A Prolonged Outbreak of KPC-3-Producing Enterobacter cloacae and Klebsiella pneumoniae Driven by Multiple Mechanisms of Resistance Transmission at a Large Academic Burn Center

Risk factors for in-hospital acquisition of carbapenem-resistant Enterobacterales in patients with severe burns

BACKGROUND

Although patients with severe burns are prone to severe infections with antibiotic-resistant bacteria and inevitably have some risk factors for carbapenem-resistant Enterobacterales (CRE) acquisition, risk factors for CRE infection or colonization in these patients have not been investigated.

AIM

To identify the independent risk factors for CRE acquisition in patients with severe burns.

METHODS

Patients admitted to the burn intensive care unit (BICU) for acute burn care were categorized based on culture results during BICU care into the CRE group and non-CRE group, which included the carbapenem-susceptible Enterobacterales (CSE) and control groups. Clinical and microbiological factors were compared between the CRE and non-CRE groups, and between the CRE and CSE groups to identify independent risk factors for in-hospital CRE acquisition.

FINDINGS

Among the included 489 patients, 101 (20.7%) and 388 (79.3%) patients were classified in the CRE and non-CRE groups, respectively. The non-CRE group included 91 (18.6%) and 297 (60.7%) patients in the CSE and control groups, respectively. In multivariate analysis between the CRE and non-CRE groups, exposure to other CRE-acquired patients (P = 0.018), abbreviated burn severity index score ≥9 (P = 0.012), and mechanical ventilation (P < 0.001) were associated with CRE acquisition. In multivariate analysis between the CRE and CSE groups, exposure to other CRE-acquired patients was associated with CRE acquisition (P = 0.048).

CONCLUSION

Considering the limitation of controlling the burn severity in hospitalized patients, enhanced infection control measures for preventing in-hospital CRE transmission among patients with severe burns should be emphasized.

Epidemiology of carbapenem-resistant organisms in Alameda County, California, 2019-2021

Objective

Carbapenem-resistant organisms (CROs) are an urgent health threat. Since 2017, Alameda County Health Public Health Department (ACPHD) mandates reporting of carbapenem-resistant Enterobacterales (CRE) and encourages voluntary reporting of non-CRE CROs including carbapenem-resistant Acinetobacter baumannii (CRAB) and carbapenem-resistant Pseudomonas aeruginosa (CRPA). Surveillance data from ACPHD were analyzed to describe the epidemiology of CROs and target public health interventions.

Methods

Healthcare facilities in Alameda County reported CRO cases and submitted isolates to ACPHD to characterize carbapenemase genes; deaths were identified via the California Electronic Death Registration System. CRO cases with isolates resistant to one or more carbapenems were analyzed from surveillance data from July 2019 to June 2021.

Results

Four hundred and forty-two cases of CROs were reported to Alameda County from 408 patients. The county case rate for CROs was 29 cases per 100,000 population, and cases significantly increased over the 2-year period. CRPA was most commonly reported (157 cases, 36%), and cases of CRAB increased 1.83-fold. One-hundred eighty-six (42%) cases were identified among residents of long-term care facilities; 152 (37%) patients had died by January 2022. One hundred and seven (24%) cases produced carbapenemases.

Conclusions

The high burden of CROs in Alameda County highlights the need for continued partnership on reporting, testing, and infection prevention to limit the spread of resistant organisms. A large proportion of cases were identified in vulnerable long-term care residents, and CRAB was an emerging CRO among this population. Screening for CROs and surveillance at the local level are important to understand epidemiology and implement public health interventions.

Prevention and Management of Wound Infections in Burn Patients

The leading cause of morbidity in burn patients is infection with pneumonia, urinary tract infection, cellulitis, and wound infection being the most common cause. High mortality is due to the immunocompromised status of patients and abundance of multidrug-resistant organisms in burn units. Despite the criteria set forth by American Association of Burn, the diagnosis and treatment of burn infections are not always straightforward. Topical antimicrobials, isolation, hygiene, and personal protective equipment are common preventive measures. Additionally medical and nutritional optimization of the patients is crucial to reverse the immunocompromised status triggered by burn injury.

#AMRrounds: a systematic educational approach for navigating bench to bedside antimicrobial resistance

Antimicrobial resistance (AMR) continues to serve as a major global health crisis. Clinicians practising in this modern era are faced with ongoing challenges in the therapeutic management of patients suffering from antimicrobial-resistant infections. A strong educational understanding and synergistic application of clinical microbiology, infectious disease and pharmacological concepts can assist the adventuring clinician in the navigation of such cases. Important items include mobilizing laboratory testing for pathogen identification and susceptibility data, harnessing an understanding of intrinsic pathogen resistance, acknowledging epidemiological resistance trends, recognizing acquired AMR mechanisms, and consolidating these considerations when constructing an ideal pharmacological plan. In this article, we outline a novel framework by which to systematically approach clinical AMR, encourage AMR-related education and optimize therapeutic decision-making in AMR-related illnesses.

Multidrug-Resistant Pathogens in Burn Wound, Prevention, Diagnosis, and Therapeutic Approaches (Conventional Antimicrobials and Nanoparticles)

Multidrug-resistant pathogens are one of the common causes of death in burn patients and have a high risk of nosocomial infections, especially pneumonia, urinary tract infections, and cellulitis. The role of prolonged hospitalization and empirical antibiotics administration in developing multidrug-resistant pathogens is undeniable. In the early days of admitting burn patients, Gram-positive bacteria were the dominant isolates with a more sensitive antibiotic pattern. However, the emergence of Gram-negative bacteria that are more resistant later occurs. Trustworthy guideline administration in burn wards is one of the strategies to prevent multidrug-resistant pathogens. Also, a multidisciplinary therapeutic approach is an effective way to avoid antibiotic resistance that involves infectious disease specialists, pharmacists, and burn surgeons. However, the emerging resistance to conventional antimicrobial approaches (such as systemic antibiotic exposure, traditional wound dressing, and topical antibiotic ointments) among burn patients has challenged the treatment of multidrug-resistant infections, and using nanoparticles is a suitable alternative. In this review article, we will discuss different aspects of multidrug-resistant pathogens in burn wounds, emphasizing the full role of these pathogens in burn wounds and discussing the application of nanotechnology in dealing with them. Also, some advances in various types of nanomaterials, including metallic nanoparticles, liposomes, hydrogels, carbon quantum dots, and solid lipid nanoparticles in burn wound healing, will be explained.

Burden of severe infections due to carbapenem-resistant pathogens in intensive care unit

Intensive care units (ICU) for various reasons, including the increasing age of admitted patients, comorbidities, and increasingly complex surgical procedures (e.g., transplants), have become "the epicenter" of nosocomial infections, these are characterized by the presence of multidrug-resistant organisms (MDROs) as the cause of infection. Therefore, the perfect match of fragile patients and MDROs, as the cause of infection, makes ICU mortality very high. Furthermore, carbapenems were considered for years as last-resort antibiotics for the treatment of infections caused by MDROs; unfortunately, nowadays carbapenem resistance, mainly among Gram-negative pathogens, is a matter of the highest concern for worldwide public health. This comprehensive review aims to outline the problem from the intensivist's perspective, focusing on the new definition and epidemiology of the most common carbapenem-resistant MDROs (Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacterales) to emphasize the importance of the problem that must be permeating clinicians dealing with these diseases.

Infections in Burn Patients

Infections are the leading cause of mortality in burn patients who survive their initial resuscitation. Burn injury leads to immunosuppression and a dysregulated inflammatory response which can have a prolonged impact. Early surgical excision along with support of the multidisciplinary burn team has improved mortality in burn patients. The authors review diagnostic and therapeutic challenges as well as strategies for management of burn related infections.

Dissemination of carbapenemase-producing Enterobacterales in Ireland from 2012 to 2017: a retrospective genomic surveillance study

The spread of carbapenemase-producing Enterobacterales (CPE) is of major public health concern. The transmission dynamics of CPE in hospitals, particularly at the national level, are not well understood. Here, we describe a retrospective nationwide genomic surveillance study of CPE in Ireland between 2012 and 2017. We sequenced 746 national surveillance CPE samples obtained between 2012 and 2017. After clustering the sequences, we used thresholds based on pairwise SNPs, and reported within-host diversity along with epidemiological data to infer recent putative transmissions. All clusters in circulating clones, derived from high-resolution phylogenies, of a species (Klebsiella pneumoniae, Escherichia coli, Klebsiella oxytoca, Enterobacter cloacae, Enterobacter hormaechei and Citrobacter freundii) were individually examined for evidence of transmission. Antimicrobial resistance trends over time were also assessed. We identified 352 putative transmission events in six species including widespread and frequent transmissions in three species. We detected putative outbreaks in 4/6 species with three hospitals experiencing prolonged outbreaks. The bla OXA-48 gene was the main cause of carbapenem resistance in Ireland in almost all species. An expansion in the number of sequence types carrying bla OXA-48 was an additional cause of the increasing prevalence of carbapenemase-producing K. pneumoniae and E. coli.

