotaxime (MIC_90s: 64 versus 4 μg/mL), ceftazidime (MIC_90s: 32 versus 4 μg/mL), cefepime (MIC_90s: 8 versus 4 μg/mL) and associated resistance to non-β-lactams (e.g., trimethoprim-sulfamethoxazole: 90.9% versus 14.3%, respectively). However, a clear phenotype-based distinction between the two groups was difficult. Therefore, we evaluated 10 different inhibitor-based confirmatory tests to allow such categorization. All tests showed a sensitivity of 100%. However, only combination disk tests (CDTs) with cefepime/cefepime-clavulanate and ceftazidime/ceftazidime-clavulanate or the double-disk synergy test (DDST) showed high specificity (100%, 95.5%, and 100%, respectively). All confirmatory tests in BMD or using the MIC gradient strip did not perform well (specificity, ≤87.5%). Of note, ceftazidime/ceftazidime-avibactam tests also exhibited low specificity (CDT, 87.5%; MIC gradient strip, 77.8%). Our results indicate that standard antimicrobial susceptibility profiles can raise some suspicion, but only the use of cefepime/cefepime-clavulanate CDT or DDST can guarantee distinction between ESBL-producing KoC strains and those hyperproducing OXY enzymes.

Clinical Implementation of Routine Whole-genome Sequencing for Hospital Infection Control of Multi-drug Resistant Pathogens

BACKGROUND

Prospective whole-genome sequencing (WGS)-based surveillance may be the optimal approach to rapidly identify transmission of multi-drug resistant (MDR) bacteria in the healthcare setting.

METHODS

We prospectively collected methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), carbapenem-resistant Acinetobacter baumannii (CRAB), extended-spectrum beta-lactamase (ESBL-E), and carbapenemase-producing Enterobacterales (CPE) isolated from blood cultures, sterile sites, or screening specimens across three large tertiary referral hospitals (2 adult, 1 paediatric) in Brisbane, Australia. WGS was used to determine in silico multi-locus sequence typing (MLST) and resistance gene profiling via a bespoke genomic analysis pipeline. Putative transmission events were identified by comparison of core genome single nucleotide polymorphisms (SNPs). Relevant clinical meta-data were combined with genomic analyses via customised automation, collated into hospital-specific reports regularly distributed to infection control teams.

RESULTS

Over 4 years (April 2017 to July 2021) 2660 isolates were sequenced. This included MDR gram-negative bacilli (n = 293 CPE, n = 1309 ESBL), MRSA (n = 620), and VRE (n = 433). A total of 379 clinical reports were issued. Core genome SNP data identified that 33% of isolates formed 76 distinct clusters. Of the 76 clusters, 43 were contained to the 3 target hospitals, suggesting ongoing transmission within the clinical environment. The remaining 33 clusters represented possible inter-hospital transmission events or strains circulating in the community. In 1 hospital, proven negligible transmission of non-multi-resistant MRSA enabled changes to infection control policy.

CONCLUSIONS

Implementation of routine WGS for MDR pathogens in clinical laboratories is feasible and can enable targeted infection prevention and control interventions.

A clinical KPC-producing Klebsiella michiganensis strain carrying IncFII/IncFIA (HI1)/IncFIB (K) multiple replicon plasmid

Klebsiella michiganensis is an increasingly important bacterial pathogen causing nosocomial infections in clinical patients. In this study, we described the molecular and genomic characteristics of a carbapenem-resistant K. michiganensis strain KM166 cultured from a one-month premature baby's blood sample. KM166 showed lower biofilm forming ability in optical density (OD) than K. pneumoniae NTUH-K2044 (0.271 ± 0.027 vs. 0.595 ± 0.054, p = 0.001), and the median lethal dose (0.684 lg CFU/mL) was lower than K. pneumoniae strain NTUH-K2044 (6.679 lg CFU/mL). A IncFII/IncFIA(HI1)/IncFIB(K) multiple replicon plasmid in KM166 was identified carrying three replicon types. It has low homology to Escherichia coli pMRY09-581ECO_1 and the highest homology similarity to the INcFIA/INcFII(p14)-type plasmid in K. michiganensis strain fxq plasmid pB_KPC, suggesting that this multiple replicon plasmid was unlikely to have been transmitted from E. coli and probably a transfer of repFIB replicon genes from other K. michiganensis strains into the INcFIA/INcFII(p14)-type plasmid of KM166 had occurred. Mapping of the gene environment revealed that bla _KPC-2 in KM166 plasmid 3 had high identity and same Tn3-tnpR-IS481-bla _KPC-2-klcA_1 genomic context structure with K. pneumoniae strain JKP55, plasmid pKPC-J5501, and bla _KPC-2-carrying plasmid proved to be autonomously transferred under the help of mobile genetic elements into Escherichia coli 600 by plasmid conjugation experiment. In conclusion, we have characterized a K. michiganensis strain carrying multi-replicon IncFII/IncFIA(HI1)/IncFIB(K) plasmid and bla _KPC-2-carrying IncFII(p14)/IncFIA plasmid in this study, which provided insights about the evolutionary diversity of plasmids carried by K. michiganensis.

