Epidemiology and control measures of an OXA-48-producing Enterobacteriaceae hospital-wide oligoclonal outbreak

Carbapenemase-producing Enterobacteriaceae and vancomycin-resistant Enterococcus faecium: The value of a computerized monitoring system to limit their spread

OBJECTIVE

To quickly implement Infection Prevention and Control measures ("search and isolate" strategy), a computerized monitoring system for carbapenemase-producing Enterobacteriaceae (CPE) and Vancomycin-resistant Enterococcus faecium (VRE) carrier and contact patients has been developed in our hospital since 2014. The objectives were to assess the value of a computerized monitoring system in CPE and VRE management and to evaluate the relevance of extended monitoring of all contact patients.

METHODS

Using the data extracted from the computerized system, we conducted a descriptive analysis of CPE and VRE carriers detected from 2004 to 2019 and CPE and VRE extensive contact patients (when hospital stay overlapped with the stay of a carrier in the same unit) from 2014 to 2019.

RESULTS

Between 2015 and 2019 (microbiological data only available during this period), 113 CPE and 558 VRE carriers were registered in the database (DB). Among them, 33.9% CPE and 12.8% VRE carriers were infected (p = 0.02). The most frequent infections were urinary tract infections (52.0%), bloodstream infections (20.0%) and pneumonia (16.0%). Close to 8000 (7679) extended contact patients were exposed. Only 26.2% of them were removed from the DB because of appropriate negative post-exposure rectal screenings. No rectal screening was performed in 33.5% of contact patients. Between 2014 and 2019, 16 outbreaks occurred. The proportion of infected carriers differed significantly between outbreaks (index cases) and non-epidemic episodes (50.0% and 20.5% respectively, p = 0.03). The detection system was able to control diffusion in 99.7% of readmissions of known carriers. Among the 360 readmissions detected by the system, only one was involved in an outbreak due to non-compliance with infection control measures.

CONCLUSION

Given the low screening completion rate (26.2%) and the low detection rate (1.3%), extended monitoring of contact patients does not seem relevant. After five years of use, the computerized monitoring system has demonstrated its effectiveness in terms of responsiveness and limitation of the spread of multidrug-resistant organisms.

Intestinal Carriage of Carbapenemase-Producing Enterobacteriaceae Members in Immunocompromised Children During COVID-19 Pandemic

Background: Hospital-acquired infection with carbapenem-resistant Enterobacteriaceae (CRE) is a global concern. The administration of antibiotics among the infected and non-infected immunocompromised children with SARS-CoV-2 is associated with an increased risk of intestinal CRE colonization and bacteremia during hospitalization. Objectives: The present study aimed to detect the correlation between the intestinal colonization of carbapenemase encoding Enterobacteriaceae with SARS-CoV-2 infection and antibiotic prescription among immunocompromised children admitted to the oncology and Bone Marrow Transplantation (BMT) wards. Methods: Stool samples were collected from the immunocompromised children, and the members of Enterobacteriaceae were isolated using standard microbiological laboratory methods. Carbapenem resistance isolates were initially characterized by the disc diffusion method according to CLSI 2021 and further confirmed by the PCR assay. SARS-CoV-2 infection was also recorded according to documented real-time PCR results. Results: In this study, 102 Enterobacteriaceae isolates were collected from the stool samples. The isolates were from Escherichia spp. (59/102, 57.8%), Klebsiella spp. (34/102, 33.3%), Enterobacter spp. (5/102, 4.9%), Citrobacter spp. (2/102, 1.9%), and Serratia spp. (2/102, 1.9%). The carbapenem resistance phenotype was detected among 42.37%, 73.52%, 40%, 50%, and 100% of Escherichia spp., Klebsiella spp., Enterobacter spp., Citrobacter spp., and Serratia spp., respectively. Moreover, blaOXA-48 (49.1%) and blaNDM-1 (29.4%), as well as blaVIM (19.6%) and blaKPC (17.6%) were common in the CRE isolates. SARS-CoV-2 infection was detected in 50% of the participants; however, it was confirmed in 65.45% (36/55) of the intestinal CRE carriers. The administration of antibiotics, mainly broad-spectrum antibiotics, had a significant correlation with the CRE colonization in both the infected and non-infected children with SARS-CoV-2 infection. Conclusions: Regardless of the COVID-19 status, prolonged hospitalization and antibiotic prescription are major risk factors associated with the CRE intestinal colonization in immunocompromised children.