Recent Approaches for Downplaying Antibiotic Resistance: Molecular Mechanisms

Antimicrobial resistance (AMR) is a ubiquitous public health menace. AMR emergence causes complications in treating infections contributing to an upsurge in the mortality rate. The epidemic of AMR in sync with a high utilization rate of antimicrobial drugs signifies an alarming situation for the fleet recovery of both animals and humans. The emergence of resistant species calls for new treatments and therapeutics. Current records propose that health drug dependency, veterinary medicine, agricultural application, and vaccination reluctance are the primary etymology of AMR gene emergence and spread. Recently, several encouraging avenues have been presented to contest resistance, such as antivirulent therapy, passive immunization, antimicrobial peptides, vaccines, phage therapy, and botanical and liposomal nanoparticles. Most of these therapies are used as cutting-edge methodologies to downplay antibacterial drugs to subdue the resistance pressure, which is a featured motive of discussion in this review article. AMR can fade away through the potential use of current cutting-edge therapeutics, advancement in antimicrobial susceptibility testing, new diagnostic testing, prompt clinical response, and probing of new pharmacodynamic properties of antimicrobials. It also needs to promote future research on contemporary methods to maintain host homeostasis after infections caused by AMR. Referable to the microbial ability to break resistance, there is a great ultimatum for using not only appropriate and advanced antimicrobial drugs but also other neoteric diverse cutting-edge therapeutics.

Clinical and Genomic Epidemiology of mcr-9-Carrying Carbapenem-Resistant Enterobacterales Isolates in Metropolitan Atlanta, 2012 to 2017

Colistin is a last-resort antibiotic for multidrug-resistant Gram-negative infections. Recently, the ninth allele of the mobile colistin resistance (mcr) gene family, designated mcr-9, was reported. However, its clinical and public health significance remains unclear. We queried genomes of carbapenem-resistant Enterobacterales (CRE) for mcr-9 from a convenience sample of clinical isolates collected between 2012 and 2017 through the Georgia Emerging Infections Program, a population- and laboratory-based surveillance program. Isolates underwent phenotypic characterization and whole-genome sequencing. Phenotypic characteristics, genomic features, and clinical outcomes of mcr-9-positive and -negative CRE cases were then compared. Among 235 sequenced CRE genomes, 13 (6%) were found to harbor mcr-9, all of which were Enterobacter cloacae complex. The median MIC and rates of heteroresistance and inducible resistance to colistin were similar between mcr-9-positive and -negative isolates. However, rates of resistance were higher among mcr-9-positive isolates across most antibiotic classes. All cases had significant health care exposures. The 90-day mortality was similarly high in both mcr-9-positive (31%) and -negative (7%) CRE cases. Nucleotide identity and phylogenetic analysis did not reveal geotemporal clustering. mcr-9-positive isolates had a significantly higher number of median [range] antimicrobial resistance (AMR) genes (16 [4 to 22] versus 6 [2 to 15]; P < 0.001) than did mcr-9-negative isolates. Pangenome tests confirmed a significant association of mcr-9 detection with mobile genetic element and heavy metal resistance genes. Overall, the presence of mcr-9 was not associated with significant changes in colistin resistance or clinical outcomes, but continued genomic surveillance to monitor for emergence of AMR genes is warranted. IMPORTANCE Colistin is a last-resort antibiotic for multidrug-resistant Gram-negative infections. A recently described allele of the mobile colistin resistance (mcr) gene family, designated mcr-9, has been widely reported among Enterobacterales species. However, its clinical and public health significance remains unclear. We compared characteristics and outcomes of mcr-9-positive and -negative CRE cases. All cases were acquired in the health care setting and associated with a high rate of mortality. The presence of mcr-9 was not associated with significant changes in colistin resistance, heteroresistance, or inducible resistance but was associated with resistance to other antimicrobials and antimicrobial resistance (AMR), virulence, and heavy metal resistance (HMR) genes. Overall, the presence of mcr-9 was not associated with significant phenotypic changes or clinical outcomes. However, given the increase in AMR and HMR gene content and potential clinical impact, continued genomic surveillance of multidrug-resistant organisms to monitor for emergence of AMR genes is warranted.

Whole genome sequencing reveals hidden transmission of carbapenemase-producing Enterobacterales

Carbapenemase-producing Enterobacterales (CPE) infection control practices are based on the paradigm that detected carriers in the hospital transmit to other patients who stay in the same ward. The role of plasmid-mediated transmission at population level remains largely unknown. In this retrospective cohort study over 4.7 years involving all multi-disciplinary public hospitals in Singapore, we analysed 779 patients who acquired CPE (1215 CPE isolates) detected by clinical or surveillance cultures. 42.0% met putative clonal transmission criteria, 44.8% met putative plasmid-mediated transmission criteria and 13.2% were unlinked. Only putative clonal transmissions associated with direct ward contact decreased in the second half of the study. Both putative clonal and plasmid-mediated transmission associated with indirect (no temporal overlap in patients’ admission period) ward and hospital contact did not decrease during the study period. Indirect ward and hospital contact were identified as independent risk factors associated with clonal transmission. In conclusion, undetected CPE reservoirs continue to evade hospital infection prevention measures. New measures are needed to address plasmid-mediated transmission, which accounted for 50% of CPE dissemination.

Carbapenemase-producing Enterobacterales cause healthcare-associated infections but modes of transmission are not well understood. Here, the authors find evidence of transmission without direct patient contact, indicating presence of undetected environmental reservoirs, whilst half of the transmission events are likely due to plasmid-mediated transmission.

Global Threat of Carbapenem-Resistant Gram-Negative Bacteria

Infections caused by multidrug-resistant (MDR) and extensively drug-resistant (XDR) Gram-negative bacteria (GNB), including carbapenem-resistant (CR) Enterobacterales (CRE; harboring mainly bla_KPC, bla_NDM, and bla_OXA-48-like genes), CR- or MDR/XDR-Pseudomonas aeruginosa (production of VIM, IMP, or NDM carbapenemases combined with porin alteration), and Acinetobacter baumannii complex (producing mainly OXA-23, OXA-58-like carbapenemases), have gradually worsened and become a major challenge to public health because of limited antibiotic choice and high case-fatality rates. Diverse MDR/XDR-GNB isolates have been predominantly cultured from inpatients and hospital equipment/settings, but CRE has also been identified in community settings and long-term care facilities. Several CRE outbreaks cost hospitals and healthcare institutions huge economic burdens for disinfection and containment of their disseminations. Parenteral polymyxin B/E has been observed to have a poor pharmacokinetic profile for the treatment of CR- and XDR-GNB. It has been determined that tigecycline is suitable for the treatment of bloodstream infections owing to GNB, with a minimum inhibitory concentration of ≤ 0.5 mg/L. Ceftazidime-avibactam is a last-resort antibiotic against GNB of Ambler class A/C/D enzyme-producers and a majority of CR-P. aeruginosa isolates. Furthermore, ceftolozane-tazobactam is shown to exhibit excellent in vitro activity against CR- and XDR-P. aeruginosa isolates. Several pharmaceuticals have devoted to exploring novel antibiotics to combat these troublesome XDR-GNBs. Nevertheless, only few antibiotics are shown to be effective in vitro against CR/XDR-A. baumannii complex isolates. In this era of antibiotic pipelines, strict implementation of antibiotic stewardship is as important as in-time isolation cohorts in limiting the spread of CR/XDR-GNB and alleviating the worsening trends of resistance.

Molecular Characterization of Carbapenem-Resistant Enterobacterales Collected in the United States

Carbapenem-resistant Enterobacterales (CRE) are a growing public health concern due to resistance to multiple antibiotics and potential to cause health care-associated infections with high mortality. Carbapenemase-producing CRE are of particular concern given that carbapenemase-encoding genes often are located on mobile genetic elements that may spread between different organisms and species. In this study, we performed phenotypic and genotypic characterization of CRE collected at eight U.S. sites participating in active population- and laboratory-based surveillance of carbapenem-resistant organisms. Among 421 CRE tested, the majority were isolated from urine (n = 349, 83%). Klebsiella pneumoniae was the most common organism (n = 265, 63%), followed by Enterobacter cloacae complex (n = 77, 18%) and Escherichia coli (n = 50, 12%). Of 419 isolates analyzed by whole genome sequencing, 307 (73%) harbored a carbapenemase gene; variants of bla_KPC predominated (n = 299, 97%). The occurrence of carbapenemase-producing K. pneumoniae, E. cloacae complex, and E. coli varied by region; the predominant sequence type within each genus was ST258, ST171, and ST131, respectively. None of the carbapenemase-producing CRE isolates displayed resistance to all antimicrobials tested; susceptibility to amikacin and tigecycline was generally retained.

