Coexistence of OXA-48-Producing Klebsiella pneumoniae and Escherichia coli in a Hospitalized Patient Who Returned from Europe to China

Antimicrobial Resistance Patterns, Sequence Types, Virulence and Carbapenemase Genes of Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates from a Tertiary Care Teaching Hospital in Zunyi, China

Purpose

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has seriously threatened public health worldwide. This study aimed to investigate the antimicrobial resistance patterns, sequence types (STs), virulence and carbapenemase genes of CRKP isolates from patients in Zunyi, China.

Methods

CRKP isolates were collected from the First People's Hospital of Zunyi between January 2018 and December 2020. Antimicrobial susceptibility was determined using a VITEK^®2 analyzer and confirmed using either the broth dilution method, Kirby-Bauer method, or E-test assays. Carbapenemase production was examined using a modified carbapenem inactivation method. STs of the studied isolates were determined by multilocus sequence typing, and the presence of carbapenemase and virulence genes was examined using polymerase chain reaction assays.

Results

In total, 94 CRKP isolates were collected. All studied isolates produced carbapenemase, and the most common carbapenemase gene was New Delhi metallo-β-lactamase (NDM; 72.3%), followed by Klebsiella pneumoniae carbapenemase (KPC; 24.5%), and Verona integron-encoded metallo-β-lactamase (VIM; 3.2%). Of the studied isolates, 74.3% exhibited multidrug-resistant (MDR) phenotype, and 25.7% were either pandrug-resistant (PDR) or extensively drug-resistant (XDR) phenotypes. The most prevalent sequence type was ST2407 (37.2%), followed by ST76 (21.3%) and ST11 (11.7%). The NDM gene was present in 97.1% of ST2407 isolates and 90.0% of ST76 isolates, whereas the KPC gene was present in 90.9% of ST11 isolates. The majority of the isolates carried wabG, uge, and fimH virulence genes, with prevalence rates of 94.7%, 92.6%, and 94.7%, respectively.

Conclusion

This study describes NDM-producing ST2407 and ST76, as well as KPC-producing ST11, as the major clonal types of CRKP isolates in Zunyi, China. All CRKP isolates were resistant to multiple types of antibiotics, and the majority of isolates carried carbapenemase and virulence genes. Clonal spread of NDM-producing CRKP ST2407 and ST76, and KPC-producing CRKP ST11 should be strictly monitored.

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.

Genetic characteristics of OXA-48-producing Enterobacterales from China

OBJECTIVES

In China, OXA-48-producing Enterobacterales have been identified sporadically, causing small-scale regional outbreaks. This study investigated the molecular epidemiology, transmission and evolution of OXA-48-producing Enterobacterales and pOXA48 from mainland China.

METHODS

We conducted a multicentre resistance monitoring project from 2013-2018. Genome sequencing of OXA-48-produicng isolates was performed. SNPs were analysed. Eleven isolates were selected for subsequent SMRT sequencing. Genome sequences were annotated, and alignment of the complete sequences of bla_OXA-48-carrying plasmids from a subset of isolates that underwent long-read sequencing was performed.

RESULTS

In total, 41 OXA-48-producing Enterobacterales were included in this study (34 Klebsiella pneumoniae, 3 Escherichia coli, 3 Enterobacter cloacae complex and 1 Klebsiella oxytoca). OXA-48-produicng K. pneumoniae (OXAKp) ST383, ST147 and ST11 caused outbreaks of different scales in our hospital. OXA-48-producing E. coli ST156 and ST648, E. cloacae complex ST414 and ST418, and K. oxytoca ST34 were also identified. bla_OXA-48 was embedded in a Tn1999.2 structure located in IncL plasmids with different sizes (63.58-109.14 kb). Importantly, K. pneumoniae ST11 co-producing KPC-2 and OXA-48 was identified in our hospital and it is possible that KPC-2-producing K. pneumoniae ST11 obtained the bla_OXA-48-carrying plasmid during its spread. A novel 109-kb bla_OXA-48-carrying IncL plasmid was identified from OXAKp ST11. Possibly, two plasmids in OXAKp ST383 were integrated to form this larger plasmid.