Successful Control of an Outbreak by Phenotypically Identified Extended-Spectrum Beta-Lactamase–Producing Klebsiella pneumoniae in a Neonatal Intensive Care Unit

Background: Premature newborns represent a vulnerable population, at high risk of acquiring nosocomial infections during neonatal intensive care unit (NICU) admission. Multidrug-resistant organisms represent the greatest concern due to their intrinsic virulence and the limited therapeutic options. Resistant Enterobacterales are a growing threat for critically ill neonates, with increasing numbers of NICU outbreaks caused by extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales being described. This study reports the early detection and successful control of an outbreak caused by ESBL-producing Klebsiella pneumoniae (ESBL-KP) in an Italian NICU in February 2021. Results: A total of 13 newborns tested positive for ESBL-KP between 2–9 February 2021, of whom four (31%) had a bloodstream infection. Two were critically ill, extremely premature newborns who died because of multiple comorbidities, and two were cured after treatment with meropenem. All other patients survived and were either discharged home or moved to other hospitals/wards in good clinical condition. ESBL-KP ST45 was found in all isolates by multilocus sequence typing (MLST) analysis. An outbreak control plan was set, including surveillance cultures for all neonates, NICU environments, and medical devices, along with the extended use of contact precautions and cohorting. In addition, the infection control plan was carried out through reinforcement and enhancement measures to guarantee maximal compliance. The outbreak was successfully controlled in seven days, given that no further cases were identified after 9 February. The source of the ESBL-KP outbreak was not identified through environmental sampling. Conclusions: Thanks to multidisciplinary management, a threatening outbreak of ESBL-KP in a NICU was controlled in few days. The prompt recognition of the event onset and the adoption of infection control interventions helped contain the bacteria spread on the ward.

Genomic Characterization of a Carbapenemase-Producing, Extensively Drug-Resistant Klebsiella michiganensis Strain from a Renal Abscess Patient

We describe an extensively drug-resistant Klebsiella michiganensis strain, Kmfe267, which was originally isolated from a renal abscess patient. The strain carries the blaNDM-5 gene, which encodes a New Delhi metallo-β-lactamase. The complete genome of the strain contains a 5.9-Mb chromosome and 5 plasmids.

Colorimetric Detection of Urease-Producing Microbes Using an Ammonia-Responsive Flexible Film Sensor

Urease-producing (ureolytic) microbes have given rise to environmental and public health concerns because they are thought to contribute to emissions of ammonia and to be a virulence factor for infections. Therefore, it is highly important to have the ability to detect such microbes. In this study, a poly(dimethylsiloxane) (PDMS)-based colorimetric film sensor was employed for the detection of urease-producing microbes. The sensor was able to detect the enzyme activity of commercially available urease, as the color and absorbance spectrum of the sensor was observed to change upon being exposed to the reaction catalyzed by urease. The ratio of the absorbance of the sensor at 640 nm to that at 460 nm (A₆₄₀/A₄₆₀) was linearly proportional to the amount of urease present. The performance of the sensor was validated by the results of a sensitivity and selectivity analysis towards thirteen different bacterial strains. Based on the development of blue color of the sensor, the tested bacteria were classified as strongly positive, moderately positive, weakly positive, or negative urease producers. The response of the sensor to ureolytic bacteria was verified using the urease inhibitor phenyl phosphorodiamidate (PPDA). Additionally, the sensor achieved the selective detection of ureolytic bacteria even in the presence of non-ureolytic bacteria. In addition, a used sensor could be reverted to its original state by being subjected to simple aeration, and in this way the same sensor could be used at least five times for the detection of bacterial urease activity.

Epidemiology and genomic analysis of Klebsiella oxytoca from a single hospital network in Australia

BACKGROUND

Infections caused by Klebsiella oxytoca are the second most common cause of Klebsiella infections in humans. Most studies have focused on K. oxytoca outbreaks and few have examined the broader clinical context of K. oxytoca.

