First report of 16S rRNA methylase ArmA-producing Acinetobacter baumannii and rapid spread of metallo-β-lactamase NDM-1 in Algerian hospitals

Molecular characterization of carbapenemase and extended spectrum beta-lactamase producing Acinetobacter baumannii isolates causing surgical site infections in Ethiopia

BACKGROUND

Acinetobacter baumannii is an opportunistic pathogen that can cause a variety of nosocomial infections in humans. This study aimed to molecularly characterize extended-spectrum beta-lactamase (ESBL) producing and carbapenem-resistant Acinetobacter species isolated from surgical site infections (SSI).

METHODS

A multicentre cross-sectional study was performed among SSI patients at four hospitals located in Northern, Southern, Southwest, and Central parts of Ethiopia. The isolates were identified by microbiological methods and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Antibiotic susceptibility was determined using disk diffusion. The presence of phenotypic ESBL and carbapenemase production was detected by employing standard microbiological tests, including combined disk diffusion (CDT). ESBL and carbapenem resistance determinants genes were studied by polymerase chain reaction (PCR) and sequencing.

RESULTS

A total of 8.7% Acinetobacter species were identified from 493 culture-positive isolates out of 752 SSI wounds. The species identified by MALDI-TOF MS were 88.4% A. baumannii, 4.7% Acinetobacter pittii, 4.7% Acinetobacter soli, and 2.3% Acinetobacter lactucae. Of all isolates 93% were positive for ESBL enzymes according to the CDT. Using whole genome sequencing 62.8% of the A. baumannii harbored one or more beta-lactamase genes, and 46.5% harbored one or more carbapenemase producing genes. The distribution of beta-lactamases among Acinetobacter species by hospitals was 53.8%, 64.3%, 75%, and 75% at JUSH, TASH, DTCSH, and HUCSH respectively. Among ESBL genes, blaCTX-M alleles were detected in 21.4% of isolates; of these 83.3% were blaCTX-M-15. The predominant carbapenemase gene of blaOXA type was detected in 24 carbapenem-resistant A. baumannii followed by blaNDM alleles carried in 12 A. baumannii with blaNDM-1 as the most common.

CONCLUSIONS

The frequency of Acinetobacter species that produce metallobetalactamases (MBLs) and ESBLs that were found in this study is extremely scary and calls for strict infection prevention and control procedures in health facilities helps to set effective antibiotics stewardship.

Antimicrobial Resistance Among Gram-Negative Bacteria Isolated in the Newborn Intensive Care Unit at ABDERREZAK-BOUHARA Hospital of Skikda, Algeria

Background: This study aimed to determine the epidemiology of gram-negative bacteria (GNB) isolated in the newborn intensive care unit (NICU) population, to assess their antibiotic susceptibility patterns and possible associated risk factors. Methods: All neonates admitted to the NICU of ABDERREZAK-BOUHARA hospital (Skikda, Algeria) with a clinical diagnosis of neonatal infections from March to May 2019 were included in the study. The extended-spectrum β-lactamase (ESBLs), plasmidic cephalosporinase (pAmpC), and carbapenemases genes were screened by polymerase chain reaction (PCR) and sequencing. PCR amplification of oprD among carbapenem-resistant Pseudomonas aeruginosa isolates was also performed. The clonal relatedness of the ESBLs isolates was studied using multilocus sequence typing (MLST). Results: Among 148 clinical specimens, 36 (24.3%) GNB strains were isolated from urine (n = 22), wound (n = 8), stool (n = 3), and blood (n = 3) samples. The bacterial species identified were Escherichia coli (n = 13), Klebsiella pneumoniae (n = 5), Enterobacter cloacae (n = 3), Serratia marcescens (n = 3), Salmonella spp. (n = 3), Proteus mirabilis (n = 1), P. aeruginosa (n = 5), and Acinetobacter baumannii (n = 3). PCR and sequencing showed that eleven Enterobacterales isolates harbored the bla_CTX-M-15 gene, two E. coli isolates harbored the bla_CMY-2 gene, and three A. baumannii isolates harbored both bla_OXA-23 and bla_OXA-51 genes. Also, five strains of P. aeruginosa were found to harbor mutations in the oprD gene. MLST showed that the K. pneumoniae strains belonged to ST13 and ST189, E. coli belonged to ST69, and E. cloacae belonged to ST214. Different risk factors that could predict positive GNB cultures were found, including female sex, Apgar score <8 at 5 min of life, enteral nutrition, antibiotic use, and extended length of hospitalization. Conclusion: Our study highlights the importance of determining the epidemiology of pathogens causing neonatal infections, their sequence types (ST), and their antibiotic susceptibility patterns to address rapidly a correct antibiotic treatment regimen.