Intestinal loads of extended-spectrum beta-lactamase and Carbapenemase genes in critically ill pediatric patients

Introduction

Intestinal colonization by Multi-Drug Resistant Organisms (MDROs) can pose a threat on the health of critically ill patients. The extent of colonization by these organisms is related to previous antibiotic treatments and their ability to cause infections among adult patients. The aim of this study is to determine the relationship between the intestinal Relative Loads (RLs) of selected antibiotic resistance genes, antibiotic consumption and extra-intestinal spread among critically ill pediatric patients.

Methods

RLs of bla _{CTX-M-1-Family}, bla _OXA-1, bla _OXA-48 and bla _VIM were determined in 382 rectal swabs obtained from 90 pediatric critically ill patients using qPCRs. The RLs were compared to the patients' demographics, antibiotic consumption, and detection of MDROs from extra-intestinal sites. 16SrDNA metagenomic sequencing was performed for 40 samples and clonality analyses were done for representative isolates.

Results and discussion

76 (74.45%) patients from which 340 (89.01%) rectal swabs were collected had at least one swab that was positive for one of the tested genes. Routine cultures did not identify carbapenemases in 32 (45.1%) and 78 (58.2%) swabs that were positive by PCR for bla _OXA-48 and blaVIM, respectively. RLs of above 6.5% were associated with extra-intestinal spread of blaOXA-48-harboring MDROs. Consumption of carbapenems, non-carbapenem β-lactams, and glycopeptides were statistically associated with testing negative for bla _{CTX-M-1-Family} and bla _OXA-1 while the consumption of trimethoprim/sulfamethoxazole and aminoglycosides was associated with testing negative for blaOXA-48 (P<0.05). In conclusion, targeted qPCRs can be used to determine the extent of intestinal dominance by antibiotic resistant opportunistic pathogens and their potential to cause extra-intestinal infections among a critically ill pediatric population.

Intestinal Dominance by Multidrug-Resistant Bacteria in Pediatric Liver Transplant Patients

Pediatric liver transplantation (PLTx) is commonly associated with extensive antibiotic treatments that can produce gut microbiome alterations and open the way to dominance by multidrug-resistant organisms (MDROs). In this study, the relationship between intestinal Relative Loads (RLs) of β-lactamase genes, antibiotic consumption, microbiome disruption, and the extraintestinal dissemination of MDROs among PLTx patients is investigated. 28 PLTx patients were included, from whom 169 rectal swabs were collected. Total DNA was extracted and bla_{CTX-M-1-Family}, bla_OXA-1, bla_OXA-48, and bla_VIM were quantified via quantitative polymerase chain reaction (qPCR) and normalized to the total bacterial load (16SrRNA) through LogΔΔCt to determine the RLs. 16SrRNA sequencing was performed for 18 samples, and metagenomic sequencing was performed for 2. Patients' clinical data were retrieved from the hospital's database. At least one of the genes tested were detected in all of the patients. The RLs for bla_{CTX-M-1-Family}, bla_OXA-1, bla_OXA-48, and bla_VIM were higher than 1% of the total bacterial population in 67 (80.73%), 56 (78.87%), 57 (77.03%) and 39 (61.9%) samples, respectively. High RLs for bla_{CTX-M-1-Family}, bla_OXA-1, and/or bla_OXA-48, were positively associated with the consumption of carbapenems with trimethoprim-sulfamethoxazole and coincided with low diversity in the gut microbiome. Low RLs were associated with the consumption of noncarbapenem β-lactams with aminoglycosides (P < 0.05). Extraintestinal isolates harboring the same gene(s) as those detected intraintestinally were found in 18 samples, and the RLs of the respective swabs were high. We demonstrated a relationship between the consumption of carbapenems with trimethoprim-sulfamethoxazole, intestinal dominance by MDROs and extraintestinal spread of these organisms among PLTx patients. IMPORTANCE In this study, we track the relative intestinal loads of antibiotic resistance genes among pediatric liver transplant patients and determine the relationship between this load, antibiotic consumption, and infections caused by antibiotic-resistant organisms. We demonstrate that the consumption of broad spectrum antibiotics increase this load and decrease the gut microbial diversity among these patients. Moreover, the high loads of resistance genes were related to the extraintestinal spread of multidrug-resistant organisms. Together, our data show that the tracking of the relative intestinal loads of antibiotic resistance genes can be used as a biomarker that has the potential to stop the extraintestinal spread of antibiotic-resistant bacteria via the measurement of the intestinal dominance of these organisms, thereby allowing for the application of preventive measures.

