First report of NDM-1-producing clinical isolate of Leclercia adecarboxylata in Spain

Resistance phenotype and virulence potential of Leclercia adecarboxylata strains isolated from different sources

Introduction. Leclercia adecarboxylata is a member of Enterobacterales, often considered an opportunistic pathogen. Recent reports have highlighted L. adecarboxylata as an emerging pathogen harbouring virulence and resistance determinants.Gap statement. Little information exists on virulence and resistance determinants in L. adecarboxylata strains isolated from environmental, food, and clinical samples.Aim. To determine the presence of resistance and virulence determinants and plasmid features in L. adecarboxylata strains isolated from environmental, food, and clinical samples, as well as their phylogenetic relationship.Results. All strains tested showed resistance to β-lactams and quinolones but were sensitive to aminoglycosides and nitrofurans. However, even though fosfomycin resistance is considered a characteristic trait of L. adecarboxylata, the resistance phenotype was only observed in 50 % of the strains; bla TEM was the most prevalent BLEE gene (70 %), while the quinolone qnrB gene was observed in 60 % of the strains. Virulence genes were differentially observed in the strains, with adhesion-related genes being the most abundant, followed by toxin genes. Finally, all strains carried one to seven plasmid bands ranging from 7 to 125 kbps and harboured several plasmid addiction systems, such as ParDE, VagCD, and CcdAB in 80 % of the strains.Conclusions. L. adecarboxylata is an important emerging pathogen that may harbour resistance and virulence genes. Additionally, it has mobilizable genetic elements that may contribute to the dissemination of genetic determinants to other bacterial genera.

Dissemination of NDM-producing bacteria in Southern Brazil

BACKGROUND

The dissemination of NDM-1 carbapenemases (New Delhi Metallo-β-lactamase) is a global public health problem, mainly in developing countries. The aim of this study was to characterize the spread of NDM-producing bacteria in the Southern Brazilian states analyzing epidemiological, molecular, and antimicrobial susceptibility aspects.

METHODS

A total of 10,684 carbapenem-resistant isolates of Enterobacterales, Pseudomonas spp. and Acinetobacter spp. obtained from several hospitals in eight cities in Southern Brazil were screened, and 486 NDM-producing bacteria were selected.

RESULTS

The incidence varied from 0.5 to 77 cases/100.000 habitants. ST11, ST15, ST340 and ST674 were the most common in K. pneumoniae. A total of 5 plasmids were identified in one K. pneumoniae strain: Col440I, Col440II, IncFIA(HI1), IncFIB(K), IncFIB(pQil)/ IncFII(K), and IncR.

CONCLUSIONS

The number of patients with NDM-producing bacteria has increased in Southern Brazil, whose gene is present in different plasmids, explaining the expansion of this enzyme.

Molecular investigation of an outbreak associated with total parenteral nutrition contaminated with NDM-producing Leclercia adecarboxylata

Background

This study aimed to determine the epidemiological, microbiological, and molecular characteristics of an outbreak of carbapenem-resistant Leclercia adecarboxylata in three hospitals associated with the unintended use of contaminated total parental nutrition (TPN).

Methods

For 10 days, 25 patients who received intravenous TPN from the same batch of a formula developed sepsis and had blood cultures positive for L. adecarboxylata. Antimicrobial susceptibility and carbapenemase production were performed in 31 isolates, including one from an unopened bottle of TPN. Carbapenemase-encoding genes, extended-spectrum β-lactamase–encoding genes were screened by PCR, and plasmid profiles were determined. Horizontal transfer of carbapenem resistance was performed by solid mating. Clonal diversity was performed by pulsed-field gel electrophoresis. The resistome was explored by whole-genome sequencing on two selected strains, and comparative genomics was performed using Roary.

Results

All 31 isolates were resistant to aztreonam, cephalosporins, carbapenems, trimethoprim/sulfamethoxazole, and susceptible to gentamicin, tetracycline, and colistin. Lower susceptibility to levofloxacin (51.6%) and ciprofloxacin (22.6%) was observed. All the isolates were carbapenemase producers and positive for bla_NDM-1, bla_TEM-1B, and bla_SHV-12 genes. One main lineage was detected (clone A, 83.9%; A1, 12.9%; A2, 3.2%). The bla_NDM-1 gene is embedded in a Tn125-like element.

Genome analysis showed genes encoding resistance for aminoglycosides, quinolones, trimethoprim, colistin, phenicols, and sulphonamides and the presence of IncFII (Yp), IncHI2, and IncHI2A incompatibility groups. Comparative genomics showed a major phylogenetic relationship among L. adecarboxylata I1 and USDA-ARS-USMARC-60222 genomes, followed by our two selected strains.

