Evaluation of carbapenem-resistant Enterobacteriaceae in an Italian setting: Report from the trench

Genome and transcriptomic analysis of the adaptation of Escherichia coli to environmental stresses

In natural niches, bacteria are forced to spend most of their lives under various environmental stresses, such as nutrient limitation, heavy metal pollution, heat and antibiotic stress. To cope with adverse environments, bacterial genome can during the life cycle, produce potential adaptive mutants. The genomic changes, especially mutations, in the genes that encode RNA polymerase and transcription factors, might lead to variations in the transcriptome. These variations enable bacteria to cope with environmental stresses through physiological adaptation in response to stress. This paper reviews the recent contributions of genomic and transcriptomic analyses in understanding the adaption mechanism of Escherichia coli to environmental stresses. Various genomic changes have been observed in E. coli strains in laboratory or under natural stresses, including starvation, heavy metals, acidic conditions, heat shock and antibiotics. The mutations include slight changes (one to several nucleotides), deletions, insertions, chromosomal rearrangements and variations in copy numbers. The transcriptome of E. coli largely changes due to genomic mutations. However, the transcriptional profiles vary due to variations in stress selections. Cellular adaptation to the selections is associated with transcriptional changes resulting from genomic mutations. Changes in genome and transcriptome are cooperative and jointly affect the adaptation of E. coli to different environments. This comprehensive review reveals that coordination of genome mutations and transcriptional variations needs to be explored further to provide a better understanding of the mechanisms of bacterial adaptation to stresses.

Characterization of Verona Integron-Encoded Metallo-β-Lactamase-Type Carbapenemase-Producing Escherichia coli Isolates Collected over a 16-Year Period in Bolzano (Northern Italy)

Multidrug-resistant Escherichia coli, particularly carbapenemase producers, are a major source of concern. This study aims to investigate the long-term epidemiology of Verona integron-encoded metallo-β-lactamase (VIM)-producing E. coli in the health district of Bolzano, Northern Italy, by examining the phenotypic and genotypic characteristics of 26 isolates obtained during 2005-2020. Isolates were identified with matrix-assisted laser desorption/ionization time-of-flight, susceptibility testing was by Vitek 2, Sensititre, and Etest; carbapenemase activity was confirmed by Etest and Carbapenemase Inactivation Method (CIM) test; and the VIM-antigen was identified by the NG-Test CARBA 5. Genome sequencing was performed on an Illumina MiSeq platform. Carbapenem minimum inhibitory concentrations varied across methodologies, and overall category agreement between phenotypic methods was low. All 23 sequenced isolates contained blaVIM-1. Eleven (47.8%) isolates belonged to the clonal lineage ST131, with fimH30 being the most common subclone. In Bolzano ST131-fimH30 was present as early as 2005. While the ST131 clonal lineage predominated for the first 10 years, various clonal lineages were present, especially in subsequent years, indicating the concurrent circulation of multiple clonal lineages. Future efforts should focus on the implementation of surveillance methods, including genomic analysis, as well as the use of updated infection control strategies and antibiotic stewardship programs to prevent the spread of these carbapenem-resistant strains.

Comparative genomic analysis of Escherichia coli strains obtained from continuous imipenem stress evolution

The carbapenem-resistant Escherichia coli (E. coli) has aroused increasing attention worldwide, especially in terms of imipenem (IMP) resistance. The molecular mechanism of IMP resistance remains unclear. This study aimed to explore the resistance mechanisms of IMP in E. coli. Susceptible Sx181-0-1 strain was induced into resistance strains by adaptive laboratory evolution. The drug resistance spectrum was measured using the disk diffusion and microbroth dilution methods. Whole-genome sequencing and resequencing were used to analyze the non-synonymous single-nucleotide polymorphisms (nsSNPs) between the primary susceptible strain and resistant strains. The expression levels of these genes with nsSNPs were identified by real-time quantitative PCR (RT-qPCR). Resistance phenotype appeared in the induced 15th generation (induction time = 183 h). Sx181-32 and Sx181-256, which had minimum inhibitory concentrations of IMP of 8 and 64 µg mL-1, were isolated during continuous subculture exposed to increasing concentrations of IMP, respectively. Nineteen nsSNPs were observed both in Sx181-32 and Sx181-256, including rpsU, sdaC, zwf, ttuC, araJ, dacC, mrdA, secF, dacD, lpxD, mrcB, ftsI, envZ, and two unknown function genes (orf01892 and orf01933). Among these 15 genes, five genes (dacC, mrdA, lpxD, mrcB, and ftsI) were mainly involved in cell wall synthesis. The mrdA (V338A, L378P, and M574I) and mrcB (P784L, A736V, and T708A) had three amino acid substitutions, respectively. The expression levels of rpsU, ttuC and orf01933 were elevated in both Sx181-32 and Sx181-256 compared to Sx181-0-1. The expression levels of these genes were elevated in Sx181-256, except for araJ. Bacteria developed resistance to antimicrobials by regulating various biological processes, among which the most involved is the cell wall synthesis (dacC, mrdA, lpxD, mrcB, and ftsI). The combination mutations of mrdA, envZ, and ftsI genes may increase the resistance to IMP. Our study could improve the understanding of the molecular mechanism underlying the IMP resistance of E. coli.