Epidemiology and mechanisms of tigecycline- and carbapenem- resistant Enterobacter cloacae in Southwest China: a five-year retrospective study

BACKGROUND

The prevalence and molecular epidemiology of tigecycline resistance in carbapenem-resistant Enterobacter cloacae (CREC) in mainland China is unknown. In this study, we aimed to investigate the molecular characteristics and resistance mechanism of tigecycline-resistant CREC (TCREC) in Southwest China.

METHODS

We conducted a five-year retrospective study. TCREC isolates were subjected to antimicrobial susceptibility testing, pulsed-field gel electrophoresis, and multilocus sequence typing. We determined the presence of genes, deficiency of outer membrane proteins, and expression of efflux pumps using polymerase chain reaction (PCR), reverse transcription-polymerase chain reaction (RT-PCR), and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE).

RESULTS

We found that a high incidence rate of 21.7% (36/166) of isolates were positive for TCREC. All isolates were resistant to ertapenem whereas 67% remained susceptible to imipenem and meropenem. ST88 (10/36, 27.8%) was predominant and associated with moderate resistance to tigecycline and high resistance to carbapenems, followed by ST256 (3/36, 8.3%), ST78 (2/36, 5.6%), ST577 (2/36, 5.6%), and ST102 (2/36, 5.6%). bla_NDM-1 (6/36, 16.6%) carriers was the most common carbapenemase gene and ST88 (5/6, 83.3%) was the most common type, followed by bla_IMP-8 (n=3/36, 8.3%). Coexistence of extensive-spectrum β-lactamase (ESBL) genes and outer membrane protein OmpF and/or OmpC loss were found in 27 out of 36 isolates, in addition, increased co-expression of efflux pump genes acrB and oqxA was identified in 25 out of 36 isolates, which may together contribute to co-resistance to carbapenem and tigecycline.

CONCLUSION

Most ST88 strains carried carbapenemases, especially New Delhi metallo-β-lactamase 1 (NDM-1). Overexpression of efflux pumps contributed to tigecycline resistance. The presence of carbapenemase and/or ESBL genes and lack of outer membrane proteins, but not overexpression of efflux pumps, may confer carbapenem resistance. Reasonable supervision and management the epidemic of TCREC will help to stem the transmission of the isolates.

Characterization of Enterobacter cloacae and Citrobacter freundii species complex isolates with decreased susceptibility to cephalosporins from United States hospitals and activity of ceftazidime/avibactam and comparator agents

Objectives

To evaluate the antimicrobial susceptibility and resistance mechanisms to β-lactams among Enterobacter cloacae and Citrobacter freundii from United States medical centres.

Methods

2571 E. cloacae and 1008 C. freundii species complex isolates were consecutively collected from 77 medical centres and susceptibility tested by broth microdilution method. Isolates displaying MIC values ≥16 mg/L for ceftazidime or ≥2 mg/L for cefepime (n = 914) were tested for β-lactamase-encoding genes using whole genome sequencing.

Results

Overall susceptibility to ceftazidime and cefepime were 73.9% and 91.2% among E. cloacae and 74.2% and 93.5% among C. freundii, respectively. Sixty-three isolates harboured a carbapenemase gene, including 56 bla_KPC, 2 bla_NMC-A, and 5 metallo-β-lactamase genes. Among non-carbapenemase producers, 121 isolates had at least one ESBL-encoding gene, mainly bla_SHV (81) or bla_CTX-M (61), and 15 had a transferable AmpC gene, mainly bla_DHA-1 (8) or bla_FOX-5 (6). Carbapenemase, ESBL, or transferable AmpC-encoding genes were not identified among 718 of 914 (78.6%) isolates sequenced. The most active agents against isolates with a decreased susceptibility to ceftazidime and/or cefepime were ceftazidime/avibactam (MIC_50/90, 0.5/1 mg/L; 99.3% susceptible), amikacin (MIC_50/90, 1/4 mg/L; 99.5% susceptible), and meropenem (MIC_50/90, 0.06/0.5 mg/L; 92.9% susceptible). The isolates resistant to ceftazidime/avibactam were the five MBL producers and one E. cloacae isolate with a reduced expression of OmpF and overexpression of AcrAB-TolC.

Conclusions

Hyperproduction of chromosomal AmpC appears to be the most common mechanism of resistance to ceftazidime and/or cefepime in E. cloacae and C. freundii. Ceftazidime/avibactam remained highly active against most isolates showing decreased susceptibility to ceftazidime and/or cefepime.

Pathophysiological effects of Klebsiella pneumoniae infection on Galleria mellonella as an invertebrate model organism

Klebsiella pneumoniae is an important human pathogen causing urinary tract infections and pneumonia. Due to the increase in resistant strains and being an opportunistic pathogen, it is very important to determine the virulence process, the cellular damage it causes in the host and the immunological response level of the host. In this study, invertebrate infection model Galleria mellonella larvae were used to investigate cellular damage, antioxidant response and changes in biochemical parameters due to K. pneumoniae infection. The activity of cell damage indicators alanine aminotransferase, aspartate aminotransferase and lactate dehydrogenase increased in hemolymph of G. mellonella larvae due to K. pneumoniae virulence. Creatine kinase, alkaline phosphatase, gamma glutamyl transferase and amylase activities were increased to regulate the disrupted energy metabolism due to infection. As a result of the damage caused by K. pneumoniae infection, changes occurred in the amount of non-enzymatic antioxidants, uric acid, bilirubin and albumin. Due to K. pneumoniae infection, the amount of calcium, potassium, magnesium and phosphorus altered. This study showed that G. mellonella larvae was important infection model in the investigation of infectious cell damage and physiological effects, given the opportunistic nature of the K. pneumoniae pathogen and the lack of adequate animal models.

Institutional outbreak involving multiple clades of IMP-producing Enterobacter cloacae complex sequence type 78 at a cancer center in Tokyo, Japan

Background

Information about the clinical and microbiological characteristics of IMP-producing Enterobacterales has been limited. Here, we describe an institutional outbreak of IMP-producing Enterobacter cloacae complex (ECC) involving multiple clades of ECC sequence type (ST) 78 strains.

Methods

Antimicrobial susceptibility testing, whole-genome sequencing, and conjugation experiments of 18 IMP-producing ECC strains isolated during four-year study period were performed. Species and subspecies were determined by average nucleotide identity analysis and clonal relatedness of the isolates was analyzed with multilocus sequence typing and core-genome single nucleotide polymorphism (SNP) analysis. Relevant clinical information was extracted from medical records.

Results

Fourteen of 18 IMP-producing ECC isolates were determined as Enterobacter hormaechei ST78. Sixteen isolates, including 13 isolates belonging to ST78, carried bla_IMP-1 in In316-like class 1 integron and also carried IncHI2 plasmids. Conjugation experiments were successful for 12 isolates carrying bla_IMP-1 on IncHI2 plasmids and for an isolate carrying bla_IMP-11 on an IncL/M plasmid. Although isolation of ST78 strains was clustered in a 14-months period suggesting nosocomial transmission, these strains were subdivided into three clades by SNP analysis: clade A (n = 10), clade B (n = 1), clade C (n = 3). A part of clonal relatedness was unexpected by the epidemiological information at the time of isolation of the strains. Most of the IMP-producing ECC strains were susceptible to non-β-lactam antibiotics and had relatively low minimum inhibitory concentrations to carbapenems (≤4 μg/mL). Five of six infections caused by IMP-producing ECC were treated successfully.

Conclusions

Whole-genome sequencing analysis revealed the outbreak was caused by three different clades of ST78 strains, where patients had favorable treatment outcome of the infections compared with that caused by Enterobacterales producing other carbapenemases, possibly due to their non-multidrug-resistant phenotype.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-05952-9.

BKC-2, a New BKC Variant Detected in MCR-9.1-Producing Enterobacter hormaechei subsp. xiangfangensis

We characterized a multidrug-resistant (MDR) Enterobacter spp. isolate highlighting the genetic aspects of the antimicrobial resistance genes. An Enterobacter spp. isolate (Ec61) was recovered in 2014 from a transtracheal aspirate sample from a patient admitted to a Brazilian tertiary hospital and submitted to further microbiological and genomic characterization. Ec61 was identified as Enterobacter hormaechei subsp. xiangfangensis strain ST451, showing an MDR profile and the presence of genes codifying the new β-lactamase variants BKC-2 and ACT-84 and the mobile colistin resistance gene mcr-9.1.

Characterization of the Plasmidome Encoding Carbapenemase and Mechanisms for Dissemination of Carbapenem-Resistant Enterobacteriaceae

Global dissemination of carbapenem-resistant Enterobacteriaceae (CRE) threatens human health by limiting the efficacy of antibiotics even against common bacterial infections. Carbapenem resistance, mainly due to carbapenemase, is generally encoded on plasmids and is spread across bacterial species by conjugation. Most CRE epidemiological studies have analyzed whole genomes or only contigs of CRE isolates. Here, plasmidome analysis on 230 CRE isolates carrying bla_IMP was performed to shed light into the dissemination of a single carbapenemase gene in Osaka, Japan. The predominant dissemination of bla_IMP-6 by the pKPI-6 plasmid among genetically distinct isolates was revealed, as well as the emergences of pKPI-6 derivatives that acquired advantages for further disseminations. Underlying vast clonal dissemination of a carbapenemase-encoding plasmid, heteroresistance was found in CRE offspring, which was generated by the transcriptional regulation of bla_IMP-6, stabilization of bla_IMP-6 through chromosomal integration, or broadened antimicrobial resistance due to a single point mutation in bla_IMP-6.