Dissemination of a single ST11 clone of OXA-48-producing Klebsiella pneumoniae within a large polyclonal hospital outbreak determined by genomic sequencing

The population structure of a set of OXA-48-producing Klebsiella pneumoniae isolates belonging to sequence type 11 (ST11 Kp-OXA) and obtained from two hospitals in Madrid in the period from 2012 to 2015 was studied by genome sequencing. Overall, 97 ST11 Kp-OXA isolates were sequenced and their population structure and demography were studied by Bayesian phylodynamic analysis using core-genome SNVs. In total, 92 isolates were from Hospital La Paz, 57 of them from two selected units. The remaining five isolates were from different units of Hospital Doce de Octubre. Altogether, 96 out of the 97 ST11 Kp-OXA isolates could be ascribed to a single lineage that evolved into three sublineages. Demographic inference showed an expansion of the ST11 Kp-OXA in the first half of 2013 in agreement with the registered incidences. Dated phylogeny showed transmission clusters within hospital wards, between wards and between hospitals. The ST11 Kp-OXA outbreak in Hospital La Paz was largely due to the expansion of a single clone that was transmitted between different units and to Hospital Doce de Octubre. This clone diverged into three sub-lineages and spread out following a mixed mode of neutral core-genome evolution with some features of antibiotic selection, frequent large deletions and plasmid loss and gain events.

Whole-Genome Sequencing Elucidates the Epidemiology of Multidrug-Resistant Acinetobacter baumannii in an Intensive Care Unit

The nosocomial pathogen Acinetobacter baumannii is a frequent cause of healthcare-acquired infections, particularly in critically ill patients, and is of serious concern due to its potential for acquired multidrug resistance. Whole-genome sequencing (WGS) is increasingly used to obtain a high-resolution view of relationships between isolates, which helps in controlling healthcare-acquired infections. Here, we conducted a retrospective study to identify epidemic situations and assess the percentage of transmission in intensive care units (ICUs). Multidrug-resistant A. baumannii (MDR-AB) were continuously isolated from the lower respiratory tract of different patients (at the first isolation in our ICU). We performed WGS, pulsed-field gel electrophoresis (PFGE), and multilocus-sequence typing (MLST) analyses to elucidate bacterial relatedness and to compare the performance of conventional methods with WGS for typing MDR-AB. From June 2017 to August 2018, A. baumannii complex strains were detected in 124 of 796 patients during their ICU stays, 103 of which were MDR-AB. Then we subjected 70 available MDR-AB strains to typing with WGS, PFGE, and MLST. Among the 70 A. baumannii isolates, 38 (54.29%) were isolated at admission, and 32(45.71%) were acquisition isolates. MLST identified 12 unique sequence types, a novel ST (ST2367) was founded. PFGE revealed 16 different pulsotypes. Finally, 38 genotypes and 23 transmissions were identified by WGS. Transmission was the main mode of MDR-AB acquisition in our ICU. Our results demonstrated that WGS was a discriminatory technique for epidemiological healthcare-infection studies. The technique should greatly benefit the identification of epidemic situations and controlling transmission events in the near future.

Intestinal loads of OXA-48-producing Klebsiella pneumoniae in colonized patients determined from surveillance rectal swabs

OBJECTIVES

To determine quantitatively the extent of intestinal colonization by OXA-48-producing Klebsiella pneumoniae (KpOXA) in hospitalized patients.

METHODS

The load of the OXA-48 β-lactamase gene in rectal swabs from 147 colonized patients was measured by quantitative PCR. The load was calculated relative to the total bacterial population (represented by the 16S rRNA gene) using the ΔΔCt method and pure cultures of OXA-48-producing K. pneumoniae as reference samples. The relative loads of the epidemic K. pneumoniae clones ST11 and ST405 were also measured.

RESULTS

The relative intestinal loads of the OXA-48 β-lactamase gene, RL_OXA-48, in hospitalized patients were high. The median RL_OXA-48 was -0.42 (95% confidence interval (CI): -0.60 to -0.16), close to that of a pure culture of OXA-48-producing K. pneumoniae (RL_OXA-48 = 0). In those patients colonized by the KpOXA clones ST11 (51/147, 34.7%) and ST405 (14/147, 9.5%), the relative loads of these clones were similarly high (median RL_ST11 = -1.1, 95% CI: -1.64 to -0.92; median RL_ST405 = -1.3, 95% CI: -1.76 to -0.96). Patients that had received previous antibiotic treatments and those that developed infections by KpOXA had significantly higher RL_OXA-48 values: -0.32 (95% CI: -0.58 to -0.20) vs -1.07 (95% CI: -2.43 to -0.35) and -0.26 (-0.77 to -0.23) vs -0.47 (-0.74 to -0.28), respectively.