Whole-Genome Sequencing (WGS) of Carbapenem-Resistant K. pneumoniae Isolated in Long-Term Care Facilities in the Northern Italian Region

K. pneumoniae (KPN) is one of the widest spread bacteria in which combined resistance to several antimicrobial groups is frequent. The most common β-lactamases found in K. pneumoniae are class A carbapenemases, both chromosomal-encoded (i.e., NMCA, IMI-1) and plasmid-encoded (i.e., GES-enzymes, IMI-2), VIM, IMP, NDM, OXA-48, and extended-spectrum β-lactamases (ESBLs) such as CTX-M enzymes. In the present study, a total of 68 carbapenem-resistant KPN were collected from twelve long-term care facilities (LTCFs) in the Northern Italian region. The whole-genome sequencing (WGS) of each KPN strain was determined using a MiSeq Illumina sequencing platform and analysed by a bacterial analysis pipeline (BAP) tool. The WGS analysis showed the prevalence of ST307, ST512, and ST37 as major lineages diffused among the twelve LTCFs. The other lineages found were: ST11, ST16, ST35, ST253, ST273, ST321, ST416, ST1519, ST2623, and ST3227. The bla_KPC-2, bla_KPC-3, bla_KPC-9, bla_SHV-11, bla_SHV-28, bla_CTX-M-15, bla_OXA-1, bla_OXA-9, bla_OXA-23, qnrS1, qnrB19, qnrB66, aac(6′)-Ib-cr, and fosA were the resistance genes widespread in most LTCFs. In this study, we demonstrated the spreading of thirteen KPN lineages among the LTCFs. Additionally, KPC carbapenemases are the most widespread β-lactamase.

Isolation and characterisation of colistin-resistant Enterobacterales from chickens in Southeast Nigeria

OBJECTIVES

Resistance to colistin (CST) mediated by mobile genetic elements has had a broad impact worldwide. There is an intensified call for epidemiological surveillance of mcr in different reservoirs to preserve CST for future generations. In Nigeria, the poultry industry is a key livestock sector. This study was undertaken to screen putative colistin-resistant Enterobacterales (CST-r-E) from poultry birds in Southeast Nigeria and to determine the genetic relatedness of mcr-harbouring isolates.

METHODS

Faecal and cloacal swab samples (n = 785) were collected from chickens in 17 farms located in three contiguous states in Southeast Nigeria between March-November 2018. Following selective culture, CST-r-E were isolated. Confirmation of CST resistance, antimicrobial susceptibility testing, molecular detection of genes mcr-1 to mcr-10, multilocus sequence typing (MLST) and randomly amplified polymorphic DNA (RAPD) analysis were performed on the isolates. A questionnaire was distributed to investigate the knowledge about CST and its use of chicken farm caretakers.

RESULTS

Of the 785 samples evaluated, 45 (5.7%) were positive for 48 CST-r-E, among which 23 harboured the mcr-1 gene (22 Escherichia coli and 1 Klebsiella pneumoniae). In two E.coli isolates, a new allelic variant (mcr-1.22) was detected. RAPD analysis allowed the identification of 11 different fingerprints. MLST also revealed 11 STs, with 3 of them being novel.

CONCLUSION

mcr has significantly spread in poultry birds of Southeast Nigeria, which poses a worrisome risk to veterinary and human health. Strategies to prevent indiscriminate use of CST in farms should be quickly adopted before CST resistance becomes a huge global health issue.

In vitro activity of cefiderocol and comparators against isolates of Gram-negative pathogens from a range of infection sources: SIDERO-WT-2014-2018 studies in Italy

OBJECTIVES

Antimicrobial resistance, particularly carbapenem resistance, in Gram-negative pathogens poses a significant healthcare threat. Carbapenem resistance rates in Italy are among the highest in Europe. We report the in vitro activity of cefiderocol, a novel siderophore cephalosporin, and comparator antibiotics against Gram-negative isolates from Italy as part of the SIDERO-WT studies.