Carbapenem-resistant Enterobacteriaceae (CRE) infections, high in morbidity and mortality, pose serious clinical challenges due to limited treatment options. A previous CRE surveillance study on 1,507 patients from 43 hospitals in Osaka, Japan, revealed that 12% of patients carried CRE and that 95% of the CRE isolates were IMP-type carbapenemase producers. Here, the mechanisms for this regional dissemination of a single carbapenemase gene were investigated. Since the dissemination of CRE is primarily due to the transmission of carbapenemase genes located on plasmids, we analyzed the plasmidome of 230 CRE isolates carrying bla_IMP by whole-genome sequencing and Southern blotting. bla_IMP-6 was found to be predominantly disseminated among chromosomally distinct isolates through the pKPI-6 plasmid. Underlying the vast clonal dissemination of pKPI-6, various subpopulations deriving from pKPI-6 were identified, which had acquired advantages for the dissemination of CRE isolates. A cluster exhibiting heteroresistance against meropenem by the transcriptional regulation of bla_IMP-6 caused an outbreak likely through covert transmission of bla_IMP-6. For stable carriage of bla_IMP-6, they occasionally integrated bla_IMP-6 on their chromosomes. In addition, we detected one isolate that broadened the range of antimicrobial resistance through a single point mutation in bla_IMP-6 on pKPI-6. Multifaceted analysis of the plasmidome granted us more accurate perspectives on the horizontal spread of CRE isolates, which is difficult to trace only by comparing the whole genomes. This study revealed the predominant spread of a specific carbapenemase-encoding plasmid accompanying the emergence of phenotypically diverse derivatives, which may facilitate further dissemination of CRE in various environments.

IMPORTANCE Global dissemination of carbapenem-resistant Enterobacteriaceae (CRE) threatens human health by limiting the efficacy of antibiotics even against common bacterial infections. Carbapenem resistance, mainly due to carbapenemase, is generally encoded on plasmids and is spread across bacterial species by conjugation. Most CRE epidemiological studies have analyzed whole genomes or only contigs of CRE isolates. Here, plasmidome analysis on 230 CRE isolates carrying bla_IMP was performed to shed light into the dissemination of a single carbapenemase gene in Osaka, Japan. The predominant dissemination of bla_IMP-6 by the pKPI-6 plasmid among genetically distinct isolates was revealed, as well as the emergences of pKPI-6 derivatives that acquired advantages for further disseminations. Underlying vast clonal dissemination of a carbapenemase-encoding plasmid, heteroresistance was found in CRE offspring, which was generated by the transcriptional regulation of bla_IMP-6, stabilization of bla_IMP-6 through chromosomal integration, or broadened antimicrobial resistance due to a single point mutation in bla_IMP-6.

Evaluation of patient risk factors for infection with carbapenem-resistant Enterobacteriaceae

BACKGROUND

To evaluate risk factors for infection or colonization with carbapenem-resistant Enterobacteriaceae (CRE) to develop an algorithm for targeted CRE screening.

METHODS

We conducted a case-control study of 50 CRE-positive cases and 100 CRE-negative controls to identify risk factors that were significant for CRE infection or colonization. The setting was at an acute care academic hospital. Patients who tested positive for CRE or other microbiological laboratory tests during the study period were included. We reviewed medical records of 50 patients who were CRE-positive and 100 matched controls who had a non-CRE culture at a similar anatomic site within the closest time period to the case's culture date. Risk factors were assessed using logistic regression with SAS 9.4, observing the 95% confidence interval (CI) to determine significance.

RESULTS

Significant risk factors for CRE infection or colonization included the use of fluoroquinolones (odds ratio [OR], 3.75; 95% CI, 1.35, 10.38) and cephalosporins (OR, 2.37; 95% CI, 1.17, 4.86). In addition, undergoing an invasive procedure with a scope device was also a significant risk factor for our participants (OR, 4.57; 95% CI, 1.31, 16.02). Significance of these risk factors varied within the community-acquired and hospital-acquired cases.

CONCLUSIONS

Our results suggest that exposure to certain antimicrobials and invasive procedures with a scope device (endoscopic retrograde cholangiopancreatography, duodenal endoscope) are risk factors for CRE. The findings of significant differences in antimicrobials received highlight the necessity to understand antimicrobial stewardship in the development of CRE colonization and infection. Along with antibiotics, inaccessibility to components within scope devices may be increasing the risk of CRE spread.

Cohorting KPC+ Klebsiella pneumoniae (KPC-Kp)-positive patients: A genomic exposé of cross-colonization hazards in a long-term acute-care hospital (LTACH)

OBJECTIVE

Cohorting patients who are colonized or infected with multidrug-resistant organisms (MDROs) protects uncolonized patients from acquiring MDROs in healthcare settings. The potential for cross transmission within the cohort and the possibility of colonized patients acquiring secondary isolates with additional antibiotic resistance traits is often neglected. We searched for evidence of cross transmission of KPC+ Klebsiella pneumoniae (KPC-Kp) colonization among cohorted patients in a long-term acute-care hospital (LTACH), and we evaluated the impact of secondary acquisitions on resistance potential.

DESIGN

Genomic epidemiological investigation.

SETTING

A high-prevalence LTACH during a bundled intervention that included cohorting KPC-Kp-positive patients.

METHODS

Whole-genome sequencing (WGS) and location data were analyzed to identify potential cases of cross transmission between cohorted patients.

RESULTS

Secondary KPC-Kp isolates from 19 of 28 admission-positive patients were more closely related to another patient's isolate than to their own admission isolate. Of these 19 cases, 14 showed strong genomic evidence for cross transmission (<10 single nucleotide variants or SNVs), and most of these patients occupied shared cohort floors (12 patients) or rooms (4 patients) at the same time. Of the 14 patients with strong genomic evidence of acquisition, 12 acquired antibiotic resistance genes not found in their primary isolates.

CONCLUSIONS

Acquisition of secondary KPC-Kp isolates carrying distinct antibiotic resistance genes was detected in nearly half of cohorted patients. These results highlight the importance of healthcare provider adherence to infection prevention protocols within cohort locations, and they indicate the need for future studies to assess whether multiple-strain acquisition increases risk of adverse patient outcomes.

Molecular Characteristics of Carbapenem-Resistant Enterobacter cloacae in a Tertiary Hospital in China

Background

Infections caused by the carbapenem-resistant Enterobacter cloacae (CREC) bring great challenges to the clinical treatment and pose a serious threat to public health. In this study, we investigated the molecular characteristics of CREC in a tertiary hospital.

Materials and Methods

A total of 12 non-duplicate CREC strains isolated during the period of November 2016 to July 2019 were subjected to automated microbial identification and antimicrobial susceptibility testing (AST) using the BD Phoenix-100 identification and antimicrobial susceptibility testing (ID/AST) system. The strains were also subjected to phenotypic screening for the detection of antibiotic resistance genes such as the carbapenemase and other β-lactamase genes, with the use of the polymerase chain reaction assay (PCR). Finally, multi-locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE)-based homology analysis were applied.

Results

Four types of carbapenemases namely IMP-26, NDM-5, NDM-1, and KPC-2 were identified in 12 CREC strains. IMP-26 was the most prevalent type (6/12 strains, 50 %), followed by NDM-5 (3/12 strains, 25 %). The results of MLST revealed that these 12 strains could be divided into five sequence types (STs) among which ST544 was the dominant type (6/12 strains, 50 %). The PFGE results divided the 12 strains into four clusters.

Conclusion

Our study indicated that the epidemics of the IMP-26-producing E. cloacae ST544 strain did occur in the intensive care unit (ICU) of a tertiary hospital. Therefore, early surveillance and strict implementation of control measures are crucial for the prevention of nosocomial infections and transmissions in hospitals.

