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

Abstract 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 blaNDM-1, blaTEM-1B, and blaSHV-12 genes. One main lineage was detected (clone A, 83.9%; A1, 12.9%; A2, 3.2%). The blaNDM-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.

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Prevalence and mechanisms of carbapenem resistance among Klebsiella aerogenes in a tertiary hospital in China

10.21203/rs.3.rs-19281/v1 ◽

2020 ◽

Author(s):

Luxiang Liu ◽

Jingjing Quan ◽

Dongdong Zhao ◽

Weichao Liao ◽

Jiaojian Lv ◽

...

Keyword(s):

Intensive Care ◽

Efflux Pump ◽

Carbapenem Resistance ◽

Clonal Diversity ◽

Tertiary Hospital ◽

Molecular Characteristics ◽

Klebsiella Aerogenes ◽

Carbapenem Resistant ◽

Efflux Pump Inhibition ◽

Clonal Spread

Abstract Background: Klebsiella aerogenes has emerged as one of the most important nosocomial pathogens for patients in intensive care units (ICU) in recent years. This study aims to evaluated the prevalence and molecular characteristics of clinical carbapenem-resistant K. aerogenes (CRKA) isolates in a tertiary hospital in China.Results: Twenty CRKA were identified among all the isolates, with the rate of 5.5% (20/364). Six CRKA isolates produced KPC-2 and 1 CRKA isolate produced NDM-1. PFGE and MLST indicated that the 20 CRKA strains were clonal diversity. All the bla KPC-2 gene and bla NDM-1 gene were located on plasmids and all the plasmids with bla KPC-2 and bla NDM-1 genes could successfully transferred to EC600 or J53. Twelve of 13 CRKA strains without any carbapenemase genes were positive for efflux pump inhibition test.Conclusion: Overall, the prevalence of CRKA in the tertiary hospital in Zhejiang Province of China is 5.5%. Only 35% of CRKA produce carbapenemase and efflux pumps might play an important role in the carbapenem resistance of K. aerogenes. It is necessary to strengthen the surveillance of carbapenem resistance in the hospital to prevent the horizontal and clonal spread of CRKA.

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Phenotypic and genotypic study of carbapenem-resistant Pseudomonas aeruginosa strains isolated from hospitalized patients

Revista Romana de Medicina de Laborator ◽

10.1515/rrlm-2016-0021 ◽

2016 ◽

Vol 24 (2) ◽

pp. 201-211 ◽

Cited By ~ 1

Author(s):

Luminița Matroș ◽

Tibor Ludovic Krausz ◽

Stanca Lucia Pandrea ◽

Monica Ioana Ciontea ◽

Erica Chiorean ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Dipicolinic Acid ◽

Screening Method ◽

Carbapenem Resistance ◽

Hospitalized Patients ◽

Carbapenem Resistant ◽

Genes Encoding ◽

Immunosuppressed Patients ◽

Phenotypic Methods ◽

Encoding Genes

Abstract Introduction: Nosocomial infections caused by Pseudomonas aeruginosa producing carbapenemases represent an important cause of morbidity and mortality among immunosuppressed patients. The aim of our study was to detect the production of metallo-carbapenemases (MBLs) by phenotypic methods and to detect the presence of the MBLs encoding genes (blaIMP and blaVIM) by PCR in P. aeruginosa strains isolated from hospitalized patients to the Regional Institute of Gastroenterology and Hepatology, Cluj-Napoca. Material and methods: Between September 2014-February 2015, we tested thirty-eight P. aeruginosa strains resistant to carbapenems according to CLSI 2014 breakpoints, determined by Vitek®2(BioMérieux),isolated from various clinical specimens. Phenotypic detection of the MBLs production was performed using the KPC/MBL Confirmation kit (ROSCO®) and the MBL Etest® IP/IPI (BioMérieux). We used the PCR method for detecting MBLs encoding genes: blaIMP, blaVIM. Results: The strains were obtained from surgery (55.3%), ICU (15.8%) and gastroenterology wards (28.9%), isolated from pus (25.8%), tracheal secretion (22.7%), bile (13.6%), sputum (10.6%), blood (10.6%), other secretions (16.7%). These strains were resistant to multiple classes of antibiotics. By ROSCO® method 28/38 strains (73.7%) were positive with imipenem ± dipicolinic acid (DPA) and 22/38 (57.9%) with meropenem ± DPA. Etest® waspositive for the 28/38 strains (73.7%). 11 strains (28.9%) were positive for KPC with the screening method. We identified: 6 blaIMP+ (15.8%), 2 (5.3%) blaVIM+ and 4 blaIMP+/blaVIM+ strains (10.5%). Conclusion: Both genes encoding MBL were found, alone or in combination. The increasing level of carbapenem resistance of these strains impose their routine testing to detect MBL.

