Analysis of OXA-204 carbapenemase-producing Enterobacteriaceae reveals possible endoscopy-associated transmission, France, 2012 to 2014

OXA-48-like carbapenemases in Proteus mirabilis - novel genetic environments and a challenge for detection

OXA-48-like enzymes represent the most frequently detected carbapenemases in Enterobacterales in Western Europe, North Africa and the Middle East. In contrast to other species, the presence of OXA-48-like in Proteus mirabilis leads to an unusually susceptible phenotype with low MICs for carbapenems and piperacillin-tazobactam, which is easily missed in the diagnostic laboratory. So far, there is little data available on the genetic environments of the corresponding genes, blaOXA-48-like, in P. mirabilis. In this study susceptibility phenotypes and genomic data of 13 OXA-48-like-producing P. mirabilis were investigated (OXA-48, n = 9; OXA-181, n = 3; OXA-162, n = 1). Ten isolates were susceptible to meropenem and ertapenem and three isolates were susceptible to piperacillin-tazobactam. The gene blaOXA-48 was chromosomally located in 7/9 isolates. Thereof, in three isolates blaOXA-48 was inserted into a P. mirabilis genomic island. Of the three isolates harbouring blaOXA-181 one was located on an IncX3 plasmid and two were located on a novel MOBF plasmid, pOXA-P12, within the new transposon Tn7713. In 5/6 isolates with plasmidic location of blaOXA-48-like, the plasmids could conjugate to E. coli recipients in vitro. Vice versa, blaOXA-48-carrying plasmids could conjugate from other Enterobacterales into a P. mirabilis recipient. These data show a high diversity of blaOXA-48-like genetic environments compared to other Enterobacterales, where genetic environments are quite homogenous. Given the difficult-to-detect phenotype of OXA-48-like-producing P. mirabilis and the location of blaOXA-48-like on mobile genetic elements, it is likely that OXA-48-like-producing P. mirabilis can disseminate, escape most surveillance systems, and contribute to a hidden spread of OXA-48-like.

Klebsiella pneumoniae ST147 harboring blaNDM-1, multidrug resistance and hypervirulence plasmids

The spread of hypervirulent (hv) and carbapenem-/multidrug-resistant Klebsiella pneumoniae is an emerging problem in healthcare settings. The New Delhi metallo-β-lactamase-1 (blaNDM-1) is found in Enterobacteriaceae including K. pneumoniae. The blaNDM-1 is capable of hydrolyzing β-lactam antibiotics which are used for treatment of severe infections caused by multidrug-resistant Gram-negative bacteria. This is associated with the unacceptably high mortality rate in immunocompromised burn injury patients. This study reports on the characterization of blaNDM-1 gene and virulence factors in hv carbapenem-/multidrug-resistant K. pneumoniae ST147 in the burns unit of a tertiary teaching hospital during routine surveillance. Two K. pneumoniae strains were obtained from wounds of burn-infected patients from May 2020 to July 2021. The hypervirulence genes and genetic context of the blaNDM-1 gene and mobile genetic elements potentially involved in the transposition of the gene were analyzed. We identified a conserved genetic background and an IS26 and open reading frame flanking the blaNDM-1 gene that could suggest its involvement in the mobilization of the gene. The plasmid harbored additional antibiotic resistance predicted regions that were responsible for resistance to almost all the routinely used antibiotics. To ensure the identification of potential outbreak strains during routine surveillance, investigations on resistance genes and their environment in relation to evolution are necessary for molecular epidemiology.IMPORTANCEData obtained from this study will aid in the prompt identification of disease outbreaks including evolving resistance and virulence of the outbreak bacteria. This will help establish and implement antimicrobial stewardship programs and infection prevention protocols in fragile health systems in countries with limited resources. Integration of molecular surveillance and translation of whole-genome sequencing in routine diagnosis will provide valuable data for control of infection. This study reports for the first time a high-risk clone K. pneumoniae ST147 with hypervirulence and multidrug-resistance features in Ghana.