Multilocus Sequence Typing of Carbapenem-Resistant Acinetobacter baumannii Isolates Harboring blaOXA-23 and blaIMP in Cattle from Punjab, Pakistan

Acinetobacter baumannii is a notorious bacterial pathogen that can cause an array of nosocomial infections in clinical settings. However, the data from the veterinary settings is limited and especially in Pakistan, no such study is conducted so far. To investigate the prevalence, antimicrobial resistance, and distribution of specific sequence types of A. baumannii in cattle, a total of 1,960 samples were collected from cattle over 18 months from Punjab, Pakistan. The isolates obtained were identified using the API20NE system and confirmed through PCR. The isolated A. baumannii isolates were further screened for antimicrobial susceptibility and the presence of resistance genes. Multilocus sequence typing was carried out to characterize the carbapenem-resistant A. baumannii (CRAB) isolates. Results revealed an overall prevalence of A. baumannii at 3.31% (65/1,960) with a higher prevalence of 7.38% (54/731) in dairy cattle compared to beef cattle at 4.41% (11/249). Among 65 A. baumannii isolates, 27.7% (18/65) were CRAB. All CRAB isolates harbor class D β-lactamases genes bla_OXA-23 and bla_OXA-51, whereas 94.4% (17/18) CRAB isolates carried class B β-lactamases gene bla_IMP, and only one isolate had bla_NDM-1 gene. The commonly found sequence types for CRAB isolates were ST2 and ST642 corresponding to 10 and 05 isolates, respectively. The presence of CRAB in cattle indicates an alarming situation that necessitates an urgent and efficient surveillance system to limit the transmission of CRAB among the cattle population and its possible transmission to humans and the environment.

In Vitro Screening of a 1280 FDA-Approved Drugs Library against Multidrug-Resistant and Extensively Drug-Resistant Bacteria

Alternative strategies against multidrug-resistant (MDR) bacterial infections are suggested to clinicians, such as drug repurposing, which uses rapidly available and marketed drugs. We gathered a collection of MDR bacteria from our hospital and performed a phenotypic high-throughput screening with a 1280 FDA-approved drug library. We used two Gram positive (Enterococcus faecium P5014 and Staphylococcus aureus P1943) and six Gram negative (Acinetobacter baumannii P1887, Klebsiella pneumoniae P9495, Pseudomonas aeruginosa P6540, Burkholderia multivorans P6539, Pandoraea nosoerga P8103, and Escherichia coli DSM105182 as the reference and control strain). The selected MDR strain panel carried resistance genes or displayed phenotypic resistance to last-line therapies such as carbapenems, vancomycin, or colistin. A total of 107 compounds from nine therapeutic classes inhibited >90% of the growth of the selected Gram negative and Gram positive bacteria at a drug concentration set at 10 µmol/L, and 7.5% were anticancer drugs. The common hit was the antiseptic chlorhexidine. The activity of niclosamide, carmofur, and auranofin was found against the selected methicillin-resistant S. aureus. Zidovudine was effective against colistin-resistant E. coli and carbapenem-resistant K. pneumoniae. Trifluridine, an antiviral, was effective against E. faecium. Deferoxamine mesylate inhibited the growth of XDR P. nosoerga. Drug repurposing by an in vitro screening of a drug library is a promising approach to identify effective drugs for specific bacteria.

Molecular Characterization of Clinical Carbapenem-Resistant Enterobacteriaceae Isolates from Sétif, Algeria

This study aimed to determine the incidence and the molecular mechanisms of carbapenem-resistant Enterobacteriaceae in patients from the Sétif University Hospital, Algeria. Nonduplicate clinical bacterial isolates recovered from patients attending the University Hospital of Sétif were collected between April and October 2018. Species identification was performed by MALDI-TOF/MS (matrix-assisted laser desorption ionization-time of flight mass spectrometry) method. The susceptibility of the isolates to carbapenems was determined using the disc diffusion method. The carbapenem resistant isolates were screened for the presence of common carbapenemase genes (bla_KPC, bla_OXA-48, bla_VIM, bla_IMP, and bla_NDM) and extended-spectrum β-lactamase (bla_CTX, bla_TEM, and bla_SHV) using PCR and sequencing technique. A total of 123 nonrepetitive Enterobacteriaceae isolates were obtained. Klebsiella pneumoniae (n = 52/42.28%), Escherichia coli (n = 24/19.51%), and Enterobacter cloacae (n = 19/15.45%) were the most prevalent species. The Carba-NP test showed that 6 out of 123 isolates carried carbapenemase enzymes. OXA-48 was found in five isolates (four K. pneumoniae and one E. coli) and NDM-5 in one E. cloacae isolate. We reported for the first time in Algeria the presence of NDM-5 carbapenemase enzyme in a clinical E. cloacae isolate.

