Outbreak of an armA methyltransferase-producing ST39 Klebsiella pneumoniae clone in a pediatric Algerian Hospital

Etiology of Bacterial Sepsis and Isolate Resistance Patterns in Hospitalized Neonates in Zambia

BACKGROUND

The Sepsis Prevention in Neonates in Zambia study is a prospective cohort study that evaluated an infection prevention and control (IPC) bundle in the University Teaching Hospital neonatal intensive care unit (NICU) in Lusaka, Zambia. We present here the etiologies, antimicrobial resistance profiles, and associated mortality of bloodstream infections (BSI) in this cohort.

METHODS

Venous blood was collected from neonates with clinically suspected sepsis and cultured with an automated blood culture system. Organism identification and susceptibility testing were done using the Vitek II system. We used the CDC National Health Safety Network criteria to define pathogens and commensals.

RESULTS

There were 1120 blood cultures performed for 1060 neonates with suspected sepsis. Overall, 38% (424/1120) of cultures were positive of which 72% (306/424) grew pathogens. Blood cultures obtained after, as compared to before, 2 days of hospitalization were more likely to yield a pathogen (77% vs. 65%; P < 0.001). Klebsiella pneumoniae was the most prevalent organism, accounting for 74% (225/306) of all pathogens . K. pneumoniae isolates were highly resistant: 98% (221/225) were extended-spectrum beta-lactamase (ESBL)-positive, while 81% were resistant to gentamicin (182/225) and fluoroquinolones (177/219). Only one isolate was carbapenem resistant. Observed mortality rate was 32% (122/380); 61% (75/122) of the deaths was related to Klebsiella BSI.

CONCLUSIONS

Multidrug-resistant ESBL-producing Klebsiella species were the main organisms responsible for BSI and were associated with increased mortality. BSI risk increased with prolonged hospitalization, underscoring the importance of IPC measures in the NICU.

Ribosome-targeting antibiotics and resistance via ribosomal RNA methylation

The rise of multidrug-resistant bacterial infections is a cause of global concern. There is an urgent need to both revitalize antibacterial agents that are ineffective due to resistance while concurrently developing new antibiotics with novel targets and mechanisms of action. Pathogen associated resistance-conferring ribosomal RNA (rRNA) methyltransferases are a growing threat that, as a group, collectively render a total of seven clinically-relevant ribosome-targeting antibiotic classes ineffective. Increasing frequency of identification and their growing prevalence relative to other resistance mechanisms suggests that these resistance determinants are rapidly spreading among human pathogens and could contribute significantly to the increased likelihood of a post-antibiotic era. Herein, with a view toward stimulating future studies to counter the effects of these rRNA methyltransferases, we summarize their prevalence, the fitness cost(s) to bacteria of their acquisition and expression, and current efforts toward targeting clinically relevant enzymes of this class.

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.

Whole Genome Sequencing of Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolated from Neonatal Bloodstream Infections at a Neonatal Care Unit, Algeria

Aims: Neonatal bloodstream infections (BSIs) are an important cause of mortality among neonates. Besides, extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBL-Kp) is one of the most frequent pathogens causing neonatal BSIs. This study aimed to characterize ESBL-Kp strains recovered from neonatal BSI and to investigate risk factors associated with ESBL-Kp BSI at the neonatal care unit of Elmeki Hospital, Bejaia, Algeria. Methodology: After isolation, identification, and antibiotic susceptibility testing, the ESBL-Kp strains were characterized by whole genome sequencing. The genomes were then analyzed using bioinformatic tools to determine the resistome, virulome, and phylogenetic relatedness. Results: From September 2019 to May 2020, 27 (8.2%) out of 328 neonates were infected by ESBL-Kp strains. These strains displayed a multidrug-resistant phenotype, and on further investigation, were found to carry an array of antibiotic resistance genes. All ESBL-Kp strains harbored the bla_CTX-M-15 gene. Using in silico multilocus sequence typing analysis, six sequence types (STs) were detected with ST268 being the most frequent (56%, n = 15) indicating a local outbreak, confirmed by single nucleotide polymorphism analysis. The yersiniabactin and colibactin gene clusters were identified in six and two ESBL-Kp strains, respectively. Conclusion: This study showed a high prevalence of CTX-M-15-producing K. pneumoniae strains coharboring different antibiotic resistance mechanisms from neonatal BSIs in Algeria. Screening of health care personnel and mothers for ESBL carriage before delivery, isolation of carriers, barrier precautions, antimicrobial usage, and control of hygiene are needed to prevent the dissemination of these pathogens.