Conclusion

We present epidemiological, microbiological, and molecular evidence of an outbreak of carbapenem-resistant L. adecarboxylata in three hospitals in western Mexico associated with the use of contaminated TPN.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-05923-0.

Leclercia Adecarboxylata Causing Necrotizing Fasciitis in an Immunocompetent Athlete Injecting Illicit Testosterone Supplements

Leclercia adecarboxylata (L. adecarboxylata) is an uncommon and often misdiagnosed cause of multiple infection types including skin and soft tissue, cholecystitis, and septicemia. It commonly afflicts immunocompromised hosts or individuals who experience trauma in aquatic environments. We present a case where this bacteria causes necrotizing fasciitis as a consequence of injecting street bought testosterone supplements. This patient was treated successfully with excisional debridement of the wound as well as a one week course of Linezolid and Bactrim. 

Retrospective Screening and Analysis of mcr-1 and bla NDM in Gram-Negative Bacteria in China, 2010-2019

Currently, Gram-negative bacteria have developed multidrug and broad-spectrum drug resistance, and the numbers of species and strains carrying mcr or bla_NDM genes are increasing. In this study, mcr-1 and bla_NDM distribution of 12,858 Gram-negative bacteria isolated from wildlife, patients, livestock, poultry and environment in 14 provinces of China from 2010 to 2019 and the antibiotics resistance in regard to polymyxins (polymyxin B and colistin) and carbapenems of positive strains were investigated. A total of 70 strains of 10 species carried the mcr-1 gene, positive rates of patients, livestock and poultry, and environmental strains were 0.62% (36/5,828), 4.07% (29/712), 5.43% (5/92), respectively. Six strains of 3 species carrying the bla_NDM gene all came from patients 0.10% (6/5,828). Two new mcr-1 gene variants (GenBank: MK965883, MK965884) were identified, one of which contains premature stop codon. The drug susceptibility results showed that all mcr-1 carriers were sensitive to carbapenems, among which, 66 strains were resistant and 4 were sensitive to polymyxins. The strains with the bla_NDM gene had different degrees of resistance to carbapenems and were sensitive to polymyxins. The findings that species carrying mcr-1 or bla_NDM genes were limited and mostly normal flora of opportunistic or low pathogenic organisms indicated that transfer of mcr-1 and bla_NDM genes between bacteria was relatively limited in China. The none detection among wildlife compared with other sources supports the speculation that the emergence of and increase in polymyxins and carbapenem-resistant strains was mainly related to the selective pressure of antibiotics.

Leclercia adecarboxylata From Human Gut Flora Carries mcr-4.3 and bla IMP-4-Bearing Plasmids

A clinical Leclercia adecarboxylata strain harboring the mcr-4.3 and bla _IMP-4 genes was isolated from active rectal screening of carbapenem-resistant Enterobacteriaceae (CRE) in a patient. The isolate was found to harbor seven plasmids, including a 94,635 bp bla _IMP-4-bearing IncN plasmid and a 9,782 bp mcr-4.3-bearing ColE10-type plasmid. The isolate was susceptible to colistin despite carrying the mcr-4.3 gene, suggesting that this MCR-4 variant may not be functional. Carriage of antibiotic resistance genes in human gut L. adecarboxylata strain suggests that close surveillance of resistance strains in the human gut flora should be included as a routine clinical practice to prevent occurrence of infections, especially among immunocompromised patients.

First Report of Coexistence of Three Different MDR Plasmids, and That of Occurrence of IMP-Encoding Plasmid in Leclercia adecarboxylata

Three different MDR plasmids p16005813A, p16005813B, and p16005813C, which carried a total of 18 non-redundant resistance genes or gene loci, were identified in a single clinical isolate of Leclercia adecarboxylata. The p16005813A backbone showed very low levels of identity to all DNA sequences available in public databases and carried a repA gene that could not assigned into any of known incompatibility groups. The IncFII-family p16005813B and pECAZ161_KPC had essentially identical backbones. p16005813C belonged to an IncR single-replicon plasmid. p16005813A, p16005813B, and p16005813C harbored three different novel MDR regions as their sole accessory modules. The MDR region of p16005813B manifested as Tn6505, which was generated from insertion of bla_IMP–8-carrying In655 instead of In4 into the Tn1696 backbone. Other key antibiotic resistance elements included Tn2, IS26–mph(A)–mrx–mphR(A)–IS6100 unit, chrA region, In27, and aacC2–tmrB region in the MDR region of p16005813A, and ΔTn9 carrying catA1, In609, and IS26–tetA(C)–tetR(C)–IS26 unit in the MDR region of p16005813C. This was the first report of coexistence of three different MDR plasmids, and that of occurrence of IMP-encoding plasmid and bla_IMP–8 gene in L. adecarboxylata.