Emergence of Metallo-β-Lactamases and OXA-48 Carbapenemase Producing Gram-Negative Bacteria in Hospital Wastewater in Algeria: A Potential Dissemination Pathway Into the Environment

Antibiotic-resistant bacteria can leave hospitals and therefore contaminate the environment and, most likely, humans and animals, through different routes, among which wastewater discharge is of great importance. This study aims to assess the possible role of hospital sewage as reservoir and dissemination pathway of carbapenem-resistant Gram-negative bacilli (GNB). Carbapenem-resistant GNB were selectively isolated from wastewater collected from a public hospital in Batna, Algeria. Species identification was carried out using matrix-assisted laser desorption and ionization time-of-flight mass spectrometry, and antibiotic susceptibility was evaluated by the disc diffusion method. β-Lactamase production was investigated phenotypically using the double-disk synergy assay and the modified CarbaNP test, then the molecular mechanisms of β-lactam-resistance were studied by PCR and sequencing. Ten Enterobacteriaceae and 14 glucose-nonfermenting GNB isolates were obtained. All Enterobacteriaceae isolates were positive for OXA-48 and TEM-1D β-lactamases, where seven of them coproduced an extended-spectrum β-lactamase. VIM-2 carbapenemase was detected in six glucose-nonfermenting GNB isolates. However, three Pseudomonas aeruginosa, one Comamonas jiangduensis and one Acinetobacter baumannii isolates were positive for VIM-4 variant. In addition, NDM-1 enzyme was detected in four A. baumannii isolates. Our findings highlight the potential impact of hospital wastewater in the spread of drug resistance mechanisms outside of hospitals.

Carbapenemase-Producing Non-Glucose-Fermenting Gram-Negative Bacilli in Africa, Pseudomonas aeruginosa and Acinetobacter baumannii: A Systematic Review and Meta-Analysis

Background

Studies have reported that the existence of CP bacteria in Africa, but, in general, comprehensive data about the molecular epidemiology of CP organisms are limited. Therefore, this systematic review and meta-analysis expound the pooled prevalence of CP P. aeruginosa and CP A. baumannii clinical isolates in Africa. It also identified the diversity of carbapenemases or their encoding genes among the isolates in Africa. Lastly, the review observed the trends of these CP isolates in Africa.

Methods

A comprehensive search was performed between July 2019 and October 2019 in the following databases: PubMed, Google Scholar, and African Journal online. The included articles were published only in English. The screening was done by two authors independently. The data extracted on Excel spreadsheet were transferred to STATA 11 software for analysis.

Results

From a total of 1,454 articles searched, 42 articles were eligible. Most of the studies were conducted in the North Africa region. But there was no report from Central Africa. The pooled prevalence of CP P. aeruginosa and CP A. baumannii among the clinical specimens in Africa was 21.36% and 56.97%, respectively. OXA-23 and VIM were the most prevailing carbapenemase among P. aeruginosa and A. baumannii, respectively. The cumulative meta-analysis revealed a relative increment of the prevalence of CP P. aeruginosa over time in Africa but it showed a higher prevalence of CP A. baumannii isolates across years.

Conclusion

The review revealed a high pooled prevalence of CP A. baumannii clinical isolates in Africa which needs urgent action. Moreover, the emergence of concomitant carbapenemases, especially OXA-23 +  NDM among CP A. baumannii, was also an alarming problem.

First Clinical Cases of KPC-2-Producing Klebsiella pneumoniae ST258 in Algeria and Outbreak of Klebsiella pneumoniae ST101 Harboring blaOXA-48 Gene in the Urology Department of Annaba Hospital

Objectives: The aim of this study was to characterize the molecular mechanisms of carbapenem resistance in Klebsiella pneumoniae isolated from the urology department of Annaba hospital, Algeria. Methods: Between January 2015 and September 2017, 14 carbapenem-resistant K. pneumoniae strains were isolated during routine surveillance work at Ibn Roched hospital of Annaba, Algeria, from the urology department. Theses strains were recovered, and carbapenem resistance mechanisms were investigated. The strains were identified by using matrix-assisted laser desorption and ionization time-of-flight mass spectrometry. Antibiotic susceptibility was assessed by using the Kirby-Bauer method, whereas minimum inhibitory concentration of imipenem/ertapenem and colistin was determined by Etest and broth microdilution methods, respectively. Carbapenem resistance determinants were studied by using PCR and sequencing methods and analyzed by BLAST against the Antibiotic Resistance Gene-ANNOTation (ARG-ANNOT) database. Clonal relationship of strains was performed by using multilocus sequence typing (MLST). Transferability of carbapenem resistance genes was assessed by conjugation and transformation experiments. Results: Fourteen carbapenem-resistant K. pneumoniae isolates were found to be resistant to the eight β-lactam antibiotics tested (except to imipenem for two isolates). Carbapenemase production was positive for all isolates. Molecular characterization revealed that bla_KPC-2 and bla_OXA-48 genes were detected in 3 (21.4%) and 11 isolates (78.6%), respectively. Other β-lactamases genes were identified, including bla_CTX-M-15, bla_{SHV-1-or 12}, and bla_TEM-1. MLST revealed that the 14 isolates belonged to 2 different sequence types (STs), including ST101 (11 OXA-48-producing K. pneumoniae) and ST258 (3 KPC-2-producing K. pneumoniae). PCR amplifications for bla_KPC-2 and bla_OXA-48 carbapenemases genes performed on extracted plasmids, showed positive results, suggesting that both carbapenemase genes were probably borne by plasmids. Conclusion: We report here the first identification of KPC-2-producing K. pneumoniae ST258 in Algerian hospitals and an outbreak of OXA-48-producing K. pneumoniae isolates ST101 in the urology department of Ibn Roched hospital located in Annaba, Algeria.