Extended-spectrum-beta-lactamases and carbapenemase-producing Klebsiella pneumoniae isolated from fresh produce farms in different governorates of Egypt

Background and Aim: Fresh produce farms represents a major source of concern since they are becoming increasingly antibiotic resistant. This study aimed to investigate t he occurrence of carbapenemase and extended-spectrum-beta-lactamases (ESBL) - producing genes in Klebsiella pneumoniae isolated from fresh produce farms in Egypt, irrigation water, and people working in these fields. Materials and Methods: One hundred tomatoes from typical farms were collected in plastic bags. The study also included 20 surface-water samples from different irrigation watersheds in fresh produce farms, as well as 50 feces samples from farmworkers. Suspected K. pneumoniae was grown on Eosin Methylene Blue agar for 24 h before being biochemically identified using the RapID ONE test. PCR was used to detect carbapenemase (blaKPC, blaOXA-48, and blaNDM) and ESBL (blaSHV, blaTEM, and blaCTX) expressing genes on isolates. Results: K. pneumoniae was identified in 30% of water and 10% of worker samples, while only one isolate was found in tomato samples. One of the six irrigation water isolates tested positive for carbapenem-resistant NDM. In contrast, two isolates tested positive for ESBL determinants, one of which was blaSHV and the other having both blaSHV and blaTEM genes. Two of the five K. pneumoniae isolates from farmworkers were positive for blaNDM, with one isolate also testing positive for blaSHV and blaTEM. The blaOXA-48 gene was also discovered in the carbapenem-resistant K. pneumoniae tomato isolate used in this study. Conclusion: Carbapenemase- and ESBL-producing K. pneumoniae were found in fresh produce farms, implying that these resistance genes were being passed down to Egyptian consumers.

Lipid A-Ara4N as an alternate pathway for (colistin) resistance in Klebsiella pneumonia isolates in Pakistan

Objectives

This study aimed to explore mechanism of colistin resistance amongst Klebsiella pneumoniae isolates through plasmid mediated mcr-1 gene in Pakistan. Carbapenem and Colistin resistant K. pneumoniae isolates (n  = 34) stored at − 80 °C as part of the Aga Khan University Clinical Laboratory strain bank were randomly selected and subjected to mcr-1 gene PCR. To investigate mechanisms of resistance, other than plasmid mediated mcr-1 gene, whole genome sequencing was performed on 8 clinical isolates, including 6 with colistin resistance (MIC  >  4 μg/ml) and 2 with intermediate resistance to colistin (MIC  >  2 μg/ml).

Results

RT-PCR conducted revealed absence of mcr-1 gene in all isolates tested. Whole genome sequencing results revealed modifications in Lipid A-Ara4N pathway. Modifications in Lipid A-Ara4N pathway were detected in ArnA_ DH/FT, UgdH, ArnC and ArnT genes. Mutation in ArnA_ DH/FT gene were detected in S3, S5, S6 and S7 isolates. UgdH gene modifications were found in all isolates except S3, mutations in ArnC were present in all except S1, S2 and S8 and ArnT were detected in all except S4 and S7. In the absence of known mutations linked with colistin resistance, lipid pathway modifications may possibly explain the phenotype resistance to colistin, but this needs further exploration.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13104-021-05867-3.

Carriage and Acquisition of Extended-spectrum β-Lactamase-producing Enterobacterales Among Neonates Admitted to Hospital in Kilifi, Kenya

Background

Infections caused by extended-spectrum β-lactamase–producing Enterobacterales (ESBL-E) among hospitalized neonates in sub-Saharan Africa pose significant clinical challenges. Data on prevalence and acquisition of ESBL-E carriage among hospitalized neonates in the region are few, and risk factors for transmission are not clearly defined.