Mutations in the two component regulator systems PmrAB and PhoPQ give rise to increased colistin resistance in Citrobacter and Enterobacter spp

Introduction. Colistin is a last resort antibiotic for treating infections caused by carbapenem-resistant isolates. Mechanisms of resistance to colistin have been widely described in Klebsiella pneumoniae and Escherichia coli but have yet to be characterized in Citrobacter and Enterobacter species.Aim. To identify the causative mutations leading to generation of colistin resistance in Citrobacter and Enterobacter spp.Methodology. Colistin resistance was generated by culturing in increasing concentrations of colistin or by direct culture in a lethal (above MIC) concentration. Whole-genome sequencing was used to identify mutations. Fitness of resistant strains was determined by changes in growth rate, and virulence in Galleria mellonella.Results. We were able to generate colistin resistance upon exposure to sub-MIC levels of colistin, in several but not all strains of Citrobacter and Enterobacter resulting in a 16-fold increase in colistin MIC values for both species. The same individual strains also developed resistance to colistin after a single exposure at 10× MIC, with a similar increase in MIC. Genetic analysis revealed that this increased resistance was attributed to mutations in PmrB for Citrobacter and PhoP in Enterobacter, although we were not able to identify causative mutations in all strains. Colistin-resistant mutants showed little difference in growth rate, and virulence in G. mellonella, although there were strain-to-strain differences.Conclusions. Stable colistin resistance may be acquired with no loss of fitness in these species. However, only select strains were able to adapt suggesting that acquisition of colistin resistance is dependent upon individual strain characteristics.

Burn Infection and Burn Sepsis

Background: Infection is the most common complication and cause of death in patients suffering burn injuries. These patients are susceptible to infection and burn wound sepsis secondary to the alterations in their physiology. Diagnosis and management of infections rely on physical examination, cultures, and the pathology of the burn wound. Method: We performed an electronic search for articles in the Google Scholar and PubMed databases using the search terms "burn sepsis," "burn infection," and "burn critical care." Results: Multiple factors increase burn patients' risk of invasive infection and sepsis, including underlying factors and co-morbidities, the percent total body surface area of the burn, delays in burn wound excision, and microbial virulence/bacterial count. Organisms causing burn wound infection differ, depending on the time since injury and its location; and diagnosis is multi-factorial. The most common pathogens remain Staphylococcus and Pseudomonas spp. Conclusion: Overall, the recognition of burn sepsis is based on clinical findings. Treatment consists of a combination of local dressings, early burn excision, and systemic antimicrobial therapy. The mortality rate has decreased significantly over the past 10 years, but continued efforts at timely management and infection prevention are essential.

ORF-based binarized structure network analysis of plasmids (OSNAp), a novel approach to core gene-independent plasmid phylogeny

OBJECTIVES

Systematic comparison of multiple plasmids remains challenging. We aimed to develop a new method for phylogenetic analysis of plasmids, open reading frame (ORF)-based binarized structure network analysis of plasmids (OSNAp).

METHODS

With the OSNAp, the genetic structures of plasmids in a given plasmid group are expressed as binary sequences based on the presence or absence of ORFs regardless of their positions or directions. As a proof-of-concept, ORFs were collected from 101 complete I1 plasmid sequences, and their corresponding binary sequences were generated. A tree was generated using the neighbor-net, an algorithm for constructing phylogenetic networks based on distance between taxa, to visualize the plasmid phylogeny drawn from binary sequences. The results were compared with those of plasmid sequence types (pSTs) defined by plasmid multilocus sequence typing (pMLST).

RESULTS

All I1 plasmids were placed on the phylogenetic tree constructed from the binary sequences. Most plasmids belonging to the same pSTs had Dice indices of ≥0.95 and were placed in the same OSNAp split. On the other hand, pST12 plasmids were distributed on separate splits due to differences in ORFs not used in pMLST, suggesting improved differentiation of the plasmids with OSNAp compared with pMLST.

CONCLUSION

OSNAp is a novel holistic approach to assess relatedness of a population of plasmids in a given plasmid group based on nucleotide sequence data. It provides higher discrimination than pMLST, which may prove useful in tracing bacteria that harbor plasmids of shared origins.

Zebrafish and Galleria mellonella: Models to Identify the Subsequent Infection and Evaluate the Immunological Differences in Different Klebsiella pneumoniae Intestinal Colonization Strains

The intestine is the main reservoir of bacterial pathogens in most organisms. Klebsiella pneumoniae is an important opportunistic pathogen associated with nosocomial bacterial infections. Intestinal colonization with K. pneumoniae has been shown to be associated with an increased risk of subsequent infections. However, not all K. pneumoniae strains in the intestine cause further infection, and the distinction of the difference among strains that cause infection after colonization and the ones causing only asymptomatic colonization is unclear. In this study, we report a case of a hospitalized patient from the ICU. We screened out two intestine colonization strains (FK4111, FK4758) to analyze the subsequent infection conditions. We set up infection models of zebrafish and Galleria mellonella to establish the differences in the potential for causing subsequent infection and the immunological specificities after K. pneumoniae intestine colonization. Sudan Black B and neutral red staining results indicated that FK4758 was more responsive to neutrophil recruitment and phagocytosis of macrophages than FK4111. The results of the assessment of the organ bacterial load revealed that FK4111 and FK4758 both had the highest bacterial loads in the zebrafish intestine compared to those in other organs. However, in the zebrafish spleen, liver, and heart, the FK4758 load was significantly higher than that of FK4111. The ST37 strain FK4111, which does not produce carbapenemase, did not cause infection after colonization, whereas the ST11 strain FK4758, which produces carbapenemase, caused infection after intestinal colonization. Our finding demonstrated that not all intestinal colonization of K. pneumoniae subsequently caused infections, and the infections of K. pneumoniae after colonization are different. Therefore, the infection models we established provided possibility for the estimation of host-microbial interactions.

Tracking KPC-3-producing ST-258 Klebsiella pneumoniae outbreak in a third-level hospital in Granada (Andalusia, Spain) by risk factors and molecular characteristics

The objective of this study was to determine clinical-epidemiological characteristics of the patients and the genetic characteristics of carbapenemase KPC-3-producing Klebsiella pneumoniae isolates belonging to sequence type ST258. The eligible study population was all patients with isolates detected between October 2015 and March 2017. Clinical-epidemiological and microbiological data were gathered on risk factors associated with infection by this clone. Antimicrobial susceptibility was determined using MicroScan system and diffusion in agar. Genes encoding carbapenemases were detected using PCR and Sanger sequencing. The sequence type was assigned by MLST, and the genetic relationship among clinical isolates was determined by pulsed field electrophoresis and by analysis of the genetic environment. The study included 23 individuals with isolates of KPC-3/ST258; the mean age was 77 year, and mean stay pre-isolation was 32 days; 81% received empirical antimicrobial treatment. Isolates were only susceptible to gentamicin (CIM ≤ 2 mg/L), tigecycline (CIM ≤ 1 mg/L), and colistin (CIM ≤ 2 mg/L). The isolates belonged to ST258, with five pulse types or subgroups. All isolates showed amplification of KPC, which was identified as KPC-3 variant. Gene _blaKPC-3 was flanked by insertion sequences Kpn6 and Kpn7 within Tn4401 transposon isoform a. We report, for the first time in Spain, an 18-month outbreak by KPC-3-producing ST258 K. pneumoniae. Its acquisition was associated with a history of antimicrobial therapy, with three treatment options, and with high mortality. The detection of different pulse types is attributable to different introductions of the clone in our setting, supporting the need for multi-resistant isolate surveillance studies.

Multiple importations and transmission of colistin-resistant Klebsiella pneumoniae in a hospital in northern India

OBJECTIVE

Resistance to colistin, a last resort antibiotic, has emerged in India. We investigated colistin-resistant Klebsiella pneumoniae(ColR-KP) in a hospital in India to describe infections, characterize resistance of isolates, compare concordance of detection methods, and identify transmission events.

DESIGN

Retrospective observational study.

METHODS

Case-patients were defined as individuals from whom ColR-KP was isolated from a clinical specimen between January 2016 and October 2017. Isolates resistant to colistin by Vitek 2 were confirmed by broth microdilution (BMD). Isolates underwent colistin susceptibility testing by disk diffusion and whole-genome sequencing. Medical records were reviewed.

RESULTS

Of 846 K. pneumoniae isolates, 34 (4%) were colistin resistant. In total, 22 case-patients were identified. Most (90%) were male; their median age was 33 years. Half were transferred from another hospital; 45% died. Case-patients were admitted for a median of 14 days before detection of ColR-KP. Also, 7 case-patients (32%) received colistin before detection of ColR-KP. All isolates were resistant to carbapenems and susceptible to tigecycline. Isolates resistant to colistin by Vitek 2 were also resistant by BMD; 2 ColR-KP isolates were resistant by disk diffusion. Moreover, 8 multilocus sequence types were identified. Isolates were negative for mobile colistin resistance (mcr) genes. Based on sequencing analysis, in-hospital transmission may have occurred with 8 case-patients (38%).

CONCLUSIONS

Multiple infections caused by highly resistant, mcr-negative ColR-KP with substantial mortality were identified. Disk diffusion correlated poorly with Vitek 2 and BMD for detection of ColR-KP. Sequencing indicated multiple importation and in-hospital transmission events. Enhanced detection for ColR-KP may be warranted in India.