Dissemination of carbapenem-resistant Acinetobacter baumannii strains carrying the bla GES, bla NDM and bla OXA23 in Morocco

Background

Acinetobacter baumannii is a microorganism which has been classified by the World Health Organization in the list of the bacterial strains that pose the biggest danger to human health. This study was performed to determine the susceptibility profile to carbapenems and to detect carbapenemases production in 111 A. baumannii isolates. Among these 30 are environmental isolates and 81 are from the three major hospitals in Morocco.

Methods

All strains of A. baumannii were tested against diverse antimicrobial agents (13 antibiotic drugs) by the agar diffusion test. Minimum inhibitory concentration (MIC) of imipenem on carbapenem-resistant strains (CRAB) was determined by the E-test technique. Simple phenotypic tests were used to detect carbapenemases and metallo-β-lactamases (MBLs) production including the modified Hodge test, EDTA test, and the cloxacillin test. The presence of carbapenemases-encoding resistance genes of CRAB strains was examined using polymerase chain reaction (PCR).

Results

Carbapenem resistance was observed in 23 clinical Acinetobacter isolates showing dissemination of the multiresistance profile. Molecular biology techniques indicated that all these strains encoded the naturally occurring bla _OXA-51-like gene and were proved as A. baumannii. The bla _OXA-23 gene was detected in 16 strains (69.6%). The metallo-β-lactamase bla _NDM gene was detected in five isolates (21.7%). GES-type carbapenemases were found in 15 strains, the existence of three classes of carbapenemases (bla _GES, bla _NDM, and bla _OXA-23) was detected in three strains, while none of the CRAB isolates contained the bla _OXA-58, bla _OXA-24, bla _VIM, bla _OXA-48 or bla _KPC encoding genes.

Conclusions

This study established baseline proof of three classes of carbapenemases producing A. baumannii in Morocco, showing the important role of surveillance in controlling their spread.

Epidemiology and Mechanisms of Resistance of Extensively Drug Resistant Gram-Negative Bacteria

Antibiotic resistance has increased markedly in gram-negative bacteria over the last two decades, and in many cases has been associated with increased mortality and healthcare costs. The adoption of genotyping and next generation whole genome sequencing of large sets of clinical bacterial isolates has greatly expanded our understanding of how antibiotic resistance develops and transmits among bacteria and between patients. Diverse mechanisms of resistance, including antibiotic degradation, antibiotic target modification, and modulation of permeability through the bacterial membrane have been demonstrated. These fundamental insights into the mechanisms of gram-negative antibiotic resistance have influenced the development of novel antibiotics and treatment practices in highly resistant infections. Here, we review the mechanisms and global epidemiology of antibiotic resistance in some of the most clinically important resistance phenotypes, including carbapenem resistant Enterobacteriaceae, extensively drug resistant (XDR) Pseudomonas aeruginosa, and XDR Acinetobacter baumannii. Understanding the resistance mechanisms and epidemiology of these pathogens is critical for the development of novel antibacterials and for individual treatment decisions, which often involve alternatives to β-lactam antibiotics.

Characterization of multidrug-resistant Gram-negative bacilli isolated from hospitals effluents: first report of a blaOXA-48-like in Klebsiella oxytoca, Algeria

The antibiotic susceptibility profile and antimicrobial resistance determinants were characterized on Gram-negative bacilli (GNB) isolated from Algerian hospital effluents. Among the 94 isolates, Enterobacteriaceae was the predominant family, with Escherichia coli and Klebsiella pneumoniae being the most isolated species. In non-Enterobacteriaceae, Acinetobacter and Aeromonas were the predominant species followed by Pseudomonas, Comamonas, Pasteurella, and Shewanella spp. The majority of the isolates were multidrug-resistant (MDR) and carried different antimicrobial resistance genes including bla_CTX-M, bla_TEM, bla_SHV, bla_OXA-48-like, bla_OXA-23, bla_OXA-51, qnrB, qnrS, tet(A), tet(B), tet(C), dfrA1, aac(3)-IIc (aacC2), aac(6')-1b, sul1, and sul2. The qacEΔ1-sul1 and intI2 signatures of class 1 and class 2 integrons, respectively, were also detected. Microarray hybridization on MDR E. coli revealed additional resistance genes (aadA1 and aph3strA, tet30, mphA, dfrA12, bla_cmy2, bla_ROB1, and cmlA1) and classified the tested strains as commensals, thus highlighting the potential role of humans in antibiotic resistance dissemination. This study is the first report of bla_OXA-48-like in Klebsiella oxytoca in Algeria and bla_OXA-23 in A. baumannii in Algerian hospital effluents. The presence of these bacteria and resistance genes in hospital effluents represents a serious public health concern since they can be disseminated in the environment and can colonize other hosts.