CONCLUSION

OXA-48-produicng Enterobacterales were sporadic in China. Importantly, K. pneumoniae ST11 co-producing KPC-2 and OXA-48 has emerged causing an outbreak in China. This high-risk multidrug-resistant clone exhibited high compatibility and strong integration ability with foreign resistance plasmids.

Intra-Abdominal Infections by Carbapenemase-Producing Enterobacteriaceae in a Surgical Unit: Counting Mortality, Stay, and Costs

Background: Carbapenemase-producing Enterobacteriaceae (CPE)-related infections are a problem in public health at present, including intra-abdominal infections (IAI) and surgical populations. The aim of this study was to determine mortality and related risk factors, length of stay (LOS,) and costs for CPE-IAI in surgical patients. Patients and Methods: Review of CPE-related IAI acquired during admission in a general surgery department from January 2013 to December 2018. A mortality analysis was performed specifically in patients with CPE-IAI, and a global analysis of IAI including patients with CPE-IAI (cases) and matched patients with IAI by non-resistant bacteria (controls). Results: Forty patients with CPE-IAI were included, OXA-48-producing Klebsiella pneumoniae was present in 85%. Global mortality rate at 30 days for CPE-IAI was 17.5%; mortality-related factors were: solid tumor (p = 0.009), metastatic disease (p = 0.005), immunodeficiency (p = 0.039), blood transfusion (p = 0.009), and septic shock (p = 0.011). Predictors related to mortality for IAI in the global analysis included age (p = 0.046), Charlson index (p = 0.036), CPE isolation (p = 0.003), and septic shock (p < 0.001). Median global LOS was 43 days (IQR 27-64) in patients with CPE-IAI, and 27 days (IQR 18-35) in controls (p < 0.001). Median global cost of admission was $31,671 (IQR 14,006-55,745) for patients with CPE-IAI and $20,306 (IQR 11,974-27,947) for controls (p = 0.064). The most relevant locations of underlying disease for CPE-IAI were: colorectal (32.5%) with 57-day LOS (IQR 34-65) and cost of $42,877 (IQR 18,780-92,607), and pancreas (25%) with 60-day LOS (IQR 32-99) and cost of $56,371 (IQR 32,590-113,979). Conclusion: Carbapenemase-producing Enterobacteriaceae-related IAI is associated with substantial mortality, LOS, and costs. Factors related to CPE-IAI mortality are solid tumor, metastatic disease, immunodeficiency, blood transfusion, and septic shock. Carbapenemase-producing Enterobacteriaceae isolation in IAI implies higher risk of mortality.

Emergence and nosocomial spread of ST11 carbapenem-resistant Klebsiella pneumoniae co-producing OXA-48 and KPC-2 in a regional hospital in Taiwan

Purpose. Carbapenem-resistant Klebsiella pneumoniae (CRKP) has emerged as a major challenge for global healthcare systems. The objectives of this study were to determine the nosocomial spread of CRKP clones and analyse the molecular characteristics of CRKP in our hospital.Methodology. Ninety-eight non-duplicated clinical CRKP isolates were collected from March 2014-June 2015. Clinical, demographic and microbiological data of patients with CRKP were reviewed. Pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing were applied to investigate the genetic relationship between the 98 isolates. Antibiotic resistance genes were identified by conventional PCR-sequencing.Results. PFGE patterns were grouped into 26 clusters. Two main PFGE clusters were identified: L (53 isolates, belonging to ST11) and N (11 isolates, belonging to ST11). The most dominant ST was ST11 (79 %, 77/98), followed by ST273 (5 %, 5/98). KPC-2 (n=82) was the predominant carbapenemase followed by OXA-48 (n=64). Fifty isolates (51 %, 50/98) harboured bla _KPC-2 and bla _OXA-48 simultaneously, and three of these isolates were detected with the third carbapenemase genes (bla _IMP-8 or bla _VIM-1).Conclusion. The clonal spread of K. pneumoniae ST11 expressing OXA-48, KPC-2 and CTX-M-14 β-lactamases was the cause of an outbreak of CRKP. To the best of our knowledge, a single strain harbouring A-, B- and D-class carbapenemase genes has not previously been identified. There is a high prevalence of plasmid-encoded KPC-2- and OXA-48-producing CRKP in our hospital; most isolates were members of ST11, which may be representative of a high-risk CRKP clone disseminating in central Taiwan.