METHODS

Here, we collected all clinical isolates identified as K. oxytoca in a hospital microbiological diagnostic lab across a 15-month period (n = 239). Whole genome sequencing was performed on a subset of 92 isolates (all invasive, third-generation cephalosporin resistant (3GCR) and non-urinary isolates collected > 48 h after admission), including long-read sequencing on a further six isolates with extended-spectrum beta-lactamase or carbapenemase genes.

RESULTS

The majority of isolates were sensitive to antimicrobials, however 22 isolates were 3GCR, of which five were also carbapenem resistant. Genomic analyses showed those identified as K. oxytoca by the clinical laboratory actually encompassed four distinct species (K. oxytoca, Klebsiella michiganensis, Klebsiella grimontii and Klebsiella pasteurii), referred to as the K. oxytoca species complex (KoSC). There was significant diversity within the population, with only 10/67 multi-locus sequence types (STs) represented by more than one isolate. Strain transmission was rare, with only one likely event identified. Six isolates had extended spectrum beta-lactamase (bla_SHV-12 and/or bla_CTX-M-9) or carbapenemase (bla_IMP-4) genes. One pair of K. michiganensis and K. pasteurii genomes carried identical bla_IMP-4 IncL/M plasmids, indicative of plasmid transmission.

CONCLUSION

Whilst antimicrobial resistance was rare, the resistance plasmids were similar to those found in other Enterobacterales, demonstrating that KoSC has access to the same plasmid reservoir and thus there is potential for multi-drug resistance. Further genomic studies are required to improve our understanding of the KoSC population and facilitate investigation into the attributes of successful nosocomial isolates.

A blaSIM-1 and mcr-9.2 harboring Klebsiella michiganensis strain reported and genomic characteristics of Klebsiella michiganensis

As a newly emerging Klebsiella pathogen, more and more Klebsiella michiganensis drug resistant strains have been reported in recent years, which posed serious threats to public health. Here we first reported a multidrug-resistant K. michiganensis strain 12084 with two blaSIM-1 and one mcr-9.2 genes isolated from the sputum specimen of a patient in the Second Affiliated Hospital of Zhejiang University School of Medicine and analyzed its genetic basis and drug-resistance phenotypes. Genetic analysis showed that this strain harbored three different incompatibility groups (IncHI2, IncHI5, and IncFIIpKPHS2:IncFIB-4.1) of plasmids (p12084-HI2, p12084-HI5, and p12084-FII). A total of 26 drug-resistance genes belonging to 12 classes of antibiotics were identified, most of which (24) were located on two plasmids (p12084-HI2 and p12084-HI5). Interestingly, two blaSIM-1 genes were identified to locate on p12084-HI2 and p12084-HI5, respectively, both of which were embedded in In630, indicating their genetic homogeny. It was noting that one blaSIM-1 gene was situated in a novel unit transposon (referred to as Tn6733) on the p12084-HI5 plasmid. We also discovered an mcr-9.2 gene on the p12084-HI2 plasmid. To the best of our knowledge, this is the first report of a blaSIM-1 and mcr-9.2 harboring K. michiganensis strain. We then investigated the population structure/classification, and antibiotic resistance for all 275 availably global K. michiganensis genomes. Population structure revealed that K. michiganensis could be divided into two main clades (Clade 1 and Clade 2); the most popular ST29 was located in Clade 1, while other common STs (such as ST50, ST27, and ST43) were located in Clade 2. Drug-resistance analysis showed 25.5% of the K. michiganensis strains (70/275) harboring at least one carbapenemase gene, indicating severe drug resistance of K. michiganensis beyond our imagination; this is a dangerous trend and should be closely monitored, especially for ST27 K. michiganensis with the most drug-resistant genes among all the STs. Overall, we reported a blaSIM-1 and mcr-9.2 harboring K. michiganensis strain, and further revealed the population structure/classification, and drug-resistance of K. michiganensis, which provided an important framework, reference, and improved understanding of K. michiganensis.

Emergence of a High-Risk Klebsiella michiganensis Clone Disseminating Carbapenemase Genes