Role of Institut Hospitalo-Universitaire Méditerranée Infection in the surveillance of resistance to antibiotics and training of students in the Mediterranean basin and in African countries

Surveillance of antibiotic resistance has become a public global concern after the rapid worldwide dissemination of several antibiotic resistance genes. Here we report the role of the Institut Hospitalo-Universitaire Méditerranée Infection created in 2011 in the identification and description of multidrug-resistant bacteria thanks to collaborations and training of students from the Mediterranean basin and from African countries. Since the creation of the institute, 95 students and researchers have come from 19 different countries from these areas to characterize 6359 bacterial isolates from 7280 samples from humans (64%), animals (28%) and the environment (8%). Most bacterial isolates studied were Gram-negative bacteria (n = 5588; 87.9%), mostly from Algeria (n = 4190), Lebanon (n = 946), Greece (n = 610), Saudi Arabia (n = 299) and Senegal (n = 278). Antibiotic resistance was diversified with the detection and characterization of extended-spectrum β-lactamases, carbapenemases and resistance to colistin, vancomycin and methicillin. All those studies led to 97 indexed international scientific papers. Over the last 6 years, our institute has created a huge network of collaborations by training students that plays a major role in the surveillance of resistance to antibiotics in these countries.

Co-occurrence of carbapenemase encoding genes in Acinetobacter baumannii, a dream or reality?

BACKGROUND

Acinetobacter baumannii is an important opportunistic pathogen that is rapidly evolving towards multidrug resistance and is responsible for life-threatening infections. Carbapenems are commonly used to treat A. baumannii infections but the emergence of carbapenemase encoding genes, such as blaOXA-23-like, blaOXA-24-like, blaOXA-58-like, and blaNDM has been reported. Moreover, several studies have reported the co-occurrence of two distinct carbapenemases in some isolates. The aim of the present study is to demonstrate whether the phenomenon of co-occurrence of two distinct carbapenemase encoding genes in a single isolate still exists.

RESULTS

We studied six strains of A. baumannii including one harboring blaOXA-23-like and blaOXA-24-like genes and five with blaOXA-23-like and blaNDM genes. One colony of each strain was inoculated in sterile water and diluted ten-fold. Each dilution was cultivated on trypticase soy agar plates for 24 h at 37 °C and the isolated bacteria were analyzed. For two of the six tested strains, we identified two different populations of A. baumannii, each with a different carbapenemase, genes encoding aminoglycoside modifying enzymes, resistance phenotype, and clonal type. In addition, the two different populations had the same aspect on the agar plate.

CONCLUSIONS

Here, we demonstrate that A. baumannii infections could be linked to multiple clones harboring different carbapenemase encoding genes in the same sample. In addition, we describe an easy method of verifying the presence of co-occurrence of carbapenemase in one isolate.

Incidence of OXA-23 and OXA-58 Carbapenemases Coexpressed in Clinical Isolates of Acinetobacter baumannii in Tunisia

Acinetobacter baumannii is an important opportunistic and multidrug-resistant pathogen responsible for nosocomial infections in health facilities. The aim of this study was to characterize the molecular mechanisms of carbapenem resistance in A. baumannii isolates isolated from Mohamed Kassab Orthopedic Institute in Tunis, Tunisia. Twenty-five imipenem-resistant A. baumannii clinical isolates collected between 2013 and 2016 were identified using API 20NE and were confirmed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS). Carbapenemase activity was detected using microbiological tests and PCR. The epidemiological relatedness of the isolates was studied using multilocus sequence typing (MLST). The isolates were resistant to all antibiotics tested with increased minimum inhibitory concentration values (>32 mg/L). The microbiological tests showed that the 25 A. baumannii were positive for modified Hodge test and for the Carba NP test; however, β-lactamase activity was not inhibited by EDTA. All the isolates harbored the naturally occurring bla_OXA-51-like gene and the bla_OXA-23-like carbapenemase gene. Among these isolates, one isolate coexpressed the bla_OXA-58 gene. MLST revealed several sequence types (STs) with the predominance of ST2 imipenem-resistant A. baumannii (14/25; 56%). In this study we report the prevalence of ST2 imipenem resistance and for the first time the coexpression of bla_OXA-23 and bla_OXA-58 in clinical isolates of A. baumannii in a Tunisian hospital.

Detection of ISAba1 in association with a novel allelic variant of the β-lactamase ADC-82 and class D β-lactamase genes mediating carbapenem resistance among the clinical isolates of MDR A. baumannii

PURPOSE

The objective of the present study is to investigate the diverse resistance determinants, their association with insertion sequence mobile elements and predilection of a particular clone for such associations in Acinetobacter baumannii.

METHODOLOGY

Fifty-four consecutive isolates collected during 2011-2012 from a tertiary care hospital were subjected to susceptibility testing followed by PCR screening of commonly reported β-lactamases and 16S rRNA methyltransferase encoding genes. The integrity of resistance-nodulation-cell division efflux pump-related genes in their respective operons was also investigated.

RESULTS

β-Lactamase genes such as blaADC (100 %), blaOXA-23 (81 %), blaPER-1 (81 %), blaIMP-1 (31 %) and blaNDM-1 (15 %) were found to be present more frequently while blaVIM-2 and blaOXA-24 were not observed in our study population. ISAba1 was associated only with blaOXA-51-like like (30 %), blaOXA-23-like (55 %) and blaADC-like (33 %). armA was found in 87 % of isolates and ISAba1 linked with one novel variant of ADC, namely blaADC-82, which was identified to have 15 nucleotide differences with blaADC-79, and this finding is of much significance. In many isolates, efflux pump genes were not intact, resulting in severely altered effluxing functions. For the first time, we have identified ISAba1-mediated disruption of adeN among the isolates of ST 195B, which would have led to overexpression of AdeIJK efflux pump causing elevated resistance. Multilocus sequence typing revealed the predominance of CC 92B (IC-IIB) and CC 447B clonal complexes.