Phenotypic and Genotypic Characterization of Carbapenem-resistant Enterobacteriaceae: Data From a Longitudinal Large-scale CRE Study in China (2012-2016)

Background

Carbapenem-resistant Enterobacteriaceae (CRE) strains are a major threat to global health. The development of effective control measures requires more detailed phenotypic and genotypic characterization of CRE.

Methods

CRE isolates were collected from 65 hospitals in 25 provinces across China between January 1, 2012, and December 31, 2016. The isolates were characterized by antimicrobial susceptibility testing and multilocus sequence typing. Genes encoding carbapenemases, mobilized colistin resistance (mcr-1), and β-lactamases were detected by polymerase chain reaction and DNA sequencing.

Results

A total of 1801 independent CRE isolates (1201 Klebsiella pneumoniae, 282 Escherichia coli, and 179 Enterobacter cloacae) were collected during the study period. Overall, 96.9%, 89.7%, 54.5%, 49.9%, and 40% of CRE strains were susceptible to colistin, tigecycline, amikacin, minocycline, and fosfomycin, respectively. Notably, 1091/1201 (91%) K. pneumoniae, 225/282 (80%) E. coli, and 129/179 (72%) E. cloacae harbored carbapenemase gene. K. pneumoniae carbapenemase (KPC) was predominant in K. pneumoniae (77%), whereas New Delhi metallo-β-lactamase (NDM) was predominant in E. coli (75%) and E. cloacae (53%). The mcr-1 gene was detected in 13 NDM-carrying E. coli isolates (4.6%). Sequence type (ST)11 and ST167 were predominant among the 100 K. pneumoniae and 47 E. coli STs, respectively. KPC-ST11, which accounted for 64% of K. pneumoniae isolates, had higher levels of resistance than non-ST11 strains to aztreonam, fosfomycin, and amikacin (P < .001). The proportions of KPC and NDM enzymes in CRE increased from 2012 to 2016 (54%-59% and 12%-28%, respectively).

Conclusions

The number of CRE strains harboring carbapenemase is increasing. KPC-ST11 K. pneumoniae, the predominant strain, shows a reduced susceptibility to most available antibiotics.

Nosocomial spread of OXA-232-producing Klebsiella pneumoniae ST15 in a teaching hospital, Shanghai, China

Background

The spread and outbreak of Enterobacteriaceae producing OXA-48-like carbapenemases have become more and more prevalent in China.

Results

A total of 62 non-duplicated OXA-232-producing K. pneumoniae (OXA232Kp) were isolated between 2015 and 2017. An outbreak of OXA232Kp was observed in burn ICU. The 62 OXA232Kp isolates were all belongs to ST15 and categorized into two PFGE types (A and B). Type A was dominated of the isolates, which contained 61 clinical isolates and divided into 10 subtypes (A1-A10). In addition, most of OXA232Kp strains exhibited low-level carbapenems resistance. All strains carried a 6141 bp ColKP3 plasmid harboring the bla_OXA-232 gene which is highly homologous to other bla_OXA-232-bearing plasmids involved in other studies in eastern China.