METHODS

Isolates were collected between 2014 and 2018. Minimum inhibitory concentrations (MICs) were determined using International Organization for Standardization and EUCAST guidelines. Antimicrobial susceptibilities were interpreted using EUCAST breakpoints; pharmacodynamic/pharmacokinetic breakpoints were used if EUCAST breakpoints were not specified.

RESULTS

The 2472 isolates [1545 (62.5%) Enterobacterales and 927 (37.5%) non-fermenters] represented a range of infection sources, including nosocomial pneumonia (902; 36.5%), complicated urinary tract infection (374; 15.1%), bloodstream infection (596; 24.1%), complicated intra-abdominal infection (257; 10.4%) and other infection sources (343; 13.9%). Cefiderocol was active against the majority of isolates, regardless of infection source (susceptibility, 94.2-97.3%). A high proportion of non-fermenters (97.6%) and Enterobacterales (95.6%) were cefiderocol-susceptible, although susceptibility was lower in Klebsiella pneumoniae (88.1%). Susceptibility to cefiderocol was significantly (P < 0.01) greater than comparators overall (96.4% vs. 71.3-81.6%) and in non-fermenters (97.6% vs. 44.3-90.3%) across infection sources. Overall 612/2472 isolates (24.8%) were meropenem-resistant (MIC > 8 mg/L), comprising 516/927 (55.7%) non-fermenters and 96/1545 (6.2%) Enterobacterales. Cefiderocol (499/516; 96.7%) activity was greater than colistin (440/516; 85.3%), ceftazidime/avibactam (123/516; 23.8%) and ceftolozane/tazobactam (89/516; 17.2%) in meropenem-resistant non-fermenter isolates.

CONCLUSION

Susceptibility to cefiderocol was significantly greater than meropenem, colistin, ceftazidime/avibactam and ceftolozane/tazobactam overall, regardless of infection source.

Incidence and risk factors of carbapenem-resistant Enterobacteriaceae infection in intensive care units: a matched case-control study

BACKGROUND

Carbapenem-resistant Enterobacteriaceae (CRE) infection is associated with intensive care admissions, morbidity, and mortality. Our study aimed to determine the incidence, risk factors, and patient outcomes of CRE in the ICU units.

METHODS

This was a retrospective matched case-control study of patients admitted to ICUs. Patients who have positive cultures of CRE and carbapenem-susceptible Enterobacteriaceae (CSE) were included in the study. Patients were randomly selected from a pool of CSE subjects in a ratio of 1:1 of CRE to CSE as control patients.

RESULTS

The infection rate with CRE among all patients admitted to ICUs was 7.6% and the incidence of CRE infection was 5.6 per 1,000 person-day. The risk factors independently associated with CRE infection were: Higher Sequential Organ Failure Assessment (SOFA) and Nutrition Risk in Critically ill (NUTRIC) scores, prolonged ICU length of stay (LOS), previous surgery, dialysis and mechanical ventilation during ICU stay, and previous use of aminoglycoside and carbapenems.

CONCLUSION

In this retrospective study, the incidence of CRE infection was relatively elevated in patients admitted to ICU. Patients with high SOFA and NUTRIC scores, prolonged ICU LOS, previous surgery, dialysis and mechanical ventilation, and prior aminoglycosides and carbapenems use, may have an increased risk of CRE infection.

Bloodstream infections due to carbapenemase-producing Enterobacteriaceae in Italy: results from nationwide surveillance, 2014 to 2017

Following the rapid increase of infections due to carbapenemase-producing Enterobacteriaceae (CPE) in Italy, the national surveillance of bloodstream infections (BSI) due to CPE (Klebsiella pneumoniae and Escherichia coli) was instituted in 2013. All CPE-BSI cases reported to the surveillance in the years 2014-17 were analysed in order to investigate incidence rate (IR), trend, main individual characteristics and enzymes involved in CPE resistance. Throughout this period, 7,632 CPE-BSI cases (IR: 3.14/100,000 inhabitants) were reported from all 21 regions and autonomous provinces in Italy, with an increasing number of reported cases (2014: 1,403; 2015: 1,838; 2016: 2,183; 2017: 2,208). CPE-BSI cases mainly occurred in subjects aged over 60 years (70.9%) and more frequently in males (62.7%) than in females. Most of the cases originated in hospitals (87.2%), mainly in intensive care units (38.0%), and were associated with central or peripheral venous catheter use (23.9%) or with urinary tract infections (21.1%). Almost all CPE-BSI (98.1%) were due to K. pneumoniae carrying the K. pneumoniae carbapenemase (KPC) enzyme (95.2%). These data show that carbapenemase-producing K. pneumoniae are endemic in our country, causing a high number of BSI and representing a threat to patient safety.