CONCLUSION

High incidence of IC-II clones, novel resistance determinants (ADC-82) and elevated resistance mediated by ISAba1 reported here will be of enormous importance while assessing the emergence of extremely resistant A. baumannii in India.

Co-existence of blaOXA-23 and blaNDM-1 genes of Acinetobacter baumannii isolated from Nepal: antimicrobial resistance and clinical significance

Background

Molecular analysis of carbapenem-resistant genes in Acinetobacter baumannii, an emerging pathogen, is less commonly reported from Nepal. In this study we determined the antibiotic susceptibility profile and genetic mechanism of carbapenem resistance in clinical isolates of A. baumannii.

Methods

A. baumannii were isolated from various clinical specimens and identified based on Gram staining, biochemical tests, and PCR amplification of organism specific 16S rRNA and bla_OXA-51 genes. The antibiotic susceptibility testing was performed using disc diffusion and E-test method. Multiplex PCR assays were used to detect the following β-lactamase genes: four class D carbapenem hydrolyzing oxacillinases (bla_OXA-51, bla_OXA-23, bla_OXA-24 and bla_OXA-58). Uniplex PCRs were used to detect three class B metallo-β-lactamases genes (bla_IMP, bla_VIM and bla_NDM-1), class C cephalosporin resistance genes (bla_ADC), aminoglycoside resistance gene (aphA6), and ISAba1 of all isolates. Insertion sequence ISAba125 among NDM-1 positive strains was detected. Clonal relatedness of all isolates were analyzed using repetitive sequence-based PCR (rep-PCR).

Results

Of total 44 analyzed isolates, 97.7% (n = 43) were carbapenem-resistant A. baumannii (CR-AB) and 97.7% (n = 43) were multidrug resistant A. baumannii (MDR-AB). One isolate was detected to be extremely drug resistant A. baumannii (XDR-AB). All the isolates were fully susceptible to colistin (MICs < 2 μg/ml). The bla_OXA-23 gene was detected in all isolates, while bla_NDM-1 was detected in 6 isolates (13.6%). Insertion sequence, ISAba1 was detected in all of bla_OXA-23 positive isolates. ISAba125 was detected in all bla_NDM-1 positive strains. The bla_ADC and aphA6 genes were detected in 90.1 and 40.1%, respectively. The rep-PCR of all isolates represented 7 different genotypes.

Conclusion

We found high prevalence of CR-AB and MDR-AB with bla_OXA-23 gene in a tertiary care hospital in Nepal. Systemic network surveillance should be established for monitoring and controlling the spread of these resistant strains.

Electronic supplementary material

The online version of this article (doi:10.1186/s13756-017-0180-5) contains supplementary material, which is available to authorized users.

Prevalence of carbapenemases among high-level aminoglycoside-resistant Acinetobacter baumannii isolates in a university hospital in China

The prevalence of aminoglycoside resistant enzymes has previously been reported and extended-spectrum β-lactamase among Acinetobacter baumannii. To track the risk of multidrug-resistant A. baumannii, the present study aimed to determine the prevalence of carbapenemases in high-level aminoglycoside resistant A. baumannii over two years. A total of 118 strains of A. baumannii were consecutively collected in the First Affiliated Hospital of Chengdu Medical College, Chengdu, China. These isolates were investigated on the genetic basis of their resistance to aminoglycosides. The results showed that 75 (63.56%) isolates were high-level resistant to aminoglycosides, including gentamicin and amikacin (minimum inhibitory concentration, ≥256 µg/ml). Aminoglycoside-resistant genes ant(2″)-Ia, aac(6′)-Ib, aph(3′)-Ia, aac(3)-Ia, aac(3)-IIa, armA, rmtA, rmtB, rmtC, rmtD, rmtE, rmtF, rmtG, rmtH and npmA, and carbapenem-resistant genes bla_OXA-23, bla_OXA-24, bla_OXA-51, bla_OXA-58, bla_SIM, bla_IMP, bla_NDM-1 and bla_KPC, were analyzed using polymerase chain reaction. The positive rate of ant(2″)-Ia, aac(6′)-Ib, aph(3′)-Ia, aac(3)-Ia and aac(3)-IIa was 66.95, 69.49, 42.37, 39.83 and 14.41%, respectively. armA was present in 72.0% (54/75) of A. baumannii isolates with high-level resistance to aminoglycosides. The remaining nine 16S ribosomal RNA methlyase genes (rmtA, rmtB, rmtC, rmtD, rmtE, rmtF, rmtG, rmtH and npmA) and aminoglycoside-modifying enzyme gene aac(6′)-Ib-cr were not detected. Among the 54 armA-positive isolates, the prevalence of the carbapenem resistant bla_OXA-23 and bla_OXA-51 genes was 79.63 and 100%, respectively. armA, ant(2″)-Ia and aac(6′)-Ib were positive in 43 isolates. The results of multilocus sequence typing revealed 31 sequence types (STs) in all clinical strains. Among these STs, the high-level aminoglycoside-resistant A. baumannii ST92, which mostly harbored bla_OXA-23, was the predominant clone (29/75). In conclusion, A. baumannii harboring carbapenemases and aminoglycoside-resistant enzymes are extremely prevalent in western China, emphasizing the need to adopt surveillance programs to solve the therapeutic challenges that this presents.