Conclusions

In this study, clone transmission of OXA232Kp ST15was observed. Highly significant homology among the bla_OXA-232-bearing plasmids indicated the important role of the 6.1 kb ColE-like plasmid on the prevalence of bla_OXA-232 gene in China.

Molecular and genetic characterization of carbapenemase-producing bacteria in Venezuela

Carbapenem-resistant Gram-negative bacteria isolated in Venezuela have been poorly characterized. The present study characterized a total of 34 isolates obtained from 27 patients; five of these patients were multi-infected. The bacterial species identified were Klebsiella pneumoniae (17), Pseudomonas aeruginosa (9), and Acinetobacter baumannii (8). From these isolates, 85% were identified as carbapenemase-producing bacteria, and the identified carbapenemase genes were bla_KPC-2 (10/29 [34.4%]), bla_VIM-type (7/29 [24.1%]), bla_OXA-23 (7/29 [24.1%]), bla_NDM-1 (8/29 [27.5%]), and the coexistence of bla_OXA-23/bla_NDM-1 (2/29 [6.8%]). Patient 1 was multi-infected by K. pneumoniae ST11 and ST2413 isolates harbouring the bla_NDM-1 and bla_KPC-2 genes, respectively. The other patients were multi-infected by two or three different bacterial species such as ESBL-producing K. pneumoniae isolates, P. aeruginosa harbouring the bla_VIM-type gene, K. pneumoniae ST147 harbouring the bla_KPC-2 gene and by A. baumannii harbouring the bla_OXA-23 gene. The bla_NDM-1 gene in A. baumannii is flanked by an uncommon genetic structure, whereas bla_NDM-1 gene in K. pneumoniae revealed a common structure described in different plasmids from Enterobacteriaceae isolates. This study provides new information about the epidemiology of carbapenemase-producing bacteria in clinical setting in Venezuela.

Emergence of OXA-232 Carbapenemase-Producing Klebsiella pneumoniae That Carries a pLVPK-Like Virulence Plasmid among Elderly Patients in China

This study reported the clonal dissemination of OXA-232-producing sequence type 15 (ST15) carbapenem-resistant Klebsiella pneumoniae among elderly patients in China. All patients were immunocompromised, suffered from multiple underlying diseases, and were hospitalized for a prolonged period; however, they slowly recovered on antimicrobial therapy. The bla _OXA-232 gene was in a 6.1-kb ColKP3-type nonconjugative plasmid. The strains displayed a multidrug resistance phenotype and were not hypervirulent despite harboring a virulence plasmid. Active surveillance should be enforced to control further transmission.

The Simplified Carbapenem Inactivation Method (sCIM) for Simple and Accurate Detection of Carbapenemase-Producing Gram-Negative Bacilli

This study reports the simplified carbapenem inactivation method (sCIM) to detect carbapenemase-producing gram-negative bacilli in a simple and accurate manner. This method is based on the modified carbapenem inactivation method (mCIM) with the improvement of experimental procedures. Instead of incubating the antibiotic disk in the organism culture media, the organism to be tested was smeared directly onto the antibiotic disk in the sCIM. For evaluating the sensitivity and specificity of the method, a total of 196 Enterobacteriaceae, 73 Acinetobacter baumannii, and 158 Pseudomonas aeruginosa isolates were collected. Polymerase chain reaction (PCR) was used to detect the carbapenemase genes. Phenotypic evaluations were performed using both the sCIM and the mCIM. PCR results showed that, of the 196 Enterobacteriaceae strains, 147 expressed the carbapenemase genes bla_KPC−2 (58.5%), bla_IMP−4 (21.8%), bla_IMP−2 (2.0%), bla_VIM−1 (6.1%), bla_NDM−1 (10.2%), and bla_OXA−48 (1.4%). sCIM results had high concordance with PCR results (99.5%) and mCIM results (100%) with the exception of one Klebsiella pneumoniae strain, which had an minimal inhibitory concentration (MIC) for imipenem of 0.25 mg/L. PCR demonstrated that 53 of the 73 A. baumannii isolates expressed the carbapenemase genes bla_OXA−23 (98.1%) and bla_VIM−2 (1.8%). sCIM and PCR results corresponded but all A. baumannii isolates were carbapenemase negative by the mCIM. PCR demonstrated that 25 of the 158 P. aeruginosa isolates expressed carbapenemase genes bla_VIM−1 (52%)_, bla_VIM−2 (8%)_, bla_VIM−4 (36%), and bla_IMP−4 (4%). sCIM results had high concordance with PCR results (100%) and the mCIM results (99.4%) with the exception of one P. aeruginosa isolate that expressed the bla_VIM−4 gene. The sCIM offers specificity and sensitivity comparable to PCR but has the advantage of being more user-friendly. This method is suitable for routine use in most clinical microbiology laboratories for the detection of carbapenemase-producing gram-negative bacilli.