Klebsiella michiganensis is emerging as an important human pathogen of concern especially strains with plasmid-mediated carbapenemase genes. The IncX3-bla_NDM-5 plasmid has been described as the primary vector for bla_NDM-5 dissemination. However, whether strains with this plasmid have any competitive edge remain largely unexplored. We characterized a bla_NDM-5-producing Klebsiella michiganensis strain (KO_408) from Japan and sought to understand the driving force behind the recent dissemination of IncX3-bla_NDM-5 plasmids in different bacterial hosts. Antibiotic susceptibility testing, conjugation, and whole-genome sequencing were performed for KO_408, a clinical isolate recovered from a respiratory culture. Fitness, stability, and competitive assays were performed using the IncX3-bla_NDM-5 plasmid, pKO_4-NDM-5. KO_408 was ascribed to a novel sequence type, ST256, and harbored resistance genes conforming to its MDR phenotype. The bla_NDM-5 gene was localized on the ~44.9 kb IncX3 plasmid (pKO_4-NDM-5), which was transferable in the conjugal assay. The acquisition of pKO_4-NDM-5 did not impose any fitness burden and showed high stability in the host cells. However, transformants with pKO_4-NDM-5 were outcompeted by their host cells and transconjugants with the IncX3-bla_OXA-181 plasmid. The genetic environment of bla_NDM-5 in pKO_4-NDM-5 has been previously described. pKO_4-NDM-5 showed a close phylogenetic distance with seven similar plasmids from China. KO_408 clustered with strains within the KoI phylogroup, which is closely associated with carbapenemase genes. This study highlights the emergence of a high-risk Klebsiella michiganensis clone harboring carbapenemase genes and affirms that the recent spread of IncX3-bla_NDM-5 plasmids might be due to their low fitness cost and stability but not their competitive prowess.

Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen

Klebsiella pneumoniae is a major cause of opportunistic healthcare-associated infections, which are increasingly complicated by the presence of extended-spectrum beta-lactamases (ESBLs) and carbapenem resistance. We conducted a year-long prospective surveillance study of K. pneumoniae clinical isolates in hospital patients. Whole-genome sequence (WGS) data reveals a diverse pathogen population, including other species within the K. pneumoniae species complex (18%). Several infections were caused by K. variicola/K. pneumoniae hybrids, one of which shows evidence of nosocomial transmission. A wide range of antimicrobial resistance (AMR) phenotypes are observed, and diverse genetic mechanisms identified (mainly plasmid-borne genes). ESBLs are correlated with presence of other acquired AMR genes (median n = 10). Bacterial genomic features associated with nosocomial onset are ESBLs (OR 2.34, p = 0.015) and rhamnose-positive capsules (OR 3.12, p < 0.001). Virulence plasmid-encoded features (aerobactin, hypermucoidy) are observed at low-prevalence (<3%), mostly in community-onset cases. WGS-confirmed nosocomial transmission is implicated in just 10% of cases, but strongly associated with ESBLs (OR 21, p < 1 × 10⁻¹¹). We estimate 28% risk of onward nosocomial transmission for ESBL-positive strains vs 1.7% for ESBL-negative strains. These data indicate that K. pneumoniae infections in hospitalised patients are due largely to opportunistic infections with diverse strains, with an additional burden from nosocomially-transmitted AMR strains and community-acquired hypervirulent strains.

Klebsiella pneumoniae is an opportunistic pathogen of increasing public health concern due to the prevalence of antimicrobial resistance. Here, the authors provide insight into the resistance profiles, bacterial genome features and virulence genes, in a year-long prospective study of K. pneumoniae clinical isolates.

CATHAI: cluster analysis tool for healthcare-associated infections

Motivation

Whole genome sequencing (WGS) is revolutionizing disease surveillance where it facilitates high-resolution clustering of related organism and outbreak detection. However, visualizing and efficiently communicating genomic data back to clinical staff is crucial for the successful deployment of a targeted infection control response.

Results

CATHAI (cluster analysis tool for healthcare-associated infections) is an interactive web-based visualization platform that couples WGS informed clustering with associated metadata, thereby converting sequencing data into informative and accessible clinical information for the management of healthcare-associated infections (HAI) and nosocomial outbreaks.

Availability and implementation

All code associated with this application are free available from https://github.com/FordeGenomics/cathai. A demonstration version of CATHAI is available online at https://cathai.fordelab.com.

Emergence and Genomic Characterization of a KPC-2-, NDM-1-, and IMP-4-Producing Klebsiella michiganensis Isolate

A rectal swab sample was collected from a patient with Guillain–Barré syndrome and enriched in lysogeny broth. Carbapenem-resistant bacteria were selected by China Blue agar plates containing 0.3 μg/ml meropenem. Carbapenemase-producing Klebsiella michiganensis was identified and characterized by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF), immune colloidal gold technique, a conjugation experiment, PCR analysis, and antimicrobial susceptibility testing. The genome of K. michiganensis was determined by whole genome sequencing. Antimicrobial susceptibility testing showed that the K. michiganensis was resistant to imipenem, meropenem, ertapenem, cefmetazole, ceftazidime, cefotaxime, piperacillin/tazobactam, sulbactam/cefoperazone, ceftazidime/avibactam, cefepime, and aztreonam while susceptible to polymyxin B, ciprofloxacin, tigecycline, and amikacin. Immune colloidal gold technique suggested that this strain co-produced three different carbapenemases [Klebsiella pneumoniae carbapenemase (KPC), New Delhi metallo-beta-lactamase (NDM), and Imipenem (IMP)]. Whole genome sequencing analysis indicated that this strain belonged to ST91, and bla_KPC–2, bla_NDM–1, and bla_IMP–4 were carried on different conjugative plasmids. Besides, the co-existence and transferability of bla_KPC–2, bla_NDM–1, and bla_IMP–4 in K. michiganensis facilitates the potential horizontal dissemination and nosocomial spread of resistance genes among multidrug-resistant organisms.