Molecular epidemiology of environmental and clinical carbapenemase-producing Gram-negative bacilli from hospitals in Guelma, Algeria: Multiple genetic lineages and first report of OXA-48 in Enterobacter cloacae

This study was designed to investigate environmental colonisation in Algerian hospitals by carbapenem-resistant Gram-negative bacilli (GNB), including molecular characterisation of their resistance, and to perform a comparative molecular analysis between clinical and environmental strains. GNB isolated from hospitalised patients and the hospital environment were identified using microbiological methods and matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Antibiotic susceptibility testing was performed by disk diffusion and Etest methods. Carbapenemase- and extended-spectrum β-lactamase (ESBL)-encoding genes were searched for using PCR and sequencing. Clonality of the environmental and clinical strains was assessed by multilocus sequencing typing (MLST). A total of 32 carbapenem-resistant GNB were isolated, including 16 (29%) of 56 multidrug-resistant (MDR) GNB from clinical specimens and 16 (48%) of 33 MDR-GNB from inanimate surfaces. Of the 32 carbapenem-resistant isolates, 14 produced a carbapenemase. The bla_OXA-48 gene was detected both in clinical and surface isolates of Klebsiella pneumoniae (n=3) and Enterobacter cloacae (n=2). Clinical and surface isolates of Acinetobacter baumannii were found to produce the carbapenemases NDM-1 (7 isolates) and OXA-23 (2 isolates). MLST revealed clonal diversity and a relationship between environmental and clinical strains with identical sequence types. Here we report the first description of an OXA-48-producing E. cloacae isolate in Algeria. We also highlight the important role of inanimate surfaces in the spread of carbapenem-resistant bacteria and the emergence of nosocomial infections.

Occurence of ArmA and RmtB Aminoglycoside Resistance 16S rRNA Methylases in Extended-Spectrum β-Lactamases Producing Escherichia coli in Algerian Hospitals

The aim of this study, was to characterize the extended-spectrum-β-lactamases (ESBLs) producing clinical strains of Escherichia coli isolated between January 2009 and June 2012 from Algerian hospitals and to determine the prevalence of 16S rRNA methylase among them. Sixty-seven ESBL-producers were detected among the 239 isolates included: 52 CTX-M-15-producers, 5 CTX-M-3-producers, 5 CTX-M-1-producers, 2 CTX-M-14-producers, 2 SHV-12-producers and one TEM-167-producer. Among the ESBL–producing strains twelve harbored 16S rRNA methylase genes: 8 rmtB and 4 armA. rmtB was located on a IncFIA plasmid and armA was located either on a IncL/M or a IncFIA plasmid. RmtB-producing isolates were genotypically related and belonged to the sequence type ST 405 whereas ArmA-producing isolates belonged to ST10, ST 167, and ST 117. This first description of 16S rRNA methylases among E. coli in Algerian hospitals pointed out the necessity to establish control measures to avoid their dissemination.

Real-time quantitative PCR assay with Taqman(®) probe for rapid detection of MCR-1 plasmid-mediated colistin resistance

Here we report the development of two rapid real-time quantitative PCR assays with TaqMan^® probes to detect the MCR-1 plasmid-mediated colistin resistance gene from bacterial isolates and faecal samples from chickens. Specificity and sensitivity of the assay were 100% on bacterial isolates including 18 colistin-resistant isolates carrying the mcr-1 gene (six Klebsiella pneumoniae and 12 Escherichia coli) with a calibration curve that was linear from 10¹ to 10⁸ DNA copies. Five out of 833 faecal samples from chickens from Algeria were positive, from which three E. coli strains were isolated and confirmed to harbour the mcr-1 gene by standard PCR and sequencing.

Co-occurrence of blaNDM-1 with blaOXA-23 or blaOXA-58 in clinical multidrug-resistant Acinetobacter baumannii isolates in Algeria