Methods

In a cohort study of consecutive neonatal admissions to Kilifi County Hospital from July 2013 through August 2014, we estimated ESBL-E carriage prevalence on admission using rectal swab cultures and identified risk factors using logistic regression. Using twice-weekly follow-up swabs, we estimated the incidence and identified risk factors for ESBL-E acquisition in hospital using Poisson regression.

Results

The prevalence of ESBL-E carriage at admission was 10% (59/569). Cesarean delivery, older neonatal age, and smaller household size were significant risk factors. Of the 510 infants admitted without ESBL-E carriage, 238 (55%) acquired carriage during their hospital stay. The incidence of acquisition was 21.4% (95% confidence interval, 19.0%–24.0%) per day. The rate was positively associated with the number of known neonatal ESBL-E carriers and with the total number of neonates on the same ward.

Conclusions

Carriage of ESBL-E was common among neonates on admission, and in-hospital acquisition was rapid. The dissemination and selection of ESBL-E appears to be driven by hospital exposures, operative delivery, and neonatal ward patient density. Further attention to infection control, patient crowding, and carriage surveillance is warranted.

Emergence of ceftazidime-avibactam resistance through distinct genomic adaptations in KPC-2-producing Klebsiella pneumoniae of sequence type 39 during treatment

Three ceftazidime-avibactam-resistant KPC-2-producing Klebsiella pneumoniae strains of ST39 were isolated in Greece, from rectal swabs of three patients after 10-15 days of treatment. The patients were treated with ceftazidime-avibactam as monotherapy or in combination with colistin. Two of these strains harbored a D179Y or a D179V substitution in the Ω loop of KPC-2, corresponding to KPC-33, or to the novel KPC-57, respectively. The third strain had a 15 amino acid insertion after position 259 in the KPC-2, corresponding to KPC-44.

IS26-Mediated Transfer of bla NDM-1 as the Main Route of Resistance Transmission During a Polyclonal, Multispecies Outbreak in a German Hospital

One of the most demanding challenges in infection control is the worldwide dissemination of multidrug-resistant (MDR) bacteria in clinical settings. Especially the increasing prevalence of carbapenemase producing Gram-negative pathogens poses an urgent threat to public health, as these enzymes confer resistance to almost all β-lactam antibiotics including carbapenems. In this study, we report a prolonged nosocomial outbreak of various NDM-1-producing Enterobacterales species due to clonal spread and cross-species exchange of plasmids and possibly transposons. Between July 2015 and September 2017, a total of 51 carbapenemase-positive isolates were collected from 38 patients and three environmental sources in a single German hospital. Combining molecular typing methods and whole genome sequencing, the metallo-β-lactamase gene bla _NDM-1 was found to be present in 35 isolates of which seven additionally carried the carbapenemase gene bla _KPC-2. Core genome MLST (cgMLST) revealed different clusters of closely related isolates of Escherichia coli, Klebsiella pneumoniae, Citrobacter freundii, Morganella morganii or Enterobacter cloacae indicating clonal spread. The detailed reconstruction of the plasmid sequences revealed that in all outbreak-associated isolates bla_NDM-1 was located on similar composite transposons, which were also very similar to Tn125 previously described for Acinetobacter baumannii. In contrast to Tn125, these structures were flanked by IS26 elements, which could facilitate horizontal gene transfer. Moreover, the identical plasmid was found to be shared by E. coli and M. morganii isolates. Our results highlight the importance of detailed genome-based analyses for complex nosocomial outbreaks, allowing the identification of causal genetic determinants and providing insights into potential mechanisms involved in the dissemination of antibiotic resistances between different bacterial species.