High Prevalence of Metallo-β-Lactamase-Producing Enterobacter cloacae From Three Tertiary Hospitals in China

Enterobacter cloacae has recently emerged as one of the most common carbapenem-resistant Enterobacteriaceae. The emergence and spread of metallo-β-lactamase-producing E. cloacae have posed an immediate threat globally. Here, we investigated the molecular characteristics of 84 carbapenem-resistant Enterobacter cloacae (CREL) collected from three tertiary hospitals in China between 2012 and 2016. Species identification and antimicrobial susceptibility testing were performed using a VITEK-2 system. Carbapenems, polymyxins B, and tigecycline were tested by broth microdilution method. The carbapenem in activation method (CIM) and cefoxitin three-dimensional test were used to detect carbapenemase and AmpC β-lactamase, respectively. Isolates were screened for β-lactam resistance genes by PCR, and expression of ompC and ompF was determined by qRT-PCR. Genetic relatedness was performed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST), while selected isolates were subjected to whole-genome sequencing. Among the 84 CREL isolates, 50 (59.5%) were detected as carbapenemase producers. NDM-1 was the dominant carbapenemase (80.0%), followed by IMP-26 (8.0%) and IMP-4 (6.0%). Notably, we identified the first NDM-1 and IMP-1 co-producing E. cloacae, carrying plasmids of several incompatibility (Inc) groups, including IncHI2, IncHI2A, and IncN. Most isolates showed decreased expression of ompC and/or ompF, and contained a broad distribution of ESBLs and AmpC β-lactamases. These findings suggested that different molecular mechanisms, including carbapenemase, ESBL and/or AmpC plus loss of porins, have contributed to carbapenem resistance. The bla_NDM−1-harboring plasmids contained highly conserved gene environment around bla_NDM−1 (bla_NDM−1-ble_MBL-trpF-dsbD-cutA1-groES-groEL), which could be associated with the potential dissemination of bla_NDM−1. IMP-type MBL was located within a variety of integrons and usually contained various gene cassettes encoding multidrug resistance. These isolates produced 54 different pulsotypes, and were classified into 42 STs by MLST. Nineteen bla_NDM−1-positive E. cloacae isolates obtained from Ningxia had the same pulsotype (PFGE type 1), belonging to ST78 within clonal complex 74 (CC74). The plasmid-based replicon typing indicated that IncX3 plasmids mediated the dissemination of bla_NDM−1 among these homologous strains. This is the first report on the outbreak of NDM-1-producing E. cloacae ST78 with contribution of IncX3 plasmids in Northwestern China. There's an immediate need to intensify surveillance attentively to prevent and control the further spread of NDM-1 in China.

Assessing genetic diversity and similarity of 435 KPC-carrying plasmids

The global spread and diversification of multidrug-resistant Gram-negative (MRGN) bacteria poses major challenges to healthcare. In particular, carbapenem-resistant Klebsiella pneumoniae strains have been frequently identified in infections and hospital-wide outbreaks. The most frequently underlying resistance gene (bla_KPC) has been spreading over the last decade in the health care setting. bla_KPC seems to have rapidly diversified and has been found in various species and on different plasmid types. To review the progress and dynamics of this diversification, all currently available KPC plasmids in the NCBI database were analysed in this work. Plasmids were grouped into 257 different representative KPC plasmids, of which 79.4% could be clearly assigned to incompatibility (Inc) group or groups. In almost half of all representative plasmids, the KPC gene is located on Tn4401 variants, emphasizing the importance of this transposon type for the transmission of KPC genes to other plasmids. The transposons also seem to be responsible for the occurrence of altered or uncommon fused plasmid types probably due to incomplete transposition. Moreover, many KPC plasmids contain genes that encode proteins promoting recombinant processes and mutagenesis; in consequence accelerating the diversification of KPC genes and other colocalized resistance genes.

Management and prevention of drug resistant infections in burn patients

Introduction: Despite modern advances, the primary cause of death after burns remains infection and sepsis. A key factor in determining outcomes is colonization with multi-drug resistant (MDR) organisms. Infections secondary to MDR organisms are challenging due to lack of adequate antibiotic treatment, subsequently prolonging hospital stay and increasing risk of adverse outcomes. Areas covered: This review highlights the most frequent organisms colonizing burn wounds as well as the most common MDR bacterial infections. Additionally, we discuss different treatment modalities and MDR infection prevention strategies as their appropriate management would minimize morbidity and mortality in this population. We conducted a search for articles on PubMed, Web of Science, Embase, Cochrane, Scopus and UpToDate with applied search strategies including a combination of: "burns, 'thermal injury,' 'infections,' 'sepsis,' 'drug resistance,' and 'antimicrobials.' Expert opinion: Management and prevention of MDR infections in burns is an ongoing challenge. We highlight the importance of preventative over therapeutic strategies, which are easy to implement and cost-effective. Additionally, targeted, limited use of antimicrobials can be beneficial in burn patients. A promising future area of investigation within this field is post-trauma microbiome profiling. Currently, the best treatment strategy for MDR in burn patients is prevention.

Carbapenemase-producing Enterobacteriaceae and Aeromonas spp. present in wastewater treatment plant effluent and nearby surface waters in the US

Carbapenemase-producing bacteria (CPB) are rare, multidrug resistant organisms most commonly associated with hospitalized patients. Metropolitan wastewater treatment plants (WWTP) treat wastewater from large geographic areas which include hospitals and may serve as epidemiologic reservoirs for the maintenance or expansion of CPB that originate from hospitals and are ultimately discharged in treated effluent. However, little is known about the potential impact of these WWTP CPB on the local surface water and their risk to the public health. In addition, CPB that are present in surface water may ultimately disseminate to intensively-managed animal agriculture facilities where there is potential for amplification by extended-spectrum cephalosporins. To better understand the role of WWTPs in the dissemination of CPB in surface waters, we obtained samples of treated effluent, and both upstream and downstream nearby surface water from 50 WWTPs throughout the US. A total of 30 CPB with clinically-relevant genotypes were recovered from 15 WWTPs (30%) of which 13 (50%) serviced large metropolitan areas and 2 (8.3%) represented small rural populations (P < 0.05). Recovery of CPB was lowest among WWTPs that utilized ultraviolet radiation for primary disinfection (12%), and higher (P = 0.11) for WWTPs that used chlorination (42%) or that did not utilize disinfection (50%). We did not detect a difference in CPB recovery by sampling site, although fewer CPB were detected in upstream (8%) compared to effluent (20%) and downstream (18%) samples. Our results indicate that WWTP effluent and nearby surface waters in the US are routinely contaminated with CPB with clinically important genotypes including those producing Klebsiella pneumoniae carbapenemase (KPC) and New Delhi metallo-beta-lactamase (NDM). This is a concern for both public health and animal agriculture because introduction of CPB into intensively managed livestock populations could lead to their amplification and foodborne dissemination.

Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains

Carbapenem-resistant Klebsiella pneumoniae (CRKP) increasingly cause high-mortality outbreaks in hospital settings globally. Following a patient fatality at a hospital in Beijing due to a blaKPC-2-positive CRKP infection, close monitoring was put in place over the course of 14 months to characterize all blaKPC-2-positive CRKP in circulation in the hospital. Whole genome sequences were generated for 100 isolates from blaKPC-2-positive isolates from infected patients, carriers and the hospital environment. Phylogenetic analyses identified a closely related cluster of 82 sequence type 11 (ST11) isolates circulating in the hospital for at least a year prior to admission of the index patient. The majority of inferred transmissions for these isolates involved patients in intensive care units. Whilst the 82 ST11 isolates collected during the surveillance effort all had closely related chromosomes, we observed extensive diversity in their antimicrobial resistance (AMR) phenotypes. We were able to reconstruct the major genomic changes underpinning this variation in AMR profiles, including multiple gains and losses of entire plasmids and recombination events between plasmids, including transposition of blaKPC-2. We also identified specific cases where variation in plasmid copy number correlated with the level of phenotypic resistance to drugs, suggesting that the number of resistance elements carried by a strain may play a role in determining the level of AMR. Our findings highlight the epidemiological value of whole genome sequencing for investigating multi-drug-resistant hospital infections and illustrate that standard typing schemes cannot capture the extraordinarily fast genome evolution of CRKP isolates.

Genomic Epidemiology of Global Carbapenemase-Producing Enterobacter spp., 2008-2014

We performed whole-genome sequencing on 170 clinical carbapenemase-producing Enterobacter spp. isolates collected globally during 2008-2014. The most common carbapenemase was VIM, followed by New Delhi metallo-β-lactamase (NDM), Klebsiella pneumoniae carbapenemase, oxacillin 48, and IMP. The isolates were of predominantly 2 species (E. xiangfangensis and E. hormaechei subsp. steigerwaltii) and 4 global clones (sequence type [ST] 114, ST93, ST90, and ST78) with different clades within ST114 and ST90. Particular genetic structures surrounding carbapenemase genes were circulating locally in various institutions within the same or between different STs in Greece, Guatemala, Italy, Spain, Serbia, and Vietnam. We found a common NDM genetic structure (NDM-GE-U.S.), previously described on pNDM-U.S. from Klebsiella pneumoniae ATCC BAA-214, in 14 different clones obtained from 6 countries spanning 4 continents. Our study highlights the importance of surveillance programs using whole-genome sequencing in providing insight into the molecular epidemiology of carbapenemase-producing Enterobacter spp.

