Rapid Detection and Typing of Carbapenemase Genes from Carbapenem-Resistant Enterobacteriaceae Isolates Collected in a Japanese Hospital Using the Xpert Carba-R Assay

Evaluation of Xpert Carba-R Assay v.2 to Detect Carbapenemase Genes in Two Hospitals in Korea

Background

As the spread of carbapenemase-producing Enterobacteriaceae poses a critical threat to public health, rapid detection of carbapenemase genes is urgently required for prompt initiation of appropriate antimicrobial therapy and infection control. We evaluated the performance of Xpert Carba-R v.2 (Cepheid, USA) compared with that of culture-based conventional PCR.

Methods

Using the results of 5,479 consecutive clinical rectal swabs, discrepant analysis (enriched culture followed by PCR) was performed for all discordant samples (N=100), which were Carba-R v.2-positive and culture-negative.

Results

Among the samples, 206 carbapenemase genes (3.6%) were detected by Carba-R v.2. The sensitivity and specificity were 95.0% and 98.1%, respectively. The positive predictive value (PPV) and negative predictive value (NPV) were 49.0% and 99.9%, respectively. Following discrepant analysis, the PPV increased to 73.5% and the low PPV (8.1%) of the 86 non-KPC improved to 48.8%. Among the 105 discrepancies, NDM was the most frequently observed (N=56), followed by KPC (N=26), VIM (N=10), IMP (N=8), OXA-48 (N=5). The threshold cycle values between discordant vs. concordant and resolved groups were significantly different (P<0.001).

Conclusions

Carba-R v.2 is a rapid and sensitive method for detecting carbapenemase-encoding genes compared with culture-based conventional PCR. Most of our discrepant results were non-KPC genes. Thus, the clinical significance of the non-KPC positive cases detected by Carba-R v.2 should be investigated. This assay would be useful for deciding whether to isolate pre-exposed patients in hospital settings, based on the high specificity and NPV.

A prolonged multispecies outbreak of IMP-6 carbapenemase-producing Enterobacterales due to horizontal transmission of the IncN plasmid

A multispecies outbreak of IMP-6 carbapenemase-producing Enterobacterales (IMP-6-CPE) occurred at an acute care hospital in Japan. This study was conducted to understand the mechanisms of IMP-6-CPE transmission by pulsed-field gel electrophoresis (PFGE), multilocus sequence typing and whole-genome sequencing (WGS), and identify risk factors for IMP-6-CPE acquisition in patients who underwent abdominal surgery. Between July 2013 and March 2014, 22 hospitalized patients infected or colonized with IMP-6-CPE (Escherichia coli [n = 8], Klebsiella oxytoca [n = 5], Enterobacter cloacae [n = 5], Klebsiella pneumoniae [n = 3] and Klebsiella aerogenes [n = 1]) were identified. There were diverse PFGE profiles and sequence types (STs) in most of the species except for K. oxytoca. All isolates of K. oxytoca belonged to ST29 with similar PFGE profiles, suggesting their clonal transmission. Plasmid analysis by WGS revealed that all 22 isolates but one shared a ca. 50-kb IncN plasmid backbone with bla_IMP-6 suggesting interspecies gene transmission, and typing of plasmids explained epidemiological links among cases. A case-control study showed pancreatoduodenectomy, changing drains in fluoroscopy room, continuous peritoneal lavage and enteric fistula were associated with IMP-6-CPE acquisition among the patients. Plasmid analysis of isolates in an outbreak of IMP-6-CPE suggested interspecies gene transmission and helped to clarify hidden epidemiological links between cases.

Screening for Carbapenemases in Ertapenem-Resistant Enterobacteriaceae Collected at a Tunisian Hospital Between 2014 and 2018

Background

Carbapenem-resistance is frequently detected in Enterobacteriaceae isolated from patients in Tunisia. The study was performed to identify frequent carbapenemases in Tunisian isolates.

Methods

Between May 2014 and January 2018, 197 ertapenem-resistant Enterobacteriaceae were isolated at the microbiological department of the Military Hospital of Tunis. The strains were phenotypically characterized and then subjected to in-house polymerase chain reaction (PCR) targeting the carbapenemase genes bla_IMP, bla_VIM, bla_NDM, bla_SPM, bla_AIM, bla_DIM,bla_GIM, bla_SIM, bla_KPC, bla_BIC, and bla_OXA-48.

Results

The assessed 197 ertapenem-resistant Enterobacteriaceae from Tunis comprised 170 Klebsiella pneumoniae, 19 Enterobacter cloacae, 6 Escherichia coli, 1 Citrobacter sedlakii, and 1 Enterobacter asburiae. Thereby, 55 out of 197 isolates (27.9%) were from blood cultures, suggesting a systemic disease. The carbapenemase gene bla_OXA-48 quantitatively dominated by far with 153 detections, followed by bla_NDM with 14 detections, which were distributed about the whole study interval. In contrast, bla_BIC and bla_VIM were only infrequently identified in 5 and 3 cases, respectively, while the other carbapenamases were not observed.

Conclusions

The carbapenemase gene bla_OXA-48 was identified in the vast majority of ertapenem-resistant Tunisian Enterobacteriaceae while all other assessed carbapenemases were much less abundant. In a quantitatively relevant minority of isolates, the applied PCR-based screening approach did not identify any carbapenemases.

Resistant Gram-Negative Bacteria and Diagnostic Point-of-Care Options for the Field Setting during Military Operations

The spread of multidrug-resistant bacteria in resource-poor settings affects the military medical service in case of deployments of soldiers to war and crisis zones. Patients with war injuries are prone to colonization or infection with multidrug-resistant bacteria. Resistant Gram-negative bacteria play a dominant role in military wound infections. Problematic hygiene conditions on deployment facilitate exposition of soldiers with subsequent colonization. Although colonizing strains are frequently cleared from their hosts after returning from deployment, transmission to close contacts of the soldiers in the home country cannot be excluded and therapeutic options are reduced if colonization progresses to invasive infection. Since sophisticated culture-based diagnostic approaches are typically not available in the field setting on deployment, molecular rapid diagnostic test systems are an option for transmission control if the locally prevalent molecular resistance mechanisms are known. Efforts for global resistance surveillance can contribute to better understanding of resistance distribution and spread at deployment sites. This review summarizes experience of the military medical services with multidrug resistance on deployment and with the influx of resistant strains to the home country and discusses potential use of available molecular rapid test systems as an option for the field setting.