Leclercia adecarboxylata Cholecystitis with Septic Shock in Immunocompetent Patient

L. adecarboxylata is a Gram-negative rod previously named Escherichia adecarboxylata, isolated as normal flora in the gut of animals including human stool. Most reported cases refer to immunocompromised patients with polymicrobial infections and water environments. Here we present a case of 51-year-old immunocompetent female presented with nausea, vomiting, malaise, and subjective fever for few days. On examination, she was drowsy but arousable and oriented to person, place, time, and situation. Her abdomen was tender globally and more tender in the epigastric area. Vitals showed a temperature of 37°C, pulse of 110 beats/min, blood pressure of 75/50 mmHg, and oxygen saturation of 91% on room air. An HIV panel and hepatitis panel were negative. Liver and gallbladder ultrasound was performed, revealing multiple nonmobile stones with shadowing noted within the gallbladder sac, a thickened gallbladder wall, and a moderate amount of pericholecystic fluid. Broad spectrum antibiotics, crystalloid fluids, and vasopressors were initiated. A few hours after admission she developed respiratory failure for which she underwent endotracheal intubation. An ultrasound guided gallbladder drain was performed. Culture of the biliary fluid yielded pure growth of pan-sensitive L. adecarboxylata; antibiotics were narrowed accordingly. The patient was on the maximum doses of vasopressin, norepinephrine, and epinephrine with a blood pressure of 75/45 and a mean arterial pressure of 51. She passed away on the fourth day of admission.

Leclercia adecarboxylata: a case report and literature review of 74 cases demonstrating its pathogenicity in immunocompromised patients

Leclercia adecarboxylata is a Gram-negative bacterium belonging to the family Enterobacteriaceae. It has been described as an emerging human pathogen with the potential to cause severe infection in immunocompromised patients. The aim of this study was to describe a clinical case of infection with L. adecarboxylata and give a review of previous reports on infection. We report the presence of L. adecarboxylata in a patient initially admitted to our hospital for a lung transplant. She had diarrhoea, urinary tract infection and pneumonia caused by L. adecarboxylata. The isolate was resistant to trimethoprim-sulfamethoxazole and susceptible to 15 other antibiotics tested. The literature search for previous reports of infection with L. adecarboxylata resulted in 61 publications describing 74 cases. Bacteremia and wound infections were most often described, and only a few cases were fatal. L. adecarboxylata was most often found as a monomicrobial infection in immunocompromised patients, and as part of a polymicrobial infection in immunocompetent patients. The previously described isolates showed a high susceptibility to antibiotics, and treatment was efficient in most cases. Due to similarities in metabolic products, L. adecarboxylata might have been mistaken as Escherichia spp., but with new identification methods such as MALDI-TOF MS, it is possible to obtain a certain identification.

Occurrence of Highly Conjugative IncX3 Epidemic Plasmid Carrying bla NDM in Enterobacteriaceae Isolates in Geographically Widespread Areas

The emergence of New Delhi metallo-β-lactamase (NDM) in common enterobacterial species is a major concern for healthcare. Early reports have revealed that the spread of NDM involved diverse and heterogeneous plasmids. Recently, the involvement of a rare, IncX3 subtype plasmid has been increasingly recognized. Here, we studied the prevalence of IncX plasmid subtypes in 198 carbapenem-resistant Enterobacteriaceae, originating from a territory-wide active surveillance in Hong Kong in 2016. The complete sequences and biological features of the bla _NDM-carrying plasmids were investigated. A total of 62 NDM-type, 21 OXA-48 type, 14 IMP-type, 8 KPC-type, 4 IMI-type producers, and 89 non-carbapenemase-producers were tested for presence of IncX subtypes. IncX3 (n = 60) was the most common subtype, followed by IncX4 (n = 6) and IncX1 (n = 2). The prevalence of IncX3 subtype in isolates producing NDM, other carbapenemase types and non-carbapenemase producers were 75.8, 21.3, and 3.4%, respectively (P < 0.001). An IncX3 plasmid (size ∼50 kb) was confirmed to carry bla _NDM in 47 isolates of different enterobacterial species. Thirteen IncX3 plasmids originating from six healthcare regions in Hong Kong were completely sequenced. The results showed that the IncX3 plasmids carrying bla _NDM share a high degree of sequence identity with a previously reported plasmid, pNDM-HN380 (GenBank accession JX104760), over the backbone and genetic load regions. A blast search further revealed the occurrence of identical or nearly identical IncX3 plasmids carrying bla _NDM in other part of China, Korea, Myanmar, India, Oman, Kuwait, Italy, and Canada. Two IncX3 carrying bla _NDM were investigated further. Conjugation experiments demonstrated that the IncX3 plasmids could be efficiently transferred to multiple enterobacterial species at frequencies that are comparable or higher than the epidemic IncFII plasmid carrying bla _CTX-M (pHK01). In addition, efficient transfer of the NDM plasmids occurred over a range of temperatures. In conclusion, this study demonstrated the important role played by IncX3 in the dissemination of NDM and the occurrence of pNDM-HN380-like plasmids in geographically widespread areas. The high mobility of IncX3 plasmid across different enterobacterial species highlights the ability of this plasmid replicon to be an important vehicle in worldwide dissemination of NDM.