Caseinolytic Proteins (Clp) in the Genus Klebsiella: Special Focus on ClpK

Caseinolytic proteins (Clp), which are present in both prokaryotes and eukaryotes, play a major role in cell protein quality control and survival of bacteria in harsh environmental conditions. Recently, a member of this protein family, ClpK was identified in a pathogenic strain of Klebsiella pneumoniae which was responsible for nosocomial infections. ClpK is linked to the thermal stress survival of this pathogen. The genome wide analysis of Clp proteins in Klebsiella spp. indicates that ClpK is present in only 34% of the investigated strains. This suggests that the uptake of the clpk gene is selective and may only be taken up by a pathogen that needs to survive harsh environmental conditions. In silico analyses and molecular dynamic simulations show that ClpK is mainly α-helical and is highly dynamic. ClpK was successfully expressed and purified to homogeneity using affinity and anion exchange chromatography. Biophysical characterization of ClpK showed that it is predominantly alpha-helical, and this is in agreement with in silico analysis of the protein structure. Furthermore, the purified protein is biologically active and hydrolyses ATP in a concentration- dependent manner.

Klebsiella oxytoca Complex: Update on Taxonomy, Antimicrobial Resistance, and Virulence

Klebsiella oxytoca is actually a complex of nine species-Klebsiella grimontii, Klebsiella huaxiensis, Klebsiella michiganensis, K. oxytoca, Klebsiella pasteurii, Klebsiella spallanzanii, and three unnamed novel species. Phenotypic tests can assign isolates to the complex, but precise species identification requires genome-based analysis. The K. oxytoca complex is a human commensal but also an opportunistic pathogen causing various infections, such as antibiotic-associated hemorrhagic colitis (AAHC), urinary tract infection, and bacteremia, and has caused outbreaks. Production of the cytotoxins tilivalline and tilimycin lead to AAHC, while many virulence factors seen in Klebsiella pneumoniae, such as capsular polysaccharides and fimbriae, have been found in the complex; however, their association with pathogenicity remains unclear. Among the 5,724 K. oxytoca clinical isolates in the SENTRY surveillance system, the rates of nonsusceptibility to carbapenems, ceftriaxone, ciprofloxacin, colistin, and tigecycline were 1.8%, 12.5%, 7.1%, 0.8%, and 0.1%, respectively. Resistance to carbapenems is increasing alarmingly. In addition to the intrinsic bla_OXY, many genes encoding β-lactamases with varying spectra of hydrolysis, including extended-spectrum β-lactamases, such as a few CTX-M variants and several TEM and SHV variants, have been found. bla_KPC-2 is the most common carbapenemase gene found in the complex and is mainly seen on IncN or IncF plasmids. Due to the ability to acquire antimicrobial resistance and the carriage of multiple virulence genes, the K. oxytoca complex has the potential to become a major threat to human health.

Phenotypic and Molecular Characterization of Commensal, Community-Acquired and Nosocomial Klebsiella spp

Klebsiella spp. is a relevant pathogen that can present acquired resistance to almost all available antibiotics, thus representing a serious threat for public health. While most studies have been focused on isolates causing community-acquired and nosocomial infections, little is known about the commensal isolates colonizing healthy subjects. We describe the molecular identification and the phenotypic characterization of commensal Klebsiella spp. from breast milk of healthy women and faeces from healthy breast-fed infants, which were compared with isolates from community-acquired infections and from a nosocomial NICU outbreak. The phylogenetic analysis of a 454-bp sequence of the rpoB gene was useful for species identification (K. pneumoniae, K. variicola, K. quasipneumoniae, K. oxytoca, K. grimontii, K. michiganensis, Raoultella planticola and R. ornithinolytica), previously misidentified as K. pneumoniae or K. oxytoca by biochemical methods. Globally, we report that commensal strains present virulence traits (virulence genes, siderophores and biofilms) comparable to community-acquired and NICU-infective isolates, thus suggesting that the human microbiota could constitute a reservoir for infection. Isolates causing NICU outbreak were multi-drug resistant (MDR) and ESBLs producers, although an imipenem-resistant commensal MDR K. quasipneumoniae isolate was also found. A commensal K. pneumoniae strain showed a potent bacteriocin-like inhibitory activity against MDR Klebsiella isolates, thus highlighting the potential role of commensal Klebsiella spp. in health and disease.