Carbapenem Resistant Enterobacteriaceae in Africa

Carbapenems are regarded as unique among the �-lactam antibiotics due to their broad spectrum of activity and ability to resist �-lactamase hydrolysis. Carbapenems are the only �-lactam antibiotics with efficacy in severe infections caused by extended-spectrum beta-lactamase (ESBL) producing bacteria. However, recent reports of carbapenem resistance particularly among members of Enterobacteriaceae that are responsible for diseases such as gastrointestinal infections, septicemia, pneumonia, meningitis, peritonitis as well as urinary tract infections, call for concerns. In Africa, the problem of carbapenem-resistant Enterobacteriaceae (CRE) is aggravated by factors such as the high rate of infections, poor diagnostic tools, sub-optimal disease surveillance, and abuse of antibiotics. Besides, the problem of CRE in Africa is understudied. This review distills available literature on the spread of CRE in Africa, CRE genes in circulation, and the need to pay attention to this emerging threat to lives in developing countries.

Molecular characterization of carbapenem-resistant Klebsiella pneumoniae ST14 and ST512 causing bloodstream infections in ICU and surgery wards of a tertiary university hospital of Verona (northern Italy): co-production of KPC-3, OXA-48, and CTX-M-15 β-lactamases

Klebsiella pneumoniae strain is an important opportunistic pathogen that causes severe nosocomial infections. In the present study a molecular characterization of carbapenem resistant K. pneumoniae, isolated from blood samples of hospitalized patients of Verona University Hospital, was performed. The simultaneous presence of SHV-1/CTX-M-15/KPC-3 and SHV-1/CTX-M-15/OXA-48 serin-β-lactamases was ascertained in the 89% and 11% of K. pneumoniae ST512 and K. pneumoniae ST14, respectively. Molecular characterization of bla genes showed that bla_KPC-3 was found in Tn4401a transposon with the tnpR, tnpA, ISKpn6, and ISKpn7 mobile elements whereas bla_CTX-M-15 was detected downstream ISEcp1 genetic element. A class 1 integron with a gene cassette of 780 bp corresponding to aadA2 gene was identified in 33 K. pneumoniae ST512 isolates.

Rectal screening for carbapenemase-producing Enterobacteriaceae: a proposed workflow

OBJECTIVES

Active screening is a crucial element for the prevention of carbapenemase-producing Enterobacteriaceae (CPE) transmission in healthcare settings. Here we propose a culture-based protocol for rectal swab CPE screening that combines CPE detection with identification of the carbapenemase type.

METHODS

The workflow integrates an automatic digital analysis of selective chromogenic media (WASPLab®; Copan), with subsequent rapid tests for the confirmation of carbapenemase production [i.e. detection of Klebsiella pneumoniae carbapenemase (KPC)-specific peak by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS) or a multiplex immunochromatographic assay identifying the five commonest carbapenemase types]. To evaluate the performance of this protocol in depth, data for 21 162 rectal swabs submitted for CPE screening to the Microbiology Unit of S. Orsola-Malpighi Hospital (Bologna, Italy) were analysed.

RESULTS

Considering its ability to correctly segregate plates with/without Enterobacteriaceae, WASPLab Image Analysis Software showed globally a sensitivity and specificity of 100% and 79.4%, respectively. Of the plates with bacterial growth (n = 901), 693 (76.9%) were found to be positive for CPE by MALDI-TOF/MS (KPC-specific peak for K. pneumoniae) or by immunochromatographic assay. Only 2.8% (16/570) of KPC-positive K. pneumoniae strains were missed by the specific MALDI-TOF/MS algorithm, being detected by the immunochromatographic assay. The mean turnaround time needed from sample arrival to the final report ranged between 18 and 24 h, representing a significant time saving compared with manual reading.

CONCLUSION

This workflow proved to be fast and reliable, being particularly suitable for areas endemic for KPC-producing K. pneumoniae and for high-throughput laboratories.