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Molecular characterization of clinical carbapenem-resistant Enterobacterales from Qatar

European Journal of Clinical Microbiology & Infectious Diseases ◽

10.1007/s10096-021-04185-7 ◽

2021 ◽

Author(s):

Fatma Ben Abid ◽

Clement K. M. Tsui ◽

Yohei Doi ◽

Anand Deshmukh ◽

Christi L. McElheny ◽

...

Keyword(s):

Common Species ◽

Clinical Samples ◽

Whole Genome ◽

E Coli ◽

Carbapenem Resistant ◽

Genes Encoding ◽

Encoding Genes ◽

Sequence Types ◽

Common Sequence

AbstractOne hundred forty-nine carbapenem-resistant Enterobacterales from clinical samples obtained between April 2014 and November 2017 were subjected to whole genome sequencing and multi-locus sequence typing. Klebsiella pneumoniae (81, 54.4%) and Escherichia coli (38, 25.5%) were the most common species. Genes encoding metallo-β-lactamases were detected in 68 (45.8%) isolates, and OXA-48-like enzymes in 60 (40.3%). blaNDM-1 (45; 30.2%) and blaOXA-48 (29; 19.5%) were the most frequent. KPC-encoding genes were identified in 5 (3.6%) isolates. Most common sequence types were E. coli ST410 (8; 21.1%) and ST38 (7; 18.4%), and K. pneumoniae ST147 (13; 16%) and ST231 (7; 8.6%).

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Emergence of Carbapenem Resistance inAcinetobacter baumanniiRecovered From Blood Cultures in Australia

Infection Control and Hospital Epidemiology ◽

10.1086/507012 ◽

2006 ◽

Vol 27 (7) ◽

pp. 759-761 ◽

Cited By ~ 27

Author(s):

Anton Y. Peleg ◽

Clare Franklin ◽

Jan M. Bell ◽

Denis W. Spelman

Keyword(s):

Acinetobacter Baumannii ◽

Linear Trend ◽

Carbapenem Resistance ◽

Blood Cultures ◽

Clonal Type ◽

Carbapenem Resistant ◽

Genes Encoding ◽

Blood Specimens

We describe the first emergence of carbapenem-resistantAcinetobacter baumanniiin Australia. NinetyA. baumanniiisolates recovered from cultures of blood specimens from 69 patients were analyzed. Overall, 58 isolates (64%) were resistant to meropenem. The χ2test for linear trend revealed that emergence of carbapenem resistance was statistically significant during the 32-month study period. Selected isolates were of the same clonal type, and no genes encoding carbapenemases were identified.