CONCLUSIONS

Colonization by KpOXA in hospital patients involves intestinal loads much higher than the K. pneumoniae loads reported in the normal microbiota, reaching levels close to those of pure KpOXA cultures in many cases and largely replacing the host microbiota.

Epidemiology and control measures of an OXA-48-producing Enterobacteriaceae hospital outbreak

Carbapenemase-producing Enterobacteriaceae (CPE) are a significant challenge to healthcare and infection prevention and control teams. In the UK, OXA-48-like carbapenemases are frequently reported. We describe an outbreak of OXA-48-like producing Enterobacteriaceae and the control measures that proved effective in containing further spread.

Aim

To describe epidemiologic and laboratory features of outbreak and highlight key control interventions.

Findings

Following the introduction of an increased sensitivity CPE screening protocol, OXA-48-like CPE were identified in screening and clinical samples from 96 patients across five hospital wards between November 2017 and July 2018. Klebsiella pneumoniae and Enterobacter cloacae were the most frequently isolated organisms, although a range of OXA-48-like positive organisms were identified. The outbreak was contained utilising certain key interventions, including the modification of laboratory screening processes, engagement of hospital senior management, clear and frequent communication and a strong ‘ward presence’ by the infection prevention and control team (IPCT).

Conclusion

Our report describes how a change in laboratory CPE screening process unmasked a CPE outbreak. The range of bacterial species harbouring the OXA-48-like mechanism suggested plasmid-mediated transfer of resistance. The timely implementation of interventions using a clinical, ‘ward-based’ approach to infection prevention and control highlights the importance of behavioural change in infection control interventions and enabled the termination of a large outbreak without recourse to environmental sampling, major remedial construction work or extensive molecular strain or plasmid typing.

Cohorting for preventing the nosocomial spread of Carbapenemase-Producing Enterobacterales, in non-epidemic settings: is it mandatory?

BACKGROUND

Worldwide dissemination of Carbapenemase-Producing Enterobacterales (CPE) has led to national and international guidance recommending the implementation of cohorting in healthcare settings (HS). However, in view of recent data regarding the spread of Extended-spectrum Beta-lactamase-producing Enterobacterales, we may wonder about the usefulness of this measure in a non-outbreak settings; here, individual contact isolation may be sufficient to control the risk of dissemination.

AIM/METHODS

We conducted a narrative review of the literature and discussed the role of cohorting.

FINDINGS

CPE are responsible for outbreaks in HS, which are considered the epicentre of spread of resistance strains. CPE are responsible for adverse effects such as increases in hospital stay and costs, less therapeutic options and thus higher risk of clinical failures and mortality. Environment and materials have also been described contaminated with CPE and can be the source of outbreak. Even if guidelines and publications have supported implementation of cohorting, there are no randomized studies demonstrating the mandatory nature of this measure. Most studies are descriptive and cohorting is usually one of several other measures to control outbreaks. Cohorting is not adapted to all HS, which requires human and material resources. Other measures must be strengthened such as compliance of hand hygiene, antibiotic stewardship and surveillance of contact patients. Individual risk factors of acquisition should also be evaluated.

CONCLUSION

Local epidemiology and resources must be assessed before implementing cohorting.

Proof-of-concept trial of the combination of lactitol with Bifidobacterium bifidum and Lactobacillus acidophilus for the eradication of intestinal OXA-48-producing Enterobacteriaceae

Background

The major reservoir of carbapenemase-producing Enterobacteriaceae (CPE) is the gastrointestinal tract of colonized patients. Colonization is silent and may last for months, but the risk of infection by CPE in colonized patients is significant.

Methods

Eight long-term intestinal carriers of OXA-48-producing Enterobacteriaceae (OXA-PE) were treated during 3 weeks with daily oral lactitol (Emportal^®), Bifidobacterium bifidum and Lactobacillus acidophilus (Infloran^®). Weekly stool samples were collected during the treatment period and 6 weeks later. The presence of OXA-PE was investigated by microbiological cultures and qPCR.

Results

At the end of treatment (EoT, secondary endpoint 1), four of the subjects had negative OXA-PE cultures. Three weeks later (secondary endpoint 2), six subjects were negative. Six weeks after the EoT (primary endpoint), three subjects had negative OXA-PE cultures. The relative intestinal load of OXA-PE decreased in all the patients during treatment.