Extended-spectrum β-lactamase, plasmid-mediated AmpC β-lactamase, fluoroquinolone resistance, and decreased susceptibility to carbapenems in Enterobacteriaceae: fecal carriage rates and associated risk factors in the community of Northern Cyprus

Background

Antibiotic-resistant Enterobacteriaceae in the gastrointestinal flora can lead to infections with limited therapeutic options. Also, the resistant bacteria can be transferred from colonized persons to others. The present study was conducted to search the fecal carriage rates of (i) Enterobacteriaceae that produce extended-spectrum β-lactamase (ESBL-E) and/or (ii) plasmid-mediated AmpC β-lactamase (pAmpC-E), (iii) ciprofloxacin-resistant Enterobacteriaceae (CIP-RE), and (iv) carbapenem-intermediate or -resistant Enterobacteriaceae (CIRE) in Northern Cyprus.

Methods

A total of 500 community-dwellers were recruited from consecutive admissions to the clinical laboratories of four hospitals. One rectal swab or stool sample was collected from each participant. A questionnaire was applied to evaluate possible risk factors associated with intestinal colonization of resistant bacteria. The samples were cultured on antibiotic containing media to screen for resistant bacteria colonization. The bacterial colonies that grew on the plates were subjected to further phenotypic tests to confirm the resistance.

Results

Of 500 volunteers, ESBL-E, pAmpC-E, CIP-RE and CIRE carriage were detected in 107 (21.4%), 15 (3.0%), 51 (10.2%) and six (1.2%) participants, respectively. Escherichia coli was the most commonly recovered species among Enterobacteriaceae isolates. A significant proportion of ESBL-producing E. coli isolates (n = 22/107; 20.6%) was found to be co-resistant to CIP (p = 0.000, OR 3.21, 95% CI 1.76-5.87). In this study, higher socioeconomic status (CIP-RE: p = 0.024, OR 1.96, 95% CI 1.09-3.53), presence of gastrointestinal symptoms (CIRE: p = 0.033; OR 6.79, 95% CI 1.34-34.39), antibiotic use (ESBL-E: p = 0.031; OR 1.67, 95% CI 1.04-2.67; and CIRE: p = 0.033; OR 6.40, 95% CI 1.16-35.39), and travelling abroad (pAmpC-E: p = 0.010; OR 4.12, 95% CI 1.45-11.66) were indentified as risk factors.

Conclusion

The study indicates that resistant Enterobacteriaceae isolates are carried by humans in the community. To prevent further spread of resistance, rational use of antibiotics should be encouraged, and antibiotic resistance should be carefully monitored in Northern Cyprus.

Molecular typing of a large nosocomial outbreak of KPC-producing bacteria in the biggest tertiary-care hospital of Quito, Ecuador

OBJECTIVES

Klebsiella pneumoniae is an opportunistic pathogen associated with nosocomial infections worldwide. Isolates with a K. pneumoniae carbapenemase (KPC)-producing phenotype show reduced susceptibility to first-choice antibiotics. Between 2012-2013, the largest public tertiary-care hospital in Quito (Ecuador) reported an outbreak of KPC-producing bacteria with more than 800 cases. We developed a molecular epidemiological approach to analyse the clonality of K. pneumoniae isolates recovered from selected hospital services and patient samples.

METHODS

A retrospective cohort study was performed based on microbial isolates and their corresponding records from the hospital and referred to Instituto Nacional de Investigación en Salud Pública (INSPI). From 800 isolates that were collected between 2012-2013, a total of 100 isolates were randomly selected for this study. Antimicrobial susceptibility testing was performed according to Clinical and Laboratory Standards Institute (CLSI) guidelines. Genotypic detection and phylogenetic relationship analysis were performed by multilocus sequence typing (MLST). The bla_KPC carbapenemase gene was also amplified by PCR and was sequenced using Sanger sequencing.

RESULTS

Molecular analysis showed that the outbreak had a polyclonal origin with two predominant genotypes, comprising sequence types ST25 and ST258, present in 38 and 36 cases, respectively. These genotypes were found in all studied hospital services including general surgery, intensive care unit and emergency. Thebla_KPC-5 gene was the most prevalent bla_KPC variant in this study.

CONCLUSION

These data indicate that KPC-producing polyclonal K. pneumoniae are frequent causes of nosocomial hospital outbreaks in South America. Similar genotypes have been reported in Colombia, Argentina, Brazil, North America and Asia.

Maternal vaginal colonization with selected potential pathogens of neonatal sepsis in the era of antimicrobial resistance, a single center experience from Sri Lanka

BACKGROUND

Maternal vaginal colonization with antibiotic resistant organisms is a growing concern in countries with high antibiotic resistance rates.