Occurrence of Third-Generation Cephalosporins-Resistant Klebsiella pneumoniae in Fresh Fruits and Vegetables Purchased at Markets in Algeria

This study aimed to characterize third-generation cephalosporin (3GC)-resistant Klebsiella pneumoniae isolated from fresh fruits and vegetables purchased at Bejaia city, Algeria. K. pneumoniae isolates were identified by MALDI-TOF. Susceptibility to antibiotics was tested by the disk diffusion method. Whole genome sequencing (WGS) was carried out to determine sequence type (ST), plasmid incompatibility group (Inc.), and acquired antimicrobial resistance gene presence. A total of 13 3GC-resistant K. pneumoniae strains were isolated. WGS identified bla_CTX-M-15 in 11 extended-spectrum-beta-lactamases (ESBL)-K. pneumoniae and bla_DHA-1 in 2 AmpC-K. pneumoniae. The aac(6')lb-cr gene was identified in 8 out of 13 isolates. Multilocus sequence typing (MLST) evidenced five different STs, namely ST14, ST45, ST219, ST236, and ST882. MDR K. pneumoniae contaminated fresh fruits and vegetables, often eaten raw and inappropriately washed, may represent an underestimated public health threat. This study highlights that hygiene measures during harvesting and retail process are of utmost importance to limit further ESBL/AmpC spread to the consumer households.

Molecular mechanisms related to colistin resistance in Enterobacteriaceae

Colistin is an effective antibiotic for treatment of most multidrug-resistant Gram-negative bacteria. It is used currently as a last-line drug for infections due to severe Gram-negative bacteria followed by an increase in resistance among Gram-negative bacteria. Colistin resistance is considered a serious problem, due to a lack of alternative antibiotics. Some bacteria, including Pseudomonas aeruginosa, Acinetobacter baumannii, Enterobacteriaceae members, such as Escherichia coli, Salmonella spp., and Klebsiella spp. have an acquired resistance against colistin. However, other bacteria, including Serratia spp., Proteus spp. and Burkholderia spp. are naturally resistant to this antibiotic. In addition, clinicians should be alert to the possibility of colistin resistance among multidrug-resistant bacteria and development through mutation or adaptation mechanisms. Rapidly emerging bacterial resistance has made it harder for us to rely completely on the discovery of new antibiotics; therefore, we need to have logical approaches to use old antibiotics, such as colistin. This review presents current knowledge about the different mechanisms of colistin resistance.

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.

A Nosocomial Outbreak of Clinical Sepsis in a Neonatal Care Unit (NCU) in Port-Au-Prince Haiti, July 2014 - September 2015

Introduction

Between July 2014 and September 2015, a neonatal care unit (NCU) in Port Au Prince, Haiti, experienced an outbreak of sepsis, most probably due to nosocomial transmission of Extended Beta Lactamase (ESBL) producing gram negative bacteria, included Klebsiella pneumoniae.

Methods

We describe the epidemiological and microbiological activities performed as part of the outbreak investigation and the control measures implemented throughout this period.

Results

During the study period 257 cases of sepsis were reported, of which 191 died. The case fatality decreased from 100% in July 2014 to 24% in September 2015 and could be attributed to an improvement in clinical management and strengthened infection prevention and control measures. Risk factors identified to be associated with having late onset sepsis (sepsis onset >48 hours after birth)(n=205/257, 79. included: all categories of birthweight lower than <2500g (p=<0.0001) and all categories of gestational age younger than 36 weeks (p=0.0002). Microbiological investigations confirmed that out of 32 isolates (N=55; 58%) that were positive for gram negative bacteria, 27 (89%) were due to K. pneumoniae and most of these were from single MLST type (ST37).

Discussion 

This outbreak highlighted the importance of epidemiological and microbiological surveillance during an outbreak of sepsis in a NCU in a low resource setting, including regular point prevalence surveys.

Genome Sequencing of Extended-Spectrum β-Lactamase (ESBL)-Producing Klebsiella pneumoniae Isolated from Pigs and Abattoir Workers in Cameroon

Background and objectives: Extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae is a serious public health issue globally. In this study, the antibiotic resistance genes, virulence factors, mobile genetic elements, and genetic lineages of circulating ESBL-producing K. pneumoniae strains isolated from pigs and humans in Cameroonian abattoirs were investigated using whole genome sequencing (WGS), in order to ascertain zoonotic transmission (viz. from animals to humans and/or vice-versa) in the food chain.