IncX3 Epidemic Plasmid Carrying blaNDM-5 in Escherichia coli from Swine in Multiple Geographic Areas in China

Six imported pigs originating from Guangdong, Henan, and Hunan provinces in China during October 2015 to February 2017 were cultured and found to be positive for meropenem-resistant Escherichia coli The samples yielded 9 E. coli isolates of diverse sequence types carrying bla_NDM-5 on IncX3 (8 isolates from 5 farms) or IncFII (1 isolate from 1 farm) plasmids. The mcr-1 gene was coharbored by 4 isolates. The IncX3 plasmids (∼46 kb) carrying bla_NDM-5 were identical or nearly identical to each other.

Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance

The hospital environment is a potential reservoir of bacteria with plasmids conferring carbapenem resistance. Our Hospital Epidemiology Service routinely performs extensive sampling of high-touch surfaces, sinks, and other locations in the hospital. Over a 2-year period, additional sampling was conducted at a broader range of locations, including housekeeping closets, wastewater from hospital internal pipes, and external manholes. We compared these data with previously collected information from 5 years of patient clinical and surveillance isolates. Whole-genome sequencing and analysis of 108 isolates provided comprehensive characterization of bla_KPC/bla_NDM-positive isolates, enabling an in-depth genetic comparison. Strikingly, despite a very low prevalence of patient infections with bla_KPC-positive organisms, all samples from the intensive care unit pipe wastewater and external manholes contained carbapenemase-producing organisms (CPOs), suggesting a vast, resilient reservoir. We observed a diverse set of species and plasmids, and we noted species and susceptibility profile differences between environmental and patient populations of CPOs. However, there were plasmid backbones common to both populations, highlighting a potential environmental reservoir of mobile elements that may contribute to the spread of resistance genes. Clear associations between patient and environmental isolates were uncommon based on sequence analysis and epidemiology, suggesting reasonable infection control compliance at our institution. Nonetheless, a probable nosocomial transmission of Leclercia sp. from the housekeeping environment to a patient was detected by this extensive surveillance. These data and analyses further our understanding of CPOs in the hospital environment and are broadly relevant to the design of infection control strategies in many infrastructure settings.

Carbapenemase-producing organisms (CPOs) are a global concern because of the morbidity and mortality associated with these resistant Gram-negative bacteria. Horizontal plasmid transfer spreads the resistance mechanism to new bacteria, and understanding the plasmid ecology of the hospital environment can assist in the design of control strategies to prevent nosocomial infections. A 5-year genomic and epidemiological survey was undertaken to study the CPOs in the patient-accessible environment, as well as in the plumbing system removed from the patient. This comprehensive survey revealed a vast, unappreciated reservoir of CPOs in wastewater, which was in contrast to the low positivity rate in both the patient population and the patient-accessible environment. While there were few patient-environmental isolate associations, there were plasmid backbones common to both populations. These results are relevant to all hospitals for which CPO colonization may not yet be defined through extensive surveillance.

Isolation and characterization of multidrug-resistant Leclercia species from animal clinical case

Leclercia adecarboxylata, a Gram-negative bacillus of family Enterobacteriaceae, is an uncommonly identified pathogen isolated from environmental and clinical specimens. Most of the human infections are polymicrobial and commonly occur in immunocompromised hosts, although nosocomial infections in immunocompetent hosts have been documented. Here, we describe the case of isolation of Leclercia species as polymicrobial infection from bovine suffering from respiratory distress in Chhattisgarh state of India. The isolates were identified by their phenotypes, 16S rDNA sequencing and MALDI-TOF-MS. The isolate was found to be resistant to aminoglycosides and fluoroquinolone antibiotics and intermediate resistant to cephalosporins and evidenced for uncertain clinical relevance and could act as hidden source of public health hazard.

SIGNIFICANCE AND IMPACT OF THE STUDY

Leclercia adecarboxylata is a rarely reported human pathogen. We report here the case from bovine suffering from respiratory distress; the sample yielded Leclercia species as polymicrobial culture. The isolate was found to be multidrug resistant and evidenced for uncertain clinical relevance and could act as hidden source of public health hazard. The limited literature available on this organism is reviewed, and the potential implications of findings are discussed. To the best of our knowledge, this is the first report of isolation and characterization of multidrug-resistant Leclercia species from animal clinical case from India.