METHODS

A low vaginal swab was collected from mothers on admission, on discharge and a peri-rectal swab was collected from the neonates born to these mothers on discharge. Routine microbiological methods were used to identify the colonization rates for Escherichia coli, Klebsiella spp. and Streptococcus agalactiae.

RESULTS

The pre-delivery colonization rate among the 250 participants for total Enterobacteriaceae was 18.8%. The colonization rates for Klebsiella spp., E. coli and S. agalactiae were, 12.4, 5.6 and 14.8% respectively. Two Klebsiella spp. and two E. coli isolates were confirmed to be exentend spectrum β lactamase (ESBL) producers with the commonest resistant determinant being blaCTX-M. Post-delivery swabs were collected from 130 participants and the colonization rates were 41.5% for Enterobacteriaceae, 25.4% for Klebsiella spp., 10.8% for E. coli, and 10.8% for S. agalacteiae. Three Klebsiella isolates and one E. coli isolate were confirmed to be ESBL producers with the commonest resistant determinant being blaCTX-M. Considering the 130 participants with both samples, there was a significant increase in the colonization with any Enterobacteriaceae and Klebsiella spp. (p < 0.05). Peri-rectal swabs were collected from neonates in 159 instances. The isolation rates for Enterobacteriaceae was 34%. The genus specific isolation rate for Klebsiella was 21.4% while the rates for E. coli and S.agalactiae were 10.1 and 5.7% respectively. Two of the E. coli were confirmed to be ESBL producers while none of the klebsiellae were identified to be so. Considering these 159 instances where both the mother and baby were sampled, random amplification of polymorphic DNA (RAPD) analysis revealed that Enterbacteriaceae with same strain type was present in 6.9% of the instances, indicating possible transfer between the mother and neonate. The transfer rate for ESBL producers were 0.6%.

CONCLUSIONS

The lower level of antimicrobial resistance among these potentially community acquired isolates is encouraging. However, in view of the increasing level of resistance reported elsewhere in the region, regular monitoring is warranted.

Multicenter Evaluation of the Xpert Carba-R Assay for Detection of Carbapenemase Genes in Gram-Negative Isolates

This multicenter study evaluated the performance of the Cepheid Xpert Carba-R assay, a qualitative PCR test designed for the rapid detection of bla_KPC, bla_NDM, bla_VIM, bla_IMP, and bla_OXA-48 carbapenem resistance genes from bacterial isolates grown on blood agar or MacConkey agar. The results were compared to those obtained from bidirectional DNA sequence analysis of nucleic acid extracted from pure colonies. Isolates of Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii that tested as either intermediate or resistant to a carbapenem antibiotic were analyzed. A total of 467 isolates were evaluated, including prospectively collected clinical isolates, frozen isolates, and a group of contrived broth specimens sent by a central reference laboratory. The assay was run on the GeneXpert platform and took 48 min, with less than 1 min of hands-on time. Compared to the results of the reference methods, the overall sensitivity of the assay was 100% (95% confidence interval [CI], 99.0 to 100%) for isolates grown on both blood and MacConkey agars. Overall specificity was 98.1% (95% CI, 93.1 to 99.8%) and 97.1% (95% CI, 91.7 to 99.4%) for blood and MacConkey agars, respectively. This platform, previously demonstrated to be effective for the detection of carbapenemase genes in rectal swabs, is also adequate for the detection of these genes in bacterial colonies isolated from blood and MacConkey agars.

First literature review of carbapenem-resistant Providencia

Providencia species are Gram-negative bacteria that belong to the Enterobacteriaceae family. They have intrinsic resistance to colistin and tigecycline, which makes treatment of the multidrug-resistant strains of Providencia challenging. Carbapenem-resistant Providencia species are increasingly reported. In this review, patients' characteristics, resistance mechanisms, treatment and infection control measures of carbapenem-resistant Providencia species in the literature are described.