Conclusions

The combination of prebiotics and probiotics was well tolerated. A rapid reduction on the OXA-PE intestinal loads was observed. At the EoT, decolonization was achieved in three patients.

Clinical Trials Registration: NCT02307383. EudraCT Number: 2014-000449-65.

Epidemiology of β-Lactamase-Producing Pathogens

β-Lactam antibiotics have been widely used as therapeutic agents for the past 70 years, resulting in emergence of an abundance of β-lactam-inactivating β-lactamases. Although penicillinases in Staphylococcus aureus challenged the initial uses of penicillin, β-lactamases are most important in Gram-negative bacteria, particularly in enteric and nonfermentative pathogens, where collectively they confer resistance to all β-lactam-containing antibiotics. Critical β-lactamases are those enzymes whose genes are encoded on mobile elements that are transferable among species. Major β-lactamase families include plasmid-mediated extended-spectrum β-lactamases (ESBLs), AmpC cephalosporinases, and carbapenemases now appearing globally, with geographic preferences for specific variants. CTX-M enzymes include the most common ESBLs that are prevalent in all areas of the world. In contrast, KPC serine carbapenemases are present more frequently in the Americas, the Mediterranean countries, and China, whereas NDM metallo-β-lactamases are more prevalent in the Indian subcontinent and Eastern Europe. As selective pressure from β-lactam use continues, multiple β-lactamases per organism are increasingly common, including pathogens carrying three different carbapenemase genes. These organisms may be spread throughout health care facilities as well as in the community, warranting close attention to increased infection control measures and stewardship of the β-lactam-containing drugs in an effort to control selection of even more deleterious pathogens.

A hybrid simulation model approach to examine bacterial genome sequencing during a hospital outbreak

Background

Hospital infection control requires timely detection and identification of organisms, and their antimicrobial susceptibility. We describe a hybrid modeling approach to evaluate whole genome sequencing of pathogens for improving clinical decisions during a 2017 hospital outbreak of OXA-181 carbapenemase-producing Escherichia coli and the associated economic effects.

Methods

Combining agent-based and discrete-event paradigms, we built a hybrid simulation model to assess hospital ward dynamics, pathogen transmission and colonizations. The model was calibrated to exactly replicate the real-life outcomes of the outbreak at the ward-level. Seven scenarios were assessed including genome sequencing (early or late) and no sequencing (usual care). Model inputs included extent of microbiology and sequencing tests, patient-level data on length of stay, hospital ward movement, cost data and local clinical knowledge. The main outcomes were outbreak size and hospital costs. Model validation and sensitivity analyses were performed to address uncertainty around data inputs and calibration.

Results

An estimated 197 patients were colonized during the outbreak with 75 patients detected. The total outbreak cost was US$318,654 with 6.1% of total costs spent on sequencing. Without sequencing, the outbreak was estimated to result in 352 colonized patients costing US$531,109. Microbiology tests were the largest cost component across all scenarios.

Conclusion

A hybrid simulation approach using the advantages of both agent-based and discrete-event modeling successfully replicated a real-life bacterial hospital outbreak as a foundation for evaluating clinical outcomes and efficiency of outbreak management. Whole genome sequencing of a potentially serious pathogen appears effective in containing an outbreak and minimizing hospital costs.

The Global Ascendency of OXA-48-Type Carbapenemases

Surveillance studies have shown that OXA-48-like carbapenemases are the most common carbapenemases in Enterobacterales in certain regions of the world and are being introduced on a regular basis into regions of nonendemicity, where they are responsible for nosocomial outbreaks. OXA-48, OXA-181, OXA-232, OXA-204, OXA-162, and OXA-244, in that order, are the most common enzymes identified among the OXA-48-like carbapenemase group. OXA-48 is associated with different Tn1999 variants on IncL plasmids and is endemic in North Africa and the Middle East. OXA-162 and OXA-244 are derivatives of OXA-48 and are present in Europe. OXA-181 and OXA-232 are associated with ISEcp1, Tn2013 on ColE2, and IncX3 types of plasmids and are endemic in the Indian subcontinent (e.g., India, Bangladesh, Pakistan, and Sri Lanka) and certain sub-Saharan African countries. Overall, clonal dissemination plays a minor role in the spread of OXA-48-like carbapenemases, but certain high-risk clones (e.g., Klebsiella pneumoniae sequence type 147 [ST147], ST307, ST15, and ST14 and Escherichia coli ST38 and ST410) have been associated with the global dispersion of OXA-48, OXA-181, OXA-232, and OXA-204. Chromosomal integration of bla _OXA-48 within Tn6237 occurred among E. coli ST38 isolates, especially in the United Kingdom. The detection of Enterobacterales with OXA-48-like enzymes using phenotypic methods has improved recently but remains challenging for clinical laboratories in regions of nonendemicity. Identification of the specific type of OXA-48-like enzyme requires sequencing of the corresponding genes. Bacteria (especially K. pneumoniae and E. coli) with bla _OXA-48, bla _OXA-181, and bla _OXA-232 are emerging in different parts of the world and are most likely underreported due to problems with the laboratory detection of these enzymes. The medical community should be aware of the looming threat that is posed by bacteria with OXA-48-like carbapenemases.