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Molecular characteristics of carbapenem-resistant Acinetobacter spp. from clinical infection samples and fecal survey samples in Southern China

BMC Infectious Diseases ◽

10.1186/s12879-019-4423-3 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 5

Author(s):

Si Li ◽

Xiaonv Duan ◽

Yuan Peng ◽

Yongyu Rui

Keyword(s):

Efflux Pump ◽

Southern China ◽

Variable Region ◽

Carbapenem Resistance ◽

Resistant Bacteria ◽

Molecular Characteristics ◽

Clinical Infection ◽

High Genetic Diversity ◽

Carbapenem Resistant ◽

Opportunistic Bacteria

Abstract Background Carbapenem resistance among Acinetobacter species has become a life-threatening problem. As a last resort in the treatment of gram-negative bacteria infection, resistance to colistin is also a serious problem. The aim of study was to analyze the mechanism of resistance and perform genotyping of carbapenem-resistant Acinetobacter from clinical infection and fecal survey samples in Southern China. Methods One hundred seventy and 74 carbapenem-resistant Acinetobacter were isolated from clinical infection samples and fecal survey samples, respectively. We detected the related genes, including carbapenemase genes (blaKPC, blaIMP, blaSPM, blaVIM, blaNDM, blaOXA-23-like, blaOXA-24/40-like, blaOXA-51-like, and blaOXA-58-like), colistin resistance-related genes (mcr-1, mcr-2, mcr-3, mcr-4, and mcr-5), a porin gene (carO), efflux pump genes (adeA, adeB, adeC, adeI, adeJ, and adeK), mobile genetic element genes (intI1, intI2, intI3, tnpU, tnp513, IS26, ISAba1, and ISAba125), and the integron variable region. Genotyping was analyzed by enterobacterial repetitive intergenic consensus (ERIC)-PCR and dendrogram cluster analysis. Results Among the 244 carbapenem-resistant Acinetobacter, the common carbapenemase-positive genes included the following: blaOXA-51-like, 183 (75.00%); blaOXA-23-like, 174 (71.30%); blaNDM-1, 57 (23.40%); and blaOXA-58-like, 30 (12.30%). The coexistence of mcr-1 and blaNDM-1 in five strains of A. junii was found for the first time. Eleven distinct carO gene variants were detected in 164 (67.20%) strains, and ten novel variants, which shared 92–99% identity with sequences in the Genbank database, were first reported. Efflux system genes were present in approximately 70% of the isolates; adeABC and adeIJK were observed in 76.23 and 72.13%, respectively. Class 1 integrons were detected in 180 (73.80%) strains and revealed that four gene cassette arrays contained 11 distinct genes. The genotyping by ERIC-PCR demonstrated a high genetic diversity of non-baumannii Acinetobacter, and greater than 90% similarity to A. baumannii. Conclusions The blaNDM-1 gene was identified in up to 77% of the carbapenem-resistant Acinetobacter isolated from fecal survey samples, indicating that the gut might be a reservoir of resistant opportunistic bacteria. Intestinal bacteria can be transmitted through the fecal-hand, which is a clinical threat, thus, the monitoring of carbapenem-resistant bacteria from inpatients’ feces should be improved, especially for patients who have been using antibiotics for a long time.

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Comparative analysis of Clinial Carbapenem- Resistant (CR), Hypermucoviscous (HM) and CR-HM Klebsiella pneumoniae isolates in China

10.21203/rs.3.rs-17188/v1 ◽

2020 ◽

Author(s):