Methods: During March–October 2016, 288 nasal and rectal pooled samples from 432 pigs as well as nasal and hand swabs from 82 humans were collected from Cameroon and South Africa. Seven ESBL-producing K. pneumoniae circulating in Cameroonian pig abattoirs were selected and their genomic DNA sequenced using an Illumina MiSeq platform. Generated reads were de novo assembled using the Qiagen CLC Genomics Workbench and SPAdes. The assembled contigs were annotated using RAST and antibiotic resistance genes, virulence factors, plasmids, and bacteriophages were identified with ResFinder, Virulence Finder, PlasmidFinder, and PHAST, respectively.

Results: ESBL-producing K. pneumoniae were detected in pigs (34/158; 21.52%) and exposed workers (8/71; 11.26%) in Cameroon only. The circulating K. pneumoniae strains were dominated principally by the sequence type (ST) 14 and 39. In addition, the “high-risk” ST307 clone and two novel STs assigned ST2958 and ST2959 were detected. Genomic analysis identified various antibiotic resistance genes associated with resistance to β-lactams, aminoglycosides, fluoroquinolones, macrolide, lincosamide and streptogramins, rifampicin, sulfonamides, trimethoprim, phenicols and tetracycline. None of the ESBL-producing K. pneumoniae harbored virulence genes. Intermingled K. pneumoniae populations were observed between pig- and human-source within and across abattoirs in the country.

Conclusion: Our study shows that ESBL-producing K. pneumoniae is actively disseminating in pigs and occupationally exposed workers in Cameroonian pig abattoirs and is probably underestimated in the absence of molecular epidemiological studies. It suggests pigs, abattoir workers and food products as potential reservoirs and sources of zoonotic transmission in Cameroon. Our findings underline the existence of a potential unheeded food safety and public health threat associated with these resistant strains and reinforce the crucial importance of implementing appropriate food safety measures and promoting rational antibiotic use.

High Prevalence of Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae in Wild Fish from the Mediterranean Sea in Algeria

AIM

We investigated the prevalence of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae among wild fish from the coast of Bejaia (Algeria) in the Mediterranean Sea.

RESULTS

From March 2012 to August 2013, gut and gill samples of wild fish were screened for the presence of ESBL-producing Enterobacteriaceae. Strains were characterized with regard to antibiotic resistance, β-lactamase content, plasmid-mediated quinolone resistance, aminoglycoside resistance genes, and clonality (repetitive sequence-based polymerase chain reaction profiles and multilocus sequence typing). Virulence traits were performed for Escherichia coli and Klebsiella pneumoniae isolates. Of the 300 fish studied, 64 (21.3%) isolates were screened as positive for ESBL producing by the double-disc method. The isolates corresponded to E. coli, K. pneumoniae, Enterobacter cloacae, Morganella morganii, Citrobacter freundii, and Proteus vulgaris. A predominance of bla_CTX-M gene was observed with a prevalence of 60.5% (n = 46). Furthermore, our study describes the association of important coresistance and virulence factors in E. coli and K. pneumoniae. Twelve of the ESBL producers carried genes of the qnr family and oqxAB gene and six carried the aac(6')-Ib-cr gene.

CONCLUSIONS

Our results highlight for the first time the diffusion of multidrug-resistant Enterobacteriaceae isolates carrying resistance and virulence genes in fish from the Mediterranean Sea in Algeria.