Whole genome sequencing reveals resemblance between ESBL-producing and carbapenem resistant Klebsiella pneumoniae isolates from Austrian rivers and clinical isolates from hospitals

In 2016, the Austrian Agency for Health and Food Safety started a pilot project to investigate antimicrobial resistance in surface water. Here we report on the characterisation of carbapenem resistant and ESBL-producing K. pneumoniae isolates from Austrian river water samples compared to 95 clinical isolates recently obtained in Austrian hospitals. Ten water samples were taken from four main rivers, collected upstream and downstream of major cities in 2016. For subtyping and comparison, public core genome multi locus sequence typing (cgMLST) schemes were used. The presence of AMR genes, virulence genes and plasmids was extracted from whole genome sequence (WGS) data. In total three ESBL-producing strains and two carbapenem resistant strains were isolated. WGS based comparison of these five water isolates to 95 clinical isolates identified three clusters. Cluster 1 (ST11) and cluster 2 (ST985) consisted of doublets of carbapenem resistant strains (one water and one clinical isolate each). Cluster 3 (ST405) consisted of three ESBL-producing strains isolated from one water sample and two clinical specimens. The cities, in which patient isolates of cluster 2 and 3 were collected, were in concordance with the water sampling locations downstream from these cities. The genetic concordance between isolates from river water samples and patient isolates raises concerns regarding the release of wastewater treatment plant effluents into surface water. From a public health perspective these findings demand attention and strategies are required to minimize the spread of multiresistant strains to the environment.

Genomic path to pandrug resistance in a clinical isolate of Klebsiella pneumoniae

Carbapenem-resistant Klebsiella pneumoniae have spread globally throughout tertiary hospitals. Many Carbapenem-resistant K. pneumoniae clinical isolates are multidrug-resistant (MDR) and may become eventually pandrug-resistant (PDR). Here we present the closed genome of a PDR VIM-1-producing K. pneumoniae strain (KP1050) obtained in a tertiary hospital. The isolate belonged to sequence type 54 (ST54) and had five extrachromosomal elements (four plasmids and a circular phage genome). Most of the antimicrobial resistance genes (ARGs) were located in two clusters borne by two of the plasmids, comprising a class 1 integron that contained up to 14 ARGs including a VIM-1 metallo-β-lactamase gene, and an IS26 transposon that contained a mobile element from Acinetobacter baumannii encoding the amikacin resistance gene aac(6')-Ian. A MDR isolate obtained 6 years previously was identified (KP1048) retrospectively and was sequenced. Comparison of the two genomes showed that chromosomal mutations in outer membrane porins as well as mutations in the ramR and phoQ genes contributed to increase the resistance spectrum.

Population structure of OXA-48-producing Klebsiella pneumoniae ST405 isolates during a hospital outbreak characterised by genomic typing

OBJECTIVES

The aim of this study was to investigate the structure of a broad and sustained hospital outbreak of OXA-48-producing Klebsiella pneumoniae (KpO48) belonging to sequence type 405 (ST405).

METHODS

Whole-genome sequencing and comparison of ten ST405 KpO48 isolates obtained from clinical samples in our hospital was performed. Using stringent criteria, 36 single nucleotide polymorphisms (SNPs) were detected (range 0-21 in pairwise comparisons), and allele-specific PCR was used to call the SNPs among a larger set of isolates.

RESULTS

Several haplotypes were identified within the population. The haplotypes did not show a spatial structure, but a temporal evolution of sequential haplotype replacements was observed.

CONCLUSIONS

The dispersed spatial distribution suggests a reservoir formed by a large pool of colonised patients, and the temporal replacement pattern suggests that the sustained outbreak was composed of several small outbreaks that appeared and rapidly dispersed to several units.