Jun-Ying Zhu ◽

Guang-Yu Wang ◽

Qing Wei ◽

Zhen Shen ◽

Qiong Li ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Virulence Genes ◽

Carbapenem Resistance ◽

Resistance Rate ◽

Molecular Characteristics ◽

Carbapenem Resistant ◽

Recent Emergence ◽

String Test

Abstract Background: Although carbapenem-resistant Klebsiella pneumoniae (CRKP) and hypermucoviscous K. pneumoniae (HMKP) were largely non-overlapping, the recent emergence of CR-HMKP has raised great alarm in the world. We compared the molecular characteristics of CRKP, HMKP and CR-HMKP isolates.Results: 220 cases of K. pneumoniae isolates was collected and identified between Jan 2015 and Dec 2016 from Renji Hospital. Carbapenem resistance test and string test were performed to screen CRKP, HMKP and CR-HMKP isolates. All the CRKP, HMKP and CR-HMKP isolates were investigated for capsular genotyping, virulence genes and resistance genes by PCR and DNA sequencing. Multilocus sequence typing (MLST) was used to characterize isolates sequence types (STs). Serum killing assay and mouse lethality assay were respectively performed to confirm the virulence of the isolates in vitro and in vivo. Of 220 K. pneumoniae，71 HMKP, 84 CRKP and 8 CR-HMKP were identified. Resistance rate to carbapenems was significantly higher in CRKP than HMKP and CR-HMKP. For MLST and serotyping, ST23 (26.8%)，K1 (33.8%) and K2 (23.9%) serotypes were the most common in HMKP isolates while ST11 (84.5%, 100%) and K-nontypable (91.6%, 100%) were the predominant types in CRKP and CR-HMKP isolates. The existence of virulence genes rmpA, magA and iutA was significantly higher in HMKP while the prevalence of resistance gene blaKPC-2 was higher in CRKP and CR-HMKP. Virulence test in vivo and in vitro both showed the lower virulence of CRKP and CR-HMKP compared to HMKP.Conclusions: In spite of low virulence, the emergence of CR-HMKP indicates a confluence of hypermucoviscous phenotype and carbapenem resistance. Furthermore, the similar molecular characteristics between CRKP and CR-HMKP suggested that CR-HMKP might evolve from CRKP.

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Predominance of Acinetobacter spp., Harboring the blaIMP Gene, Contaminating the Hospital Environment in a Tertiary Hospital in Mwanza, Tanzania: A Cross-Sectional Laboratory-Based Study

Pathogens ◽

10.3390/pathogens11010063 ◽

2022 ◽

Vol 11 (1) ◽

pp. 63

Author(s):

Vitus Silago ◽

Eveline C. Mruma ◽

Betrand Msemwa ◽

Conjester I. Mtemisika ◽

Shukurani Phillip ◽

...

Keyword(s):

Carbapenem Resistance ◽

Tertiary Hospital ◽

Hospital Environment ◽

Pcr Assay ◽

Cross Sectional ◽

Middle Income ◽

Carbapenem Resistant ◽

Multiplex Pcr Assay ◽

Genes Encoding ◽

Acinetobacter Spp

Data on colonization and hospital contamination of carbapenem-resistant Gram-negative bacteria (CR-GNB) are limited in low- and middle-income countries. We designed this study to determine the prevalence and co-existence of carbapenemase genes among CR-GNB isolated from clinical, colonization, and hospital environmental samples at a tertiary hospital in Mwanza, Tanzania. The modified Hodge test (MHT), the combined disk test (CDT), and the double-disk synergy test (DDST) were used for the phenotypic detection of carbapenemases. A multiplex PCR assay was used to detect blaIMP and blaKPC, and a singleplex PCR assay was used to detect blaOXA-48. Data were analyzed by STATA version 13.0. Overall, 68.8% (44/64) of the CR-GNB had at least one phenotype by phenotypic methods, whereby 60.9% (39/64) were both CDT and DDST positive and 31.3% (20/64) were MHT positive. A total of 23/64 (35.9%) had at least one of the genes tested with the predominance of blaIMP (91.3%; 21/23). In addition, 47.7% (21/44) of the CR-GNB phenotypes had at least one gene. Around 47.8% (11/23) of the CR-GNB carried multiple genes encoding for carbapenem resistance, with the maximum co-existence of blaIMP/blaKPC/blaOXA-48 (45.5%; 5/11). The majority of carbapenem-resistant genes were detected in Acinetobacter spp. (82.6%; 19/23) and isolated from bed swabs (69.6%; 16/23). Acinetobacter spp. carrying the blaIMP gene predominantly contaminated the hospital environment. Therefore, we recommend routine decontamination of inanimate hospital surfaces, including patient beds.