OXA-48-Like β-Lactamases: Global Epidemiology, Treatment Options, and Development Pipeline

Modern medicine is threatened by the rising tide of antimicrobial resistance, especially among Gram-negative bacteria, where resistance to β-lactams is most often mediated by β-lactamases. The penicillin and cephalosporin ascendancies were, in their turn, ended by the proliferation of TEM penicillinases and CTX-M extended-spectrum β-lactamases. These class A β-lactamases have long been considered the most important. For carbapenems, however, the threat is increasingly from the insidious rise of a class D carbapenemase, OXA-48, and its close relatives. Over the past 20 years, OXA-48 and "OXA-48-like" enzymes have proliferated to become the most prevalent enterobacterial carbapenemases across much of Europe, Northern Africa, and the Middle East. OXA-48-like enzymes are notoriously difficult to detect because they often cause only low-level in vitro resistance to carbapenems, meaning that the true burden is likely underestimated. Despite this, they are associated with carbapenem treatment failures. A highly conserved incompatibility complex IncL plasmid scaffold often carries bla_OXA-48 and may carry other antimicrobial resistance genes, leaving limited treatment options. High conjugation efficiency means that this plasmid is sometimes carried by multiple Enterobacterales in a single patient. Producers evade most β-lactam-β-lactamase inhibitor combinations, though promising agents have recently been licensed, notably ceftazidime-avibactam and cefiderocol. The molecular machinery enabling global spread, current treatment options, and the development pipeline of potential new therapies for Enterobacterales that produce OXA-48-like β-lactamases form the focus of this review.

Epidemiology and clinical characteristics of infection/colonization due to carbapenemase-producing Enterobacterales in neonatal patients

Background

The aim of this study was to elucidate the epidemiological features of carbapenemase-producing Enterobacterales (CPE) in the pediatric and neonatal patients, to describe clinical characteristics of neonatal patients with CPE infections, and to assess risk factors for neonatal rectal colonization with CPE.

Results

A total of 439 carbapenem-resistant Enterobacterales (CRE) isolates recovered from 367 infant patients were characterised, including 397 isolates of Klebsiella pneumoniae (KP) and 42 isolates of Escherichia coli (EC). Carbapenemase gene blaNDM-1 was the most commonly detected, accounting for 86.56% (n = 380), followed by blaKPC-2 (9.11%, 40) and blaIMP-4 (4.33%, 19). MLST analysis showed 17 different STs detected within CPKP isolates, with ST20, ST2068, ST36 and ST17 being the most frequently isolated types. Eleven STs were identified within CPEC isolates, with ST325 being the dominant types. Eight isolates of NDM-1 producing KP, belonging to ST23, were identified as having hypervirulent traits. The main infections caused by CPE were pneumonia (n = 90) and sepsis (n = 16). All infected patients received monotherapy, with meropenem and ciprofloxacin being the most commonly used antibiotics. All pneumonia patients were cured or improved after treatment. Of the 16 patients with sepsis, 9 were cured or improved, 3 died, and 4 abandoned treatment without any clinical improvement. The rectal prevalences of CPE in the 0–3 days old (DO), the 4–28 DO, and the 29 DO-1 year old groups were decreased from 15.31%, 27.37% and 14.29% in the first stool screening period to 11.78%, 19.59% and 4.07% in the second stool screening period, respectively. Multivariate analysis showed that cesarean section, acidosis, respiration failure, gastric lavage and enema were independent risk factors for rectal colonization in the 0–3 DO group, whereas cesarean section, cephalosporins, gastric lavage and residence in rural area were independently associated with rectal colonization in the 4–28 DO group. The implementation of a series of evidence-based control measures eventually contained the CPE transmission.

Conclusions

Continued vigilance, epidemiological studies, and multimodal infection prevention strategies are urgently needed due to frequent importations.

Gastrointestinal Endoscopy-Associated Infections: Update on an Emerging Issue

Over 17.7 million gastrointestinal (GI) endoscopic procedures are performed annually, contributing to 68% of all endoscopic procedures in the United States. Usually, endoscopic procedures are low risk, but adverse events may occur, including cardiopulmonary complications, bleeding, perforation, pancreatitis, cholangitis, and infection. Infections after the GI endoscopies most commonly result from the patient's endogenous gut flora. Although many studies have reported infection after GI endoscopic procedures, a true estimate of the incidence rate of post-endoscopy infection is lacking. In addition, the infection profile and causative organisms have evolved over time. In recent times, multi-drug-resistant microorganisms have emerged as a cause of outbreaks of endoscope-associated infections (EAI). In addition, lapses in endoscope reprocessing have been reported, with some but not all outbreaks in recent times. This systematic review summarizes the demographical, clinical, and management data of EAI events reported in the literature. A total of 117 articles were included in the systematic review, with the majority reported from North America and Western Europe. The composite infection rate was calculated to be 0.2% following GI endoscopic procedures, 0.8% following ERCP, 0.123% following non-ERCP upper GI endoscopic procedures, and 0.073% following lower GI endoscopic procedures. Pseudomonas aeruginosa was the most common culprit organism, followed by other Enterobacteriaceae groups of organisms and Gram-positive cocci. We have also elaborated different prevention methods such as antimicrobial prophylaxis, adequate sterilization methods for reprocessing endoscopes, periodic surveillance, and current evidence supporting their utilization. Finally, we discuss disposable endoscopes, which could be an alternative to reprocessing to minimize the chances of EAIs with their effects on the environmental and financial situation.