Novel Drexlerviridae bacteriophage KMI8 with specific lytic activity against Klebsiella michiganensis and its biofilms

The bacterial genus Klebsiella includes the closely related species K. michiganensis, K. oxytoca and K. pneumoniae, which are capable of causing severe disease in humans. In this report we describe the isolation, genomic and functional characterisation of the lytic bacteriophage KMI8 specific for K. michiganensis. KMI8 belongs to the family Drexlerviridae, and has a novel genome which shares very little homology (71.89% identity over a query cover of only 8%) with that of its closest related bacteriophages (Klebsiella bacteriophage LF20 (MW417503.1); Klebsiella bacteriophage 066039 (MW042802.1). KMI8, which possess a putative endosialidase (depolymerase) enzyme, was shown to be capable of degrading mono-biofilms of a strain of K. michiganensis that carried the polysaccharide capsule KL70 locus. This is the first report of a lytic bacteriophage for K. michiganensis, which is capable of breaking down a biofilm of this species.

Queensland Genomics: an adaptive approach for integrating genomics into a public healthcare system

The establishment of genomics in health care systems has been occurring for the past decade. It is recognised that implementing genomics within a health service is challenging without a system-wide approach. Globally, as clinical genomics implementation programs have matured there is a growing body of information around program design and outcomes. Program structures vary depending on local ecosystems including the health system, politics and funding availability, however, lessons from other programs are important to the design of programs in different jurisdictions. Here we describe an adaptive approach to the implementation of genomics into a publicly funded health care system servicing a population of 5.1 million people. The adaptive approach enabled flexibility to facilitate substantial changes during the program in response to learnings and external factors. We report the benefits and challenges experienced by the program, particularly in relation to the engagement of people and services, and the design of both individual projects and the program as a whole.

Techniques in bacterial strain typing: past, present, and future

PURPOSE OF REVIEW

The advancement of molecular techniques such as whole-genome sequencing (WGS) has revolutionized the field of bacterial strain typing, with important implications for epidemiological surveillance and outbreak investigations. This review summarizes state-of-the-art techniques in strain typing and examines barriers faced by clinical and public health laboratories in implementing these new methodologies.

RECENT FINDINGS

WGS-based methodologies are on track to become the new 'gold standards' in bacterial strain typing, replacing traditional methods like pulsed-field gel electrophoresis and multilocus sequence typing. These new techniques have an improved ability to identify genetic relationships among organisms of interest. Further, advances in long-read sequencing approaches will likely provide a highly discriminatory tool to perform pangenome analyses and characterize relevant accessory genome elements, including mobile genetic elements carrying antibiotic resistance determinants in real time. Barriers to widespread integration of these approaches include a lack of standardized workflows and technical training.

SUMMARY

Genomic bacterial strain typing has facilitated a paradigm shift in clinical and molecular epidemiology. The increased resolution that these new techniques provide, along with epidemiological data, will facilitate the rapid identification of transmission routes with high confidence, leading to timely and effective deployment of infection control and public health interventions in outbreak settings.

The Gut Microbiome as a Reservoir for Antimicrobial Resistance

This review will consider the gut as a reservoir for antimicrobial resistance, colonization resistance, and how disruption of the microbiome can lead to colonization by pathogenic organisms. There is a focus on the gut as a reservoir for β-lactam and plasmid-mediated quinolone resistance. Finally, the role of functional metagenomics and long-read sequencing technologies to detect and understand antimicrobial resistance genes within the gut microbiome is discussed, along with the potential for future microbiome-directed methods to detect and prevent infection.

First report of a blaVIM-1 metallo-β-lactamase-possessing Klebsiella michiganensis

OBJECTIVES

Klebsiella michiganensis is an emerging pathogen. Like Klebsiella pneumoniae, this species is able to acquire antibiotic resistance genes (ARGs) via mobile genetic elements. In this context, K. michiganensis isolates producing carbapenemases of KPC, NDM, IMP and OXA-48-like types have already been reported. Here we characterised a strain (BD-50-Km) isolated from a rectal swab of a Turkish patient hospitalised in Switzerland.