A Systematic Review and Meta-analyses of the Clinical Epidemiology of Carbapenem-Resistant Enterobacteriaceae

Carbapenem-resistant Enterobacteriaceae (CRE) are major health care-associated pathogens and responsible for hospital outbreaks worldwide. To prevent a further increase in CRE infections and to improve infection prevention strategies, it is important to summarize the current knowledge about CRE infection prevention in hospital settings. This systematic review aimed to identify risk factors for CRE acquisition among hospitalized patients. In addition, we summarized the environmental sources/reservoirs and the most successful infection prevention strategies related to CRE. A total of 3,983 potentially relevant articles were identified and screened. Finally, we included 162 studies in the systematic review, of which 69 studies regarding risk factors for CRE acquisition were included in the random-effects meta-analysis studies. The meta-analyses regarding risk factors for CRE acquisition showed that the use of medical devices generated the highest pooled estimate (odds ratio [OR] = 5.09; 95% confidence interval [CI] = 3.38 to 7.67), followed by carbapenem use (OR = 4.71; 95% CI = 3.54 to 6.26). To control hospital outbreaks, bundled interventions, including the use of barrier/contact precautions for patients colonized or infected with CRE, are needed. In addition, it is necessary to optimize the therapeutic approach, which is an important message to infectious disease specialists, who need to be actively involved in a timely manner in the treatment of patients with known CRE infections or suspected carriers of CRE.

A Lytic Providencia rettgeri Virus of Potential Therapeutic Value Is a Deep-Branching Member of the T5virus Genus

Providencia rettgeri is emerging as a new opportunistic pathogen with high antibiotic resistance. The need to find alternative methods to control antibiotic-resistant bacteria and the recent advances in phage therapy motivate the search for new phages able to infect Providencia spp. This study describes the isolation and characterization of an obligatory lytic phage, vB_PreS_PR1 (PR1), with therapeutic potential against drug-resistant P. rettgeri PR1 is a siphovirus. Its virion DNA size (118,537 bp), transcriptional organization, terminal repeats (10,461 bp), and nicks in the 3'-to-5' strand are similar to those of phage T5. However, sequence similarities of PR1 to phages of the T5virus genus at the DNA and protein levels are limited, suggesting that it belongs to a new species within the Siphoviridae family. PR1 exhibits the ability to kill P. rettgeri antibiotic-resistant strains, is highly specific to the species, and did not present known genomic markers indicating a temperate lifestyle. The lack of homologies between its proteins and proteins of the only other sequenced Providencia prophage, Redjac, suggests that these two phages evolved separately and may target different host proteins.IMPORTANCE The alarming increase in the number of bacteria resistant to antibiotics has been observed worldwide. This is particularly true for Gram-negative bacteria. For certain of their strains, no effective antibiotics are available. Providencia sp. has been a neglected pathogen but is emerging as a multidrug-resistant bacterium. This has revived interest in bacteriophages as alternative therapeutic agents against this bacterium. We describe the morphological, physiological, and genomic characterization of a novel lytic virus, PR1, which is able to kill drug-resistant P. rettgeri clinical isolates. Genomic and phylogenetic analyses indicate that PR1 is a distant relative of T5virus genus representatives. The lack of known virulence- or temperate lifestyle-associated genes in the genome of PR1 makes this phage a potential candidate for therapeutic use. Analysis of its genome also improves our knowledge of the ecology and diversity of T5-like siphoviruses, providing a new link for evolutionary studies of this phage group.

Spread of resistant gram negatives in a Sri Lankan intensive care unit

Background

Infections with multi drug resistant (MDR) organisms are a major problem in intensive care units (ICUs). Proper infection control procedures are mandatory to combat the spread of resistant organisms within ICUs. Well stablished surveillance programmes will enhance the adherence of the staff to infection control protocols. The study was conducted to assess the feasibility of using basic molecular typing methods and routine hospital data for laboratory surveillance of resistance organisms in resource limited settings.

Methods

A retrospective study was conducted using consecutive Gram negative isolates obtained from an ICU over a six month period. Antibiotic sensitivity patterns and random amplified polymorphic DNA (RAPD) based typing was performed on the given isolates.

Results

Of the seventy isolates included in the study, seven were E.coli. All E.coli were MDRs and Extended Spectrum β lactamse (ESBL) producers carrying bla_CTX-M. Fourteen isolates were K.pneumoniae, and all were MDRs and ESBL producers. All K.pneumoniae harboured bla_SHV while 13 harboured bla_CTX-M. The MDR rate among P.aeruginosa was 13% (n=15) while all acinetobacters (n=30) were MDRs. Predominant clusters were identified within all four types of Gram negatives using RAPD and the ICU stay of patients overlapped temporally.

Conclusion

We propose that simple surveillance methods like RAPD based typing and basic hospital data can be used to convince hospital staff to adhere to infection control protocols more effectively, in low and middle income countries.