The aim of this study was to characterise the mechanisms of carbapenem resistance in Acinetobacter baumannii strains isolated in an Algerian hospital. A total of 43 imipenem-resistant A. baumannii clinical isolates collected between 2010 and 2013 were identified using API 20NE and were confirmed by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Antibiotic susceptibility testing was performed by the disk diffusion and Etest methods. Carbapenemase activity was detected using microbiological tests and PCR. Genetic transfer of the blaNDM-1 gene was performed by conjugation using sodium azide-resistant Escherichia coli J53 as recipient strain. Clonal relationships were studied by multilocus sequence typing (MLST) using partial sequences of the csuE and blaOXA-51 genes. All 43 A. baumannii isolates were resistant to imipenem with high minimum inhibitory concentrations (MICs) (>32μg/mL). The strains harboured blaOXA-23, blaNDM-1, blaOXA-58 and/or blaOXA-24 genes. Co-existence of blaNDM-1 and blaOXA-23 or blaOXA-58 was detected in two isolates and one isolate, respectively. NDM-1 plasmid transfer to E. coli J53 was successful only for one of the three strains harbouring both blaNDM-1 and blaOXA-23 or blaOXA-58. The phylogenetic tree obtained from concatenation of the partial sequences of csuE and blaOXA-51 showed that there was no genetic relationship between the isolates and the blaNDM-1 resistance gene. Here we report for the first time the co-occurrence of blaNDM-1 along with blaOXA-23 or blaOXA-58 in recent clinical isolates of A. baumannii from Northeast Algeria. These findings re-emphasise the dissemination and rapid spread of blaNDM-1 carbapenemase genes in multidrug-resistant clinical A. baumannii isolates in Algeria.

Coexistence of blaOXA-23 with armA in quinolone-resistant Acinetobacter baumannii from a Chinese university hospital

A total of 101 Acinetobacter baumannii isolates were collected to determine the mechanisms of quinolone resistance and investigate the occurrence of carbapenem and high-level aminoglycoside resistance genes among quinolone-resistant strains. Among 77 quinolone-resistant A. baumannii harbored mutations of gyrA and parC, 41 isolates, which belonged to European clone II, had resistance to aminoglycosides and carbapenems due to the expression of armA and acquisition of blaOXA-23. Most of sequence type belonged to clonal complex 92. These results suggested hospital dissemination of multidrug-resistant A. baumannii carrying blaOXA-23, armA, and mutations of quinolone resistance-determining regions in western China.

Emergence of Carbapenemase-Producing Escherichia coli Isolated from Companion Animals in Algeria

The emergence and worldwide spread of carbapenemase-producing Enterobacteriaceae is of great concern to public health. The aim of this study was to investigate the occurrence of carbapenemase-producing Escherichia coli in companion animals in Algeria. Two hundred fecal samples were obtained from healthy and diseased dogs and cats in one veterinary office and private owners in Bejaia city, Algeria, during November 2014 to March 2015. Isolates were screened by polymerase chain reaction for the presence of carbapenemase, acquired plasmidic AmpC (pAmpC) and extended-spectrum beta-lactamase genes. Five carbapenemase-producing E. coli isolates were detected including four OXA-48-producing isolates and one isolate producing NDM-5. Coexpression of ESBL and pAmpC genes was observed in these isolates. Phylogenetic grouping revealed that these isolates belonged to A and D phylogroups. The results of this study show that carbapenemase-producing E. coli spread to the companion animals in Algeria.

The Molecular Epidemiology and Genetic Environment of Carbapenemases Detected in Africa

Research articles describing carbapenemases and their genetic environments in Gram-negative bacteria were reviewed to determine the molecular epidemiology of carbapenemases in Africa. The emergence of resistance to the carbapenems, the last resort antibiotic for difficult to treat bacterial infections, affords clinicians few therapeutic options, with a resulting increase in morbidities, mortalities, and healthcare costs. However, the molecular epidemiology of carbapenemases throughout Africa is less described. Research articles and conference proceedings describing the genetic environment and molecular epidemiology of carbapenemases in Africa were retrieved from Google Scholar, Scifinder, Pubmed, Web of Science, and Science Direct databases. Predominant carbapenemase genes so far described in Africa include the blaOXA-48 type, blaIMP, blaVIM, and blaNDM in Acinetobacter baumannii, Klebsiella pneumoniae, Enterobacter cloacae, Citrobacter spp., and Escherichia coli carried on various plasmid types and sizes, transposons, and integrons. Class D and class B carbapenemases, mainly prevalent in A. baumannii, K. pneumoniae, E. cloacae, Citrobacter spp., and E. coli were the commonest carbapenemases. Carbapenemases are mainly reported in North and South Africa as under-resourced laboratories, lack of awareness and funding preclude the detection and reporting of carbapenemase-mediated resistance. Consequently, the true molecular epidemiology of carbapenemases and their genetic environment in Africa is still unknown.

Emerging broad-spectrum resistance in Pseudomonas aeruginosa and Acinetobacter baumannii: Mechanisms and epidemiology

Multidrug resistance is quite common among non-fermenting Gram-negative rods, in particular among clinically relevant species including Pseudomonas aeruginosa and Acinetobacter baumannii. These bacterial species, which are mainly nosocomial pathogens, possess a diversity of resistance mechanisms that may lead to multidrug or even pandrug resistance. Extended-spectrum β-lactamases (ESBLs) conferring resistance to broad-spectrum cephalosporins, carbapenemases conferring resistance to carbapenems, and 16S rRNA methylases conferring resistance to all clinically relevant aminoglycosides are the most important causes of concern. Concomitant resistance to fluoroquinolones, polymyxins (colistin) and tigecycline may lead to pandrug resistance. The most important mechanisms of resistance in P. aeruginosa and A. baumannii and their most recent dissemination worldwide are detailed here.