METHODS

Species identification was initially performed using MALDI-TOF/MS. Antimicrobial susceptibility testing was done by the microdilution method. Whole-genome sequencing (WGS) was performed with both Illumina and Nanopore platforms and was used to confirm species identification, to characterise plasmids and to perform core-genome analyses.

RESULTS

BD-50-Km was initially identified as Klebsiella oxytoca and showed reduced susceptibility to imipenem. However, WGS indicated that the isolate was actually K. michiganensis. BD-50-Km carried the bla_VIM-1 gene associated with a rare class 1 integron (In87) located on a pST1 196 kb IncC plasmid. This plasmid shares its backbone with many other IncC plasmids found in different species (including five K. michiganensis), but not the same In87 and the remaining region harbouring various ARGs. BD-50-Km belongs to the novel ST342. Moreover, core-genome analysis (single nucleotide variant analysis) showed that BD-50-Km was not closely related to any K. michiganensis strains deposited in NCBI (n = 212), including the 38 so far reported as possessing carbapenemase genes.

CONCLUSION

This is the first report of a bla_VIM-possessing K. michiganensis clinical isolate. The spread of plasmid-mediated VIM carbapenemases in this emerging pathogen represents an additional threat to our therapeutic armamentarium.

Genotypic Characterization of Clinical Klebsiella spp. Isolates Collected From Patients With Suspected Community-Onset Sepsis, Sweden

Klebsiella is a genus of Gram-negative bacteria known to be opportunistic pathogens that may cause a variety of infections in humans. Highly drug-resistant Klebsiella species, especially K. pneumoniae, have emerged rapidly and are becoming a major concern in clinical management. Although K. pneumoniae is considered the most important pathogen within the genus, the true clinical significance of the other species is likely underrecognized due to the inability of conventional microbiological methods to distinguish between the species leading to high rates of misidentification. Bacterial whole-genome sequencing (WGS) enables precise species identification and characterization that other technologies do not allow. Herein, we have characterized the diversity and traits of Klebsiella spp. in community-onset infections by WGS of clinical isolates (n = 105) collected during a prospective sepsis study in Sweden. The sequencing revealed that 32 of the 82 isolates (39.0%) initially identified as K. pneumoniae with routine microbiological methods based on cultures followed by matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS) had been misidentified. Of these, 23 were identified as Klebsiella variicola and nine as other members of the K. pneumoniae complex. Comparisons of the number of resistance genes showed that significantly fewer resistance genes were detected in Klebsiella oxytoca compared to K. pneumoniae and K. variicola (both values of p < 0.001). Moreover, a high proportion of the isolates within the K. pneumoniae complex were predicted to be genotypically multidrug-resistant (MDR; 79/84, 94.0%) in contrast to K. oxytoca (3/16, 18.8%) and Klebsiella michiganensis (0/4, 0.0%). All isolates predicted as genotypically MDR were found to harbor the combination of β-lactam, fosfomycin, and quinolone resistance markers. Multi-locus sequence typing (MLST) revealed a high diversity of sequence types among the Klebsiella spp. with ST14 (10.0%) and ST5429 (10.0%) as the most prevalent ones for K. pneumoniae, ST146 for K. variicola (12.0%), and ST176 for K. oxytoca (25.0%). In conclusion, the results from this study highlight the importance of using high-resolution genotypic methods for identification and characterization of clinical Klebsiella spp. isolates. Our findings indicate that infections caused by other members of the K. pneumoniae complex than K. pneumoniae are a more common clinical problem than previously described, mainly due to high rates of misidentifications.

Finding Order in the Chaos: Outstanding Questions in Klebsiella pneumoniae Pathogenesis

Klebsiella pneumoniae are Gram-negative facultative anaerobes that are found within host-associated commensal microbiomes, but they can also cause a wide range of infections that are often difficult to treat. These infections are caused by different pathotypes of K. pneumoniae, called either classical or hypervirulent strains.

Klebsiella pneumoniae are Gram-negative facultative anaerobes that are found within host-associated commensal microbiomes, but they can also cause a wide range of infections that are often difficult to treat. These infections are caused by different pathotypes of K. pneumoniae, called either classical or hypervirulent strains. These two groups are genetically distinct, inhabit nonoverlapping geographies, and cause different types of harmful infections in humans. These distinct bacterial groups have also been found to interact differently with the host immune system. Initial innate immune defenses against K. pneumoniae infection include complement, macrophages, neutrophils, and monocytes; these defenses are primary strategies employed by the host to clear infections. K. pneumoniae pathogenesis depends upon the interactions between the microbe and each of these host defenses, and it is becoming increasingly apparent that bacterial genetic diversity impacts the outcomes of these interactions. Here, we highlight recent advances in our understanding of K. pneumoniae pathogenesis, with a focus on how bacterial evolution and diversity impact K. pneumoniae interactions with mammalian innate immune host defenses. We also discuss outstanding questions regarding how K. pneumoniae can frustrate normal immune responses, capitalize upon states of immunocompromise, and cause infections with high mortality.