Clonal Spread of 16S rRNA Methyltransferase-Producing Klebsiella pneumoniae ST37 with High Prevalence of ESBLs from Companion Animals in China

We screened 30 Klebsiella pneumoniae isolates from dogs and cats at a single animal hospital in Guangdong Province, China. Among them, 12 K. pneumoniae strains possessed high-level resistance to amikacin and gentamicin and these were screened for 16S rRNA methyltransferase (16S-RMTase) genes. And then the genes positive isolates were detected for ESBLs (extended spectrum β-lactamases) and analyzed by pulsed-field gel electrophoresis, multilocus sequence typing, PCR-based replicon typing and plasmid analysis. The genetic profiles of rmtB were also determined by PCR mapping. The twelve 16S-RMTase gene-positive isolates were rmtB (11/30) and armA (2/30) with one isolate carrying both genes. Extended spectrum β-lactamases genes were represented by bla_CTX-M-55 (9/12), bla_CTX-M-27 (2/12) and bla_CTX-M-14 (1/12). The twelve 16S-RMTase containing strains were grouped into five clonal patterns and ST37 was the most prevalent sequence type. Ten rmtB-bearing plasmids conjugated successfully and all belonged to IncN and IncF (F33:A-:B-) incompatibility groups. Nine of the transconjugants carried a 97 kb plasmid and the other harbored both ∼60 and ∼200 kb plasmids. rmtB and bla_CTX-M-55 were present on the same plasmid and indicated the co-transfer of these two genes, with the rmtB gene showing highly relevant relationships with IS26 and Tn3. Our findings suggested a high prevalence of 16S-RMTase genes in K. pneumonia ST37 from dogs and cats. Additional studies are needed to trace the evolutionary path of this type of resistance among the K. pneumonia isolates, and to determine whether they have been transferred to humans.

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.

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.

Clinical features and molecular epidemiology of plasmid-mediated DHA-type AmpC β-lactamase-producing Klebsiella pneumoniae blood culture isolates, Hong Kong

Knowledge of risk factors and clinical characteristics of bacteraemia caused by plasmid-mediated AmpC β-lactamase (pAmpC)-producing Klebsiella pneumoniae (pAmpC-Kp) is not well described. This was a retrospective cohort study of patients with K. pneumoniae bacteraemia in three Hong Kong regional hospitals. Demographic and clinical data were retrieved from medical records. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were performed for molecular epidemiology. A total of 109 patients were included, divided into four groups: bacteraemia due to K. pneumoniae with (i) DHA-type pAmpC (n=23), (ii) extended-spectrum β-lactamase (ESBL) (n=37), (iii) DHA-type pAmpC+ESBL (n=26) and (iv) controls (n=23). Nursing home residence was independently associated with pAmpC-Kp bacteraemia compared with ESBL-Kp bacteraemia [adjusted odds ratio (aOR)=7.13, 95% confidence interval (CI) 1.36-37.54] and controls (aOR=41.47, 95% CI 4.55-377.75). Compared with controls, patients with pAmpC-Kp bacteraemia also suffered from more severe illness [median Acute Physiology and Chronic Health Evaluation (APACHE) II scores 16 and 25, respectively; P=0.006]. Importantly, the pAmpC group received discordant empirical antimicrobial therapy more frequently (OR=24.00, 95% CI 5.01-114.97), resulting in higher 7-day mortality (OR=20.17, 95% CI 2.32-175.67) and 30-day mortality (OR 4.68, 95% CI 1.29-16.98). PFGE detected six pulsotypes, corresponding to the predominant sequence type 11. Severity of illness and mortality of patients with bacteraemia caused by pAmpC-Kp were high. Patients who are nursing home residents presenting nosocomial sepsis should be treated with broad-spectrum antimicrobials.

Molecular epidemiology and distribution of serotypes, genotypes, and antibiotic resistance genes of Streptococcus agalactiae clinical isolates from Guelma, Algeria and Marseille, France