Specificities and Commonalities of Carbapenemase-Producing Escherichia coli Isolated in France from 2012 to 2015

Carbapenemase-producing Escherichia coli (CP-Ec) represents a major public health threat with a risk of dissemination in the community as has occurred for lineages producing extended-spectrum β-lactamases. To characterize the extent of CP-Ec spread in France, isolates from screening and infection samples received at the French National Reference Center (F-NRC) laboratory for carbapenemase-producing Enterobacterales were investigated. A total of 691 CP-Ec isolates collected between 2012 and 2015 and 22 isolates collected before 2012 were fully sequenced. Analysis of their genome sequences revealed some disseminating multidrug-resistant (MDR) lineages frequently acquiring diverse carbapenemase genes mainly belonging to clonal complex 23 (CC23) (sequence type 410 [ST410]) and CC10 (ST10 and ST167) and sporadic isolates, including rare ST131 isolates (n = 17). However, the most represented sequence type (ST) was ST38 (n = 92) with four disseminated lineages carrying bla_OXA-48-like genes inserted in the chromosome. Globally, the most frequent carbapenemase gene (n = 457) was bla_OXA-48. It was also less frequently associated with MDR isolates being the only resistance gene in 119 isolates. Thus, outside the ST38 clades, its acquisition was frequently sporadic with no sign of dissemination, reflecting the circulation of the IncL plasmid pOXA-48 in France and its high frequency of conjugation. In contrast, bla_OXA-181 and bla_NDM genes were often associated with the evolution of MDR E. coli lineages characterized by mutations in ftsI and ompC.

IMPORTANCE Carbapenemase-producing Escherichia coli (CP-Ec) might be difficult to detect, as MICs can be very low. However, their absolute number and their proportion among carbapenem-resistant Enterobacterales have been increasing, as reported by WHO and national surveillance programs. This suggests a still largely uncharacterized community spread of these isolates. Here, we have characterized the diversity and evolution of CP-Ec isolated in France before 2016. We show that carbapenemase genes are associated with a wide variety of E. coli genomic backgrounds and a small number of dominant phylogenetic lineages. In a significant proportion of CP-Ec, the most frequent carbapenemase gene bla_OXA-48, was detected in isolates lacking any other resistance gene, reflecting the dissemination of pOXA-48 plasmids, likely in the absence of any antibiotic pressure. In contrast, carbapenemase gene transfer may also occur in multidrug-resistant E. coli, ultimately giving rise to at-risk lineages encoding carbapenemases with a high potential of dissemination.

A narrative review on current duodenoscope reprocessing techniques and novel developments

Duodenoscopy-associated infections occur worldwide despite strict adherence to reprocessing standards. The exact scope of the problem remains unknown because a standardized sampling protocol and uniform sampling techniques are lacking. The currently available multi-society protocol for microbial culturing by the Centers for Disease Control and Prevention, the United States Food and Drug Administration (FDA) and the American Society for Microbiology, published in 2018 is too laborious for broad clinical implementation. A more practical sampling protocol would result in increased accessibility and widespread implementation. This will aid to reduce the prevalence of duodenoscope contamination. To reduce the risk of duodenoscopy-associated pathogen transmission the FDA advised four supplemental reprocessing measures. These measures include double high-level disinfection, microbiological culturing and quarantine, ethylene oxide gas sterilization and liquid chemical sterilization. When the supplemental measures were advised in 2015 data evaluating their efficacy were sparse. Over the past five years data regarding the supplemental measures have become available that place the efficacy of the supplemental measures into context. As expected the advised supplemental measures have resulted in increased costs and reprocessing time. Unfortunately, it has also become clear that the efficacy of the supplemental measures falls short and that duodenoscope contamination remains a problem. There is a lot of research into new reprocessing methods and technical applications trying to solve the problem of duodenoscope contamination. Several promising developments such as single-use duodenoscopes, electrolyzed acidic water, and vaporized hydrogen peroxide plasma are already applied in a clinical setting.

Arrival of the rare carbapenemase OXA-204 in Canada causing a multispecies outbreak over 3 years

OBJECTIVES

To investigate a persistent multispecies OXA-204 outbreak occurring simultaneously in multiple distant hospitals in the province of Quebec, Canada.