Acquisition of Carbapenemase-Producing Enterobacteriaceae in Solid Organ Transplantation Recipients

BACKGROUND

Carbapenemase-producing Enterobacteriaceae (CPE) can lead to life-threatening outcomes with rapid spread of the carbapenemase gene in solid organ transplantation (SOT) recipients because of limitations of available antibiotics. We examined the characteristics and importance of CPE acquisition in SOT recipients with large numbers of CPE isolates.

METHODS

Between November 2015 and October 2016, 584 CPE isolates were found in 37 recipients and verified by carbapenemase gene multiplex polymerase chain reaction (PCR). One hundred recipients with at least 2 negative results in carbapenemase PCR for stool surveillance and no CPE isolates in clinical samples were retrospectively included.

RESULTS

Most CPE isolates were Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae (546, 93.5%). The most frequent transplantation organ was lung (43.3%), and the most common sample with CPE isolates other than stool was respiratory tract (22.6%). The median time between SOT and first CPE acquisition was 7 days. All-cause mortality was significantly higher in recipients with CPE than in those without CPE (24.3% vs 10.0%; P = .03). In multivariate regression analysis, stool colonization of vancomycin-resistant Enterococci and/or Clostridium difficile during 30 days before SOT (odds ratio [OR], 3.28; 95% CI, 1.24-8.68; P = .02), lung transplantation (OR, 4.50; 95% CI, 1.19-17.03; P = .03), and intensive care unit stay ≥2 weeks (OR, 6.21; 95% CI, 1.72-22.45; P = .005) were associated with acquisition of CPE.

CONCLUSIONS

Early posttransplantation CPE acquisition may affect the clinical outcome of SOT recipients. Careful screening for CPE during the early posttransplantation period would be meaningful in recipients with risk factors.

Multidrug-Resistant Enterobacter cloacae Complex Emerging as a Global, Diversifying Threat

The Enterobacter cloacae complex (ECC) includes common nosocomial pathogens capable of producing a wide variety of infections. Broad-spectrum antibiotic resistance, including the recent emergence of resistance to last-resort carbapenems, has led to increased interest in this group of organisms and carbapenem-resistant E. cloacae complex (CREC) in particular. Molecular typing methods based on heat-shock protein sequence, pulsed-field gel electrophoresis, comparative genomic hybridization, and, most recently, multilocus sequence typing have led to the identification of over 1069 ECC sequence types in 18 phylogenetic clusters across the globe. Whole-genome sequencing and comparative genomics, moreover, have facilitated global analyses of clonal composition of ECC and specifically of CREC. Epidemiological and genomic studies have revealed diverse multidrug-resistant ECC clones including several potential epidemic lineages. Together with intrinsic β-lactam resistance, members of the ECC exhibit a unique ability to acquire genes encoding resistance to multiple classes of antibiotics, including a variety of carbapenemase genes. In this review, we address recent advances in the molecular epidemiology of multidrug-resistant E. cloacae complex, focusing on the global expansion of CREC.

Whole Genome Sequencing detects Inter-Facility Transmission of Carbapenem-resistant Klebsiella pneumoniae

OBJECTIVES

To identify transmission patterns of Carbapenem-resistant Klebsiella pneumoniae infection during an outbreak at a large, tertiary care hospital and to detect whether the outbreak organisms spread to other facilities in the integrated healthcare network.

METHODS

We analyzed 71 K. pneumoniae whole genome sequences collected from clinical specimens before, during and after the outbreak and reviewed corresponding patient medical records. Sequence and patient data were used to model probable transmissions and assess factors associated with the outbreak.

RESULTS

We identified close genetic relationships among carbapenem-resistant K. pneumoniae isolates sampled during the study period. Transmission tree analysis combined with patient records uncovered extended periods of silent colonization in many study patients and transmission routes that were likely the result of asymptomatic patients transitioning between facilities.

CONCLUSIONS

Detecting how and where Carbapenem-resistant K. pneumoniae infections spread is challenging in an environment of rising prevalence, asymptomatic carriage and mobility of patients. Whole genome sequencing improved the precision of investigating inter-facility transmissions. Our results emphasize that containment of Carbapenem-resistant K. pneumoniae infections requires coordinated efforts between healthcare networks and settings of care that acknowledge and mitigate transmission risk conferred by undetected carriage and by patient transfers between facilities.

Investigation of a Carbapenemase-producing Acinetobacter baumannii outbreak using whole genome sequencing versus a standard epidemiologic investigation

Background

The standard epidemiologic investigation of outbreaks typically relies on spatiotemporal data and pulsed-field gel electrophoresis (PFGE), but whole genome sequencing (WGS) is becoming increasingly used. This investigation aimed to characterize a carbapenemase-producing Acinetobacter baumannii (CPAb) nosocomial outbreak using WGS compared to a standard outbreak investigation.

Methods

The CPAb outbreak occurred in a single center between 2012 and 2014. The standard investigation used spatiotemporal data and PFGE to generate a chain of transmission. A separate WGS investigation generated a chain of transmission based solely on WGS and date of sampling and was blinded to all other spatiotemporal data and PFGE. Core single nucleotide variant (SNV) phylogenetic analysis was performed on WGS data generated using the Illumina MiSeq platform. The chains of transmission were compared quantitatively and qualitatively to assess the concordance between both methods.

Results

28 colonized and infected cases were included. Of the 27 transmission events identified using the standard investigation, 12 (44%) were identical to the transmission events using WGS. WGS identified several transmission events that had not been detected by traditional method, and numerous transmission events that had occurred on different hospital wards than suspected by standard methods. The average number (standard deviation [SD]) of SNVs per transmission events was 1.63 (SD, 1.31) by traditional method and 0.63 (SD, 0.79) by WGS (p = 0.001) All isolates harbored the rare carbapenemase bla_OXA-237.

Conclusions

The traditional and WGS investigations had moderate concordance. When used alongside epidemiologic data and clinical information, WGS could help improve the mapping of transmission events.

Colonization with Multidrug-Resistant Enterobacteriaceae is Associated with Increased Mortality Following Burn Injury in Sub-Saharan Africa

BACKGROUND

Multidrug-resistant (MDR) bacteria are an emerging international concern in low- and middle-income countries that threaten recent public health gains. These challenges are exacerbated in immunocompromised hosts, such as those with burn injury. This study sought to describe the epidemiology and associated clinical outcomes of burn wound colonization in a Malawian tertiary burn center.

METHODS

This is a prospective analysis of burn patients presenting to Kamuzu Central Hospital in Lilongwe, Malawi, within 72 h of burn injury. A swab of each patient's primary wound was collected at admission and each subsequent week. The primary exposure was burn wound colonization with MDR bacteria, particularly Enterobacteriaceae. The primary outcome was in-hospital mortality. A log binomial model estimated the association between the exposure and outcome, adjusted for confounders.

RESULTS

Ninety-nine patients were enrolled with a median age of 4 years (IQR 2-12) and a male preponderance (54%). Median total body surface area burn (TBSA) was 14% (IQR 9-25), and crude in-hospital mortality was 19%. Enterobacteriaceae were the most common MDR bacteria with 36% of patients becoming colonized. Wound colonization with MDR Enterobacteriaceae was associated with increased in-hospital mortality with a risk ratio of 1.86 (95% CI 1.38, 2.50, p < 0.001) adjusted for TBSA, burn type (scald vs. flame), sex, age, length of stay, and methicillin-resistant Staphylococcus aureus colonization.

CONCLUSION

MDR bacteria, especially Enterobacteriaceae, are common and are associated with worse burn injury outcomes. In resource-poor environments, a greater emphasis on prevention of MDR bacterial colonization, improved isolation precautions, affordable diagnostics, and antibiotic stewardship are imperative.

In Vitro Activity of LYS228, a Novel Monobactam Antibiotic, against Multidrug-Resistant Enterobacteriaceae

LYS228 is a novel monobactam with potent activity against Enterobacteriaceae LYS228 is stable to metallo-β-lactamases (MBLs) and serine carbapenemases, including Klebsiella pneumoniae carbapenemases (KPCs), resulting in potency against the majority of extended-spectrum β-lactamase (ESBL)-producing and carbapenem-resistant Enterobacteriaceae strains tested. Overall, LYS228 demonstrated potent activity against 271 Enterobacteriaceae strains, including multidrug-resistant isolates. Based on MIC₉₀ values, LYS228 (MIC₉₀, 1 μg/ml) was ≥32-fold more active against those strains than were aztreonam, ceftazidime, ceftazidime-avibactam, cefepime, and meropenem. The tigecycline MIC₉₀ was 4 μg/ml against the strains tested. Against Enterobacteriaceae isolates expressing ESBLs (n = 37) or displaying carbapenem resistance (n = 77), LYS228 had MIC₉₀ values of 1 and 4 μg/ml, respectively. LYS228 exhibited potent bactericidal activity, as indicated by low minimal bactericidal concentration (MBC) to MIC ratios (MBC/MIC ratios of ≤4) against 97.4% of the Enterobacteriaceae strains tested (264/271 strains). In time-kill studies, LYS228 consistently achieved reductions in CFU per milliliter of 3 log₁₀ units (≥99.9% killing) at concentrations ≥4× MIC for Escherichia coli and K. pneumoniae reference strains, as well as isolates encoding TEM-1, SHV-1, CTX-M-14, CTX-M-15, KPC-2, KPC-3, and NDM-1 β-lactamases.