This study describes, for the first time, the genetic and phenotypic diversity among 93 Streptococcus agalactiae (group B Streptococcus, GBS) isolates collected from Guelma, Algeria and Marseille, France. All strains were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The molecular support of antibiotic resistance and serotyping were investigated by polymerase chain reaction (PCR). The phylogenetic lineage of each GBS isolate was determined by multilocus sequence typing (MLST) and grouped into clonal complexes (CCs) using eBURST. The isolates represented 37 sequence types (STs), 16 of which were novel, grouped into five CCs, and belonging to seven serotypes. Serotype V was the most prevalent serotype in our collection (44.1%). GBS isolates of each serotype were distributed among multiple CCs, including cps III/CC19, cps V/CC1, cps Ia/CC23, cps II/CC10, and cps III/CC17. All isolates presented susceptibility to penicillin, whereas resistance to erythromycin was detected in 40% and tetracycline in 82.2% of isolates. Of the 37 erythromycin-resistant isolates, 75.7% showed the macrolide-lincosamide-streptogramin B (MLSB)-resistant phenotype and 24.3% exhibited the macrolide (M)-resistant phenotype. Constitutive MLSB resistance (46%) mediated by the ermB gene was significantly associated with the Guelma isolates, whereas the M resistance phenotype (24.3%) mediated by the mefA/E gene dominated among the Marseille isolates and belonged to ST-23. Tetracycline resistance was predominantly due to tetM, which was detected alone (95.1%) or associated with tetO (3.7%). These results provide epidemiological data in these regions that establish a basis for monitoring increased resistance to erythromycin and also provide insight into correlations among clones, serotypes, and resistance genes.

Mechanisms of Resistance to Aminoglycoside Antibiotics: Overview and Perspectives

Aminoglycoside (AG) antibiotics are used to treat many Gram-negative and some Gram-positive infections and, importantly, multidrug-resistant tuberculosis. Among various bacterial species, resistance to AGs arises through a variety of intrinsic and acquired mechanisms. The bacterial cell wall serves as a natural barrier for small molecules such as AGs and may be further fortified via acquired mutations. Efflux pumps work to expel AGs from bacterial cells, and modifications here too may cause further resistance to AGs. Mutations in the ribosomal target of AGs, while rare, also contribute to resistance. Of growing clinical prominence is resistance caused by ribosome methyltransferases. By far the most widespread mechanism of resistance to AGs is the inactivation of these antibiotics by AG-modifying enzymes. We provide here an overview of these mechanisms by which bacteria become resistant to AGs and discuss their prevalence and potential for clinical relevance.

MALDI-TOF MS as a Tool To Detect a Nosocomial Outbreak of Extended-Spectrum-β-Lactamase- and ArmA Methyltransferase-Producing Enterobacter cloacae Clinical Isolates in Algeria

Enterobacter cloacae is among the most important pathogens responsible for nosocomial infections and outbreaks. In this study, 77 Enterobacter isolates were collected: 27 isolates from Algerian hospitals (in Constantine, Annaba, and Skikda) and 50 isolates from Marseille, France. All strains were identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Antibiotic susceptibility testing was performed by the disk diffusion method. PCR was used to detect extended-spectrum-beta-lactamase (ESBL)-encoding, fluoroquinolone resistance-encoding, and aminoglycoside-modifying enzyme (AME) genes. Epidemiological typing was performed using MALDI-TOF MS with data mining approaches, along with multilocus sequence typing (MLST). Sixty-eight isolates (27 from Algeria, 41 from Marseille) were identified by MALDI-TOF MS as E. cloacae. Resistance to antibiotics in the Algerian isolates was significantly higher than that in the strains from Marseille, especially for beta-lactams and aminoglycosides. Eighteen of the 27 Algerian isolates and 11 of the 41 Marseille isolates possessed at least one ESBL-encoding gene: blaCTX-M and/or blaTEM. AME genes were detected in 20 of the 27 Algerian isolates and 8 of the 41 Marseille isolates [ant(2″)-Ia, aac(6')-Ib-cr, aadA1, aadA2, and armA]. Conjugation experiments showed that armA was carried on a transferable plasmid. MALDI-TOF typing showed three separate clusters according to the geographical distribution and species level. An MLST-based phylogenetic tree showed a clade of 14 E. cloacae isolates from a urology unit clustering together in the MALDI-TOF dendrogram, suggesting the occurrence of an outbreak in this unit. In conclusion, the ability of MALDI-TOF to biotype strains was confirmed, and surveillance measures should be implemented, especially for Algerian patients hospitalized in France.