METHODS

OXA-204 carbapenemase-producing Enterobacterales (CPE) isolated from multiple hospitals between January 2016 and October 2018 were included in the study. An epidemiological inquiry was conducted in order to elucidate possible transmission routes and a putative source. Isolates were characterized by standardized antibiotic susceptibility testing and by WGS, using Illumina short-read data and MinION long-read data.

RESULTS

The outbreak comprised 65 patients and 82 isolates from four hospital sites. Most patients were ≥65 years old, had multiple comorbidities and had received antibiotics recently. The infection to colonization ratio was 1:20. No persistent environmental reservoir was identified. The most frequent organism was Citrobacter freundii (n = 78), followed by Klebsiella spp. (n = 3) and Escherichia coli (n = 1). WGS analysis showed 77/78 C. freundii isolates differing by 0-26 single nucleotide variants (SNVs). Results of WGS analysis showed blaOXA-204 was present on three plasmids types (IncX1, IncA/C2 and IncFII/FIB/A/C2) and on a prophage. All C. freundii isolates harboured multiple copies of blaOXA-204, both on the chromosome and a plasmid. Plasmid IncFII/FIB/A/C2 was observed in all three species.

CONCLUSIONS

Transfer of OXA-204 plasmids likely occurred between species within the same patient, highlighting the plasticity of these plasmids and potential for widespread dissemination. OXA-204 carbapenemase has been introduced into Quebec and has rapidly disseminated. Although the infection to colonization ratio was low in this outbreak, this carbapenemase has been associated with severe infection elsewhere.

Clonal CTX-M-15-Producing Escherichia coli ST-949 Are Present in German Surface Water

Extended-spectrum beta-lactamase (ESBL)-producing bacterial isolates are emerging within the last years. To understand this emergence, a thorough genome-based analysis of ESBL isolates from different sources (One Health approach) is needed. Among these, analysis of surface water is underrepresented. Therefore, we performed a genome-based analysis of ESBL-producing Escherichia coli isolates from surface water samples. Water samples were collected from eleven different surface water sites (lakes, river). ESBL-producing E. coli were recovered from these samples using filters and chromogenic media. Whole-genome sequencing of ESBL-producing E. coli was performed followed by determination of the multilocus sequence type (ST), ESBL-type, and virulence genes. Phylogenetic analysis was done using single nucleotide analysis. From all water samples taken, nineteen ESBL-producing E. coli were recovered. All of them harbored an ESBL gene. Nine different multilocus STs were determined, among which ST-949 was the ST detected most frequently. Phylogenetic analysis of ST-949 isolates revealed that all those isolates were closely related. In addition, they harbored an identical chromosomal insertion of bla _CTX-M-15 , indicating a clonal relationship among these isolates. Genetic comparison with isolates from all over the world revealed that these isolates were closely related to human clinical isolates derived from New Zealand and Sweden. An ESBL-producing E. coli ST-949 clone was detected in German surface waters. Its close relationship to human clinical isolates suggests its ability to colonize or even infect humans. Our findings reveal that water sources indeed may play a hitherto underreported role in spread of ESBL-producing isolates.

Burden of carbapenem non-susceptible infections in high-risk patients: systematic literature review and meta-analysis

Background

Owing to their resistance to an important class of antibiotics, the prevention and treatment of carbapenem-resistant (CR)/non-susceptible Gram-negative (GN) infections has become an important public health objective. We conducted a systematic review and meta-analysis of published literature to evaluate the burden of CR GN infections, focusing on high-risk patients such as transplant recipients, or patients with cancer, renal impairment, or sepsis.

Methods

MEDLINE®, Cochrane Central, and Embase® were searched between 2010 and March 2019. Abstracts and full-text articles were screened in duplicate. Random effects meta-analysis was conducted when reported outcomes were sufficiently similar.

Results

Twenty-six publications were eligible. Meta-analyses found increased mortality associated with CR infections among high-risk patients in both unadjusted analysis (8 studies; summary unadjusted odds ratio [OR]: 5.85; 95% confidence interval [CI]: 3.69, 9.26; I² = 19.8%) and adjusted analysis (5 studies; summary hazard ratio [HR]: 4.67; 95% CI: 2.18, 9.99; I² = 77.7%), compared to patients with carbapenem-susceptible (CS) infections or no infection. Increased mortality was also seen in subgroup analyses by length of follow-up (either short-term or long-term) or causative pathogen. A limited number of studies found that CR GN infections increased the risk for mechanical ventilation, adverse events such as graft failure or acute rejection in solid organ transplant recipients, increased renal failure or nephrotoxicity, and an increase in readmissions and costs, though the findings reported in the literature were not consistent.