Epidemiologic characteristics of health care-associated outbreaks and lessons learned from multiple outbreak investigations with a focus on the usefulness of routine molecular analysis

BACKGROUND

Single outbreaks have often been reported in health care settings, but the frequency of outbreaks at a hospital over time has not been described. We examined epidemiologic features of all health care-associated outbreak investigations at an academic hospital during a 5-year period.

METHODS

Health care-associated outbreak investigations at an academic hospital (2012-2016) were retrospectively reviewed through data on comprehensive hospital-wide surveillance and pulsed-field gel electrophoresis (PFGE) analysis.

RESULTS

Fifty-one health care-associated outbreaks (annual range, 8-15), including 26 (51%) outbreaks in intensive care units (ICUs), and 263 infected-colonized patients involved in these outbreaks were identified. The frequency of pathogens varied by affected location, specifically multidrug-resistant organisms (20/26 outbreaks, 77% in ICUs vs 2/25 outbreaks, 8% in non-ICUs; P < .0001) and gastroenteritis because of Clostridium difficile, norovirus, or adenovirus (1/26 outbreaks, 4% in ICUs vs 17/25 outbreaks, 68% in non-ICUs; P < .0001). Outbreaks occurred in approximately one-third of all units (37%) with some repeated instances of the same pathogens. Of 16 outbreaks caused by a bacterial pathogen evaluated by PFGE, 12 (75%) included some indistinguishable strains, suggesting person-to-person transmission or a common source.

CONCLUSIONS

This study demonstrated epidemiologic characteristics of multiple outbreaks between ICUs and non-ICUs and the value of molecular typing in understanding the epidemiology of health care-associated outbreaks.

Bacterial Infections After Burn Injuries: Impact of Multidrug Resistance

Patients who are admitted to the hospital after sustaining a large burn injury are at high risk for developing hospital-associated infections. If patients survive the initial 72 hours after a burn injury, infections are the most common cause of death. Ventilator-associated pneumonia is the most important infection in this patient population. The risk of infections caused by multidrug-resistant bacterial pathogens increases with hospital length of stay in burn patients. In the first days of the postburn hospitalization, more susceptible, Gram-positive organisms predominate, whereas later more resistant Gram-negative organisms are found. These findings impact the choice of empiric antibiotics in critically ill burn patients. A proactive infection control approach is essential in burn units. Furthermore, a multidisciplinary approach to burn patients with a team that includes an infectious disease specialist and a pharmacist in addition to the burn surgeon is highly recommended.

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.

Germicidal Activity against Carbapenem/Colistin-Resistant Enterobacteriaceae Using a Quantitative Carrier Test Method

Susceptibility to germicides for carbapenem/colistin-resistant Enterobacteriaceae is poorly described. We investigated the efficacy of multiple germicides against these emerging antibiotic-resistant pathogens using the disc-based quantitative carrier test method that can produce results more similar to those encountered in health care settings than a suspension test. Our study results demonstrated that germicides commonly used in health care facilities likely will be effective against carbapenem/colistin-resistant Enterobacteriaceae when used appropriately in health care facilities.

Genomic and Geographic Context for the Evolution of High-Risk Carbapenem-Resistant Enterobacter cloacae Complex Clones ST171 and ST78

Recent reports have established the escalating threat of carbapenem-resistant Enterobacter cloacae complex (CREC). Here, we demonstrate that CREC has evolved as a highly antibiotic-resistant rather than highly virulent nosocomial pathogen. Applying genomics and Bayesian phylogenetic analyses to a 7-year collection of CREC isolates from a northern Manhattan hospital system and to a large set of publicly available, geographically diverse genomes, we demonstrate clonal spread of a single clone, ST171. We estimate that two major clades of epidemic ST171 diverged prior to 1962, subsequently spreading in parallel from the Northeastern to the Mid-Atlantic and Midwestern United States and demonstrating links to international sites. Acquisition of carbapenem and fluoroquinolone resistance determinants by both clades preceded widespread use of these drugs in the mid-1980s, suggesting that antibiotic pressure contributed substantially to its spread. Despite a unique mobile repertoire, ST171 isolates showed decreased virulence in vitro While a second clone, ST78, substantially contributed to the emergence of CREC, it encompasses diverse carbapenemase-harboring plasmids, including a potentially hypertransmissible IncN plasmid, also present in other sequence types. Rather than heightened virulence, CREC demonstrates lineage-specific, multifactorial adaptations to nosocomial environments coupled with a unique potential to acquire and disseminate carbapenem resistance genes. These findings indicate a need for robust surveillance efforts that are attentive to the potential for local and international spread of high-risk CREC clones.IMPORTANCE Carbapenem-resistant Enterobacter cloacae complex (CREC) has emerged as a formidable nosocomial pathogen. While sporadic acquisition of plasmid-encoded carbapenemases has been implicated as a major driver of CREC, ST171 and ST78 clones demonstrate epidemic potential. However, a lack of reliable genomic references and rigorous statistical analyses has left many gaps in knowledge regarding the phylogenetic context and evolutionary pathways of successful CREC. Our reconstruction of recent ST171 and ST78 evolution represents a significant addition to current understanding of CREC and the directionality of its spread from the Eastern United States to the northern Midwestern United States with links to international collections. Our results indicate that the remarkable ability of E. cloacae to acquire and disseminate cross-class antibiotic resistance rather than virulence determinants, coupled with its ability to adapt under conditions of antibiotic pressure, likely led to the wide dissemination of CREC.

Using Patient Risk Factors to Identify Whether Carbapenem-Resistant Enterobacteriaceae Infections Are Caused by Carbapenemase-Producing Organisms

Evaluating all inpatient carbapenem-resistant Enterobacteriaceae (CRE) infections over a 1-year period, 47% were caused by carbapenemase-producing (CP) organisms. Compared with non-CP-CRE patients, patients with CP-CRE had an 18-fold greater odds of a recent stay in a foreign health care facility and a 3-fold greater odds of transfer from a post–acute care facility.

Clinically Relevant Plasmid-Host Interactions Indicate that Transcriptional and Not Genomic Modifications Ameliorate Fitness Costs of Klebsiella pneumoniae Carbapenemase-Carrying Plasmids

The rapid dissemination of antimicrobial resistance (AMR) around the globe is largely due to mobile genetic elements, such as plasmids. They confer resistance to critically important drugs, including extended-spectrum beta-lactams, carbapenems, and colistin. Large, complex resistance plasmids have evolved alongside their host bacteria. However, much of the research on plasmid-host evolution has focused on small, simple laboratory plasmids in laboratory-adapted bacterial hosts. These and other studies have documented mutations in both host and plasmid genes which occur after plasmid introduction to ameliorate fitness costs of plasmid carriage. We describe here the impact of two naturally occurring variants of a large AMR plasmid (pKpQIL) on a globally successful pathogen. In our study, after pKpQIL plasmid introduction, no changes in coding domain sequences were observed in their natural host, Klebsiella pneumoniae However, significant changes in chromosomal and plasmid gene expression may have allowed the bacterium to adapt to the acquisition of the AMR plasmid. We hypothesize that this was sufficient to ameliorate the associated fitness costs of plasmid carriage, as pKpQIL plasmids were maintained without selection pressure. The dogma that removal of selection pressure (e.g., antimicrobial exposure) results in plasmid loss due to bacterial fitness costs is not true for all plasmid/host combinations. We also show that pKpQIL impacted the ability of K. pneumoniae to form a biofilm, an important aspect of virulence. This study used highly relevant models to study the interaction between AMR plasmids and pathogens and revealed striking differences from results of studies done on laboratory-adapted plasmids and strains.IMPORTANCE Antimicrobial resistance is a serious problem facing society. Many of the genes that confer resistance can be shared between bacteria through mobile genetic elements, such as plasmids. Our work shows that when two clinically relevant AMR plasmids enter their natural host bacteria, there are changes in gene expression, rather than changes to gene coding sequences. These changes in gene expression ameliorate the potential fitness costs of carriage of these AMR plasmids. In line with this, the plasmids were stable within their natural host and were not lost in the absence of selective pressure. We also show that better understanding of the impact of resistance plasmids on fundamental pathogen biology, including biofilm formation, is crucial for fighting drug-resistant infections.