Extended-spectrum β-lactamase-producing and carbapenemase-producing Enterobacteriaceae

Antimicrobial resistance (AMR) is a global public-health emergency, which threatens the advances made by modern medical care over the past century. The World Health Organization has recently published a global priority list of antibiotic-resistant bacteria, which includes extended-spectrum β-lactamase-producing Enterobacteriaceae and carbapenemase-producing Enterobacteriaceae. In this review, we highlight the mechanisms of resistance and the genomic epidemiology of these organisms, and the impact of AMR.

Emergence and mechanism of carbapenem-resistant Escherichia coli in Henan, China, 2014

The emergence and dissemination of carbapenem-resistant Escherichia coli (E. coli) strains is a main risk for global public health, but little is known of carbapenemase producing E. coli in Henan, China. The study was undertaken to investigate the prevalence and mechanism of carbapenem-resistant E. coli strains in a hospital in Xinxiang, Henan, China, 2014. A total of 5 carbapenemase-producing E. coli strains were screened from 1014 isolates. We found that they were all resistant to meropenem and imipenem. Amikacin showed the best sensitivity, with gentamicin coming up next. The positive rate of bla_NDM was 80% (4/5). The sequencing results showed that two isolates belonged to bla_NDM-1 whereas other 2 isolates carried the bla_NDM-5. Other carbapenemase genes including bla_IMP,bla_VIM, bla_KPC and bla_OXA-48 were not detected. The bla_CTX-M-15,bla_TEM-1,sul2, aad, and aac(6")-Ib-cr were also detected. MLST analysis showed that NDM-producing E. coli were sporadic. Conjugation test indicated bla_NDM could be transferred. In conclusion, the bla_NDM was the principal resistance mechanism of carbapenem-resistant E. coli in the hospital, Henan, China.

OXA-48-like carbapenemases producing Enterobacteriaceae in different niches

The emergence of carbapenem-resistant enterobacterial species poses a serious threat to public health worldwide. OXA-48-type carbapenem-hydrolyzing class D β-lactamases are widely distributed among Enterobacteriaceae, with significant geographical differences. To date, 11 OXA-48-like variants have been identified, with classical OXA-48 being the most widespread. These enzymes show high-level hydrolytic activity against penicillins and low-level hydrolysis towards carbapenems. Since the first description of the OXA-48 carbapenemase in Turkey, bacterial strains producing the enzyme have been extensively reported in nosocomial and community outbreaks in many parts of the word, particularly in the Mediterranean area and European countries. The rapid spread of Enterobacteriaceae producing OXA-48-like enzymes in different ecosystems has become a serious issue recently. The number of reservoirs for such organisms is increasing, not only in hospitals, but also in the community, among animals (e.g., livestock, companion animals, and wildlife) and in the environment. This review aims to summarize the main characteristics of the OXA-48-type carbapenemases, covering genetic and enzymatic traits, their epidemiology, clonality and associated genes, correlation with extended-spectrum β-lactamases (ESBLs) or plasmidic AmpC (pAmpC) in different bacterial species worldwide.