Budget impact analysis of routinely using whole-genomic sequencing of six multidrug-resistant bacterial pathogens in Queensland, Australia

OBJECTIVE

To predict the cost and health effects of routine use of whole-genome sequencing (WGS) of bacterial pathogens compared with those of standard of care.

DESIGN

Budget impact analysis was performed over the following 5 years. Data were primarily from sequencing results on clusters of multidrug-resistant organisms across 27 hospitals. Model inputs were derived from hospitalisation and sequencing data, and epidemiological and costing reports, and included multidrug resistance rates and their trends.

SETTING

Queensland, Australia.

PARTICIPANTS

Hospitalised patients.

INTERVENTIONS

WGS surveillance of six common multidrug-resistant organisms (Staphylococcus aureus, Escherichia coli, Enterococcus faecium, Klebsiella pneumoniae, Enterobacter sp and Acinetobacter baumannii) compared with standard of care or routine microbiology testing.

PRIMARY AND SECONDARY OUTCOMES

Expected hospital costs, counts of patient infections and colonisations, and deaths from bloodstream infections.

RESULTS

In 2021, 97 539 patients in Queensland are expected to be infected or colonised with one of six multidrug-resistant organisms with standard of care testing. WGS surveillance strategy and earlier infection control measures could avoid 36 726 infected or colonised patients and avoid 650 deaths. The total cost under standard of care was $A170.8 million in 2021. WGS surveillance costs an additional $A26.8 million but was offset by fewer costs for cleaning, nursing, personal protective equipment, shorter hospital stays and antimicrobials to produce an overall cost savings of $30.9 million in 2021. Sensitivity analyses showed cost savings remained when input values were varied at 95% confidence limits.

CONCLUSIONS

Compared with standard of care, WGS surveillance at a state-wide level could prevent a substantial number of hospital patients infected with multidrug-resistant organisms and related deaths and save healthcare costs. Primary prevention through routine use of WGS is an investment priority for the control of serious hospital-associated infections.

Variation in Accessory Genes Within the Klebsiella oxytoca Species Complex Delineates Monophyletic Members and Simplifies Coherent Genotyping

Members of the Klebsiella oxytoca species complex (KoSC) are emerging human pathogens causing infections of increasing significance especially in healthcare settings. KoSC strains are affiliated with distinct phylogroups based on genetic variation at the beta-lactamase gene (bla _OXY) and it has been proposed that each major phylogroup represents a unique species. However, since the typing methods applied in clinical settings cannot differentiate every species within the complex, existing clinical, epidemiological and DNA sequence data is frequently misclassified. Here we systematically examined the phylogenetic relationship of KoSC strains to evaluate robustness of existing typing methods and to provide a simple typing strategy for KoSC members that cannot be differentiated biochemically. Initial analysis of a collection of K. oxytoca, K. michiganensis, K. pasteurii, and K. grimontii strains of environmental origin showed robust correlation of core phylogeny and blaOXY grouping. Moreover, we identified species-specific accessory gene loci for these strains. Extension of species correlation using database entries initially failed. However, assessment of average nucleotide identities (ANI) and phylogenetic validations showed that nearly one third of isolates in public databases have been misidentified. Reclassification resulted in a robust reference strain set for reliable species identification of new isolates or for retyping of strains previously analyzed by multi-locus sequence typing (MLST). Finally, we show convergence of ANI, core gene phylogeny, and accessory gene content for available KoSC genomes. We conclude that also the monophyletic members K. oxytoca, K. michiganensis, K. pasteurii and K. grimontii can be simply differentiated by a PCR strategy targeting bla _OXY and accessory genes defined here.

Complete Genome Sequence of a Canadian Klebsiella michiganensis Strain, Obtained Using Oxford Nanopore Technologies Sequencing

Klebsiella michiganensis is a Gram-negative opportunistic pathogen that is associated with many hospital-acquired infections in humans. Here, we report the complete genome sequence of a K. michiganensis strain isolated from a Canadian wastewater treatment facility.

Klebsiella michiganensis is a Gram-negative opportunistic pathogen that is associated with many hospital-acquired infections in humans. Here, we report the complete genome sequence of a K. michiganensis strain isolated from a Canadian wastewater treatment facility.