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Phenotypic prevalence of resistance to carbapenems, colistin and genes encoding carbapenemase in Pseudomonas aeruginosa

MedPharmRes ◽

10.32895/ump.mpr.5.1.4 ◽

2021 ◽

Vol 5 (1) ◽

pp. 18-22

Author(s):

Mai Thi Thanh Nguyen ◽

Chuong Van Le ◽

Phuong Mai Doan ◽

Chinh Van Nguyen ◽

Huy Quang Vu

Keyword(s):

Pseudomonas Aeruginosa ◽

Effective Treatment ◽

Resistance Genes ◽

Real Time Pcr ◽

Carbapenem Resistance ◽

Good Effect ◽

Colistin Resistance ◽

Carbapenem Resistant ◽

Genes Encoding

Introduction: The production of carbapenem enzyme is one of the most frequent mechanisms reported in cabapenem resistant Pseudomonas aeruginosa. Besides, a growing number of mobile colistin resistance (MCR) genes are threatening the renewed interest of colistin as a "last-resort" against carbapenem-resistant pathogens. Therefore, the detection of carbapenem-resistant and colistin-resistant phenotypes as well as preventing transmission of multi-resistant P. aeruginosa strains with genes coding for carbapenemase is extremely necessary. Material and methods: Among 159 P. aeruginosa strains were collected 46 isolates, which is resistant or intermediated to meropenem. Modified carbapenem inactivation (mCIM) and colistin broth disk elution (CBDE) methods were used to identify carbapenemase-producing strains and colistin resistance. In addition, a multiplex real-time PCR technique was applied to investigate the frequency of emergence of carbapenem resistance genes. Results: The results revealed that 25 strains (54.3%) were positive with mCIM test and none of them resistant to colistin by CBDE method. Number of strains carrying a gene blaIMP: 4 strains (16%), blaNDM: 2 strains (8%). Strains are carrying two genes: blaIMP + blaNDM: 10 strains (40%), blaVIM + blaNDM: 1 strain (4%), blaNDM + blaOXA-48: 1 strain (4%) and are carrying three genes blaIMP + blaNDM + blaOXA-48: 6 strains (24%), blaKPC + blaIMP + blaNDM: 1 strain (4%). Conclusions: All mCIM positive P. aeruginosa were contained carbapenemase genes. Colistin still reserved a good effect to combine with other antibiotics in multi-resistant treatment. Hence, the classification of genes can help clinicians selected appropriate antibiotics so that more effective treatment for patients.

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Increasing carbapenem resistance due to the clonal dissemination of oxacillinase (OXA-23 and OXA-58)-producing Acinetobacter baumannii: report from the Turkish SENTRY Program sites

Journal of Medical Microbiology ◽

10.1099/jmm.0.2008/002469-0 ◽

2008 ◽

Vol 57 (12) ◽

pp. 1529-1532 ◽

Cited By ~ 29

Author(s):

Deniz Gur ◽

Volken Korten ◽

Serhat Unal ◽

Lalitagauri M. Deshpande ◽

Mariana Castanheira

Keyword(s):

Acinetobacter Baumannii ◽

Antimicrobial Agents ◽

Carbapenem Resistance ◽

Surveillance Program ◽

Carbapenem Resistant ◽

Medical Institutions ◽

Antimicrobial Surveillance ◽

Resistant Strains ◽

Resistance Rates ◽

Encoding Genes

A significant increase in carbapenem-resistance rates among Acinetobacter baumannii isolates collected in two Turkish medical centres was detected in the 2000–2006 period (20–60 %) by the SENTRY Antimicrobial Surveillance Program. Carbapenem-resistant strains from 2006 were evaluated for the presence of encoding genes and epidemic clonality. OXA-58-like and OXA-23-like carbapenemase-producing strains were detected in both medical institutions. Seventeen out of 18 strains from Ankara were positive for bla OXA-58 primers and belonged to the same clone, whilst 26 isolates (25 from Istanbul and one from Ankara) harboured bla OXA-23-like genes and showed identical or similar PFGE patterns. Isolates producing OXA-23-like carbapenemases were more resistant than OXA-58-like carbapenemase producers to non-carbapenem antimicrobial agents. Carbapenem resistance in these institutions was observed to be largely driven by the dissemination of clones producing OXA-type carbapenemases.

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