Conclusion

This systematic literature review and meta-analysis indicates that CR GN infections in high-risk patients are associated with increased mortality, emphasizing the need for antimicrobial stewardship and infection control in hospitals which treat high-risk patients and for the development of effective antimicrobials with favorable efficacy and safety profiles for the treatment of CR GN infections.

Emerging Antimicrobial-Resistant High-Risk Klebsiella pneumoniae Clones ST307 and ST147

There is an enormous global public health burden due to antimicrobial-resistant (AMR) Klebsiella pneumoniae high-risk clones. K. pneumoniae ST307 and ST147 are recent additions to the family of successful clones in the species. Both clones likely emerged in Europe during the early to mid-1990s and, in a relatively short time, became prominent global pathogens, spreading to all continents (with the exception of Antarctica). ST307 and ST147 consist of multiple clades/clusters and are associated with various carbapenemases (i.e., KPCs, NDMs, OXA-48-like, and VIMs). ST307 is endemic in Italy, Colombia, the United States (Texas), and South Africa, while ST147 is endemic in India, Italy, Greece, and certain North African countries. Both clones have been introduced into regions of nonendemicity, leading to worldwide nosocomial outbreaks. Genomic studies showed ST307 and ST147 contain identical gyrA and parC mutations and likely obtained plasmids with bla _CTX-M-15 during the early to mid-2000s, which aided in their global distribution. ST307 and ST147 then acquired plasmids with various carbapenemases during the late 2000s, establishing themselves as important AMR pathogens in certain regions. Both clones are likely underreported due to restricted detection methodologies. ST307 and ST147 have the ability to become major threats to public health due to their worldwide distribution, ability to cause serious infections, and association with AMR, including panresistance. The medical community at large, especially those concerned with antimicrobial resistance, should be aware of the looming threat posed by emerging AMR high-risk clones such as K. pneumoniae ST307 and ST147.

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.

Persisting intrahospital transmission of multidrug-resistant Klebsiella pneumoniae and challenges for infection control

In the past several decades, the incidence of Klebsiella pneumoniae harboring resistance mechanisms against multiple antibiotic agents has increased on a global scale. We discuss reasons for ongoing transmission of multidrug-resistant K. pneumoniae in healthcare settings, which has resulted in the successful spread and establishment of this pathogen. It is now one of the most important causes of healthcare-associated infections worldwide.

Top-ten papers in Infection Control (2015-2017)

Healthcare-associated infections are a main Public Health challenge. In the era of antimicrobial resistance, more effective Infection Control Programs are needed. In this review we will discuss some publications related to hand hygiene (should the patients participate in the improvement programs?); some new strategies to enhance terminal room disinfection and important controversies on contact precautions policies (should we abandon them?). In the last year, there have been as well some reports that provide new insights in Clostridium difficile infection and in the impact of educational antimicrobial stewardship programs.

Diversity of Carbapenemase-Producing Escherichia coli Isolates in France in 2012-2013

With the dissemination of carbapenemase-producing Enterobacteriaceae (CPE) strains worldwide, carbapenem-hydrolyzing enzymes are increasingly reported among isolates of Escherichia coli, the first hospital and community-acquired opportunistic pathogen. Here, we have performed an epidemiological survey of carbapenemase-producing E. coli (CP-Ec) isolates received at the French National Reference Centre (F-NRC) in 2012 and 2013. Antimicrobial susceptibilities for last-resort antibiotics and antimicrobial compounds commonly used to treat urinary tract infections were determined by broth microdilution. Clonal relationship was assessed using repetitive sequence-based PCR (rep-PCR) and multilocus sequence typing (MLST). From this collection of 140 carbapenemase-producing E. coli isolates, 74% produced an OXA-48-like carbapenemase and 21% produced an NDM carbapenemase. A link with a foreign country was suspected for 37% of infected/colonized patients. Most of the isolates were from screening (56%) and from urine samples (26%). Colistin, fosfomycin, and nitrofurantoin possessed the most consistent activity, with 100%, 95%, and 96% isolates susceptible, respectively. A wide diversity of carbapenemase-producing E. coli isolates has been found (50 different sequence types [STs]). The most prevalent clones were (i) E. coli sequence type 38 (ST38) producing OXA-48 (n = 21), a clone linked to Turkey and North African countries, (ii) E. coli ST-90 producing OXA-204 (n = 9), which was responsible for an outbreak related to a contaminated duodenoscope, and (iii) E. coli ST-410 producing OXA-181 (n = 5), which was recovered from patients of different geographical origins. These specific clones might be considered high-risk clones for the dissemination of carbapenemases in E. coli The wide diversity of STs, combined with the increasing number of CP-Ec isolates received by the F-NRC, suggests a likely dissemination of CP-Ec isolates in the community.