Rapid Identification of Five Classes of Carbapenem Resistance Genes Directly from Rectal Swabs by Use of the Xpert Carba-R Assay

Carbapenemase-producing organisms (CPO) have been identified by global health leaders as an urgent threat. Detection of patients with gastrointestinal carriage of CPO is necessary to interrupt their spread within health care facilities. In this multisite study, we assessed the performance of the Xpert Carba-R test, a rapid real-time quantitative PCR (qPCR) assay that detects five families of carbapenemase genes (bla_IMP, bla_KPC, bla_NDM, bla_OXA-48, and bla_VIM) directly from rectal swab specimens. Using dual swabs, specimens from 755 patients were collected and tested prospectively. An additional 432 contrived specimens were prepared by seeding well-characterized carbapenem-susceptible and -nonsusceptible strains into a rectal swab matrix and inoculating them onto swabs prior to testing. Antimicrobial susceptibility testing, broth enriched culture, and DNA sequencing were performed by a central laboratory blind to the Xpert Carba-R results. The Xpert Carba-R assay demonstrated a positive percentage of agreement (PPA) between 60 and 100% for four targets (bla_KPC, bla_NDM, bla_VIM, and bla_OXA-48) and a negative percentage of agreement (NPA) ranging between 98.9 and 99.9% relative to the reference method (culture and sequencing of any carbapenem-nonsusceptible isolate). There were no prospective bla_IMP-positive samples. Contrived specimens demonstrated a PPA between 95 and 100% and an NPA of 100% for all targets. Testing of rectal swabs directly using the Xpert Carba-R assay is effective for rapid detection and identification of CPO from hospitalized patients.

Carbapenemases-producing Klebsiella pneumoniae in hospitals of two regions of Southern Italy

Carbapenem-resistant Klebsiella pneumoniae infections are reported with increasing frequency elsewhere in the world, representing a worrying phenomenon for global health. In Italy, there are hotspot data on the diffusion and type of carbapenemase-producing Enterobacteriaceae and K. pneumoniae in particular, with very few data coming from Apulia and Basilicata, two regions of Southern Italy. This study was aimed at characterizing by phenotypic and genotypic methods carbapenem-resistant K. pneumoniae isolated from several Hospitals of Apulia and Basilicata, Southern Italy. Antibiotic susceptibility was also evaluated. The relatedness of carbapenemase-producing K. pneumoniae strains was established by pulsed-field gel electrophoresis (PFGE). Among the 150 K. pneumoniae carbapenemase producers, KPC-3 genotype was the most predominant (95%), followed by VIM-1 (5%). No other genotypes were found and no co-presence of two carbapenemase genes was found. A full concordance between results obtained by both the phenotypic and the genotypic tests was observed. All strains were resistant to β-lactam antibiotics including carbapenems, and among antibiotics tested, only tetracycline and gentamycin showed low percentage of resistance (18% and 15%, respectively). Resistance to colistin was detected in 17.3% of strains studied. The analysis of PFGE profiles of the carbapenemases-positive strains shows that one group (B) of the five (A to E) main groups identified was the most prevalent and detected in almost all the hospitals considered, while the other groups were randomly distributed. Three different sequence types (ST 307, ST 258, and ST 512) were detected with the majority of isolates belonging to the ST 512. Our results demonstrated the wide diffusion of K. pneumoniae KPC-3 in the area considered, the good concordance between phenotypic and genotypic tests. Gentamicin and colistin had a good activity against these strains.

Carriage of beta-lactamase-producing Enterobacteriaceae among nursing home residents in north Lebanon

BACKGROUND

Multidrug-resistant (MDR) Enterobacteriaceae can cause severe infections with high morbidity, mortality, and health care costs. Individuals can be fecal carriers of these resistant organisms. Data on the extent of MDR Enterobacteriaceae fecal carriage in the community setting in Lebanon are very scarce. The aim of this study was to investigate the fecal carriage of MDR Enterobacteriaceae among the elderly residents of two nursing homes located in north Lebanon.

METHODS

Over a period of 4 months, five fecal swab samples were collected from each of 68 elderly persons at regular intervals of 3-4 weeks. Fecal swabs were subcultured on selective media for the screening of resistant organisms. The phenotypic detection of extended-spectrum beta-lactamase (ESBL), AmpC, metallo-beta-lactamase (MBL), and Klebsiella pneumoniae carbapenemase (KPC) production was performed using the beta-lactamase inhibitors ethylenediaminetetraacetic acid, phenylboronic acid, and cloxacillin. A temocillin disk was used for OXA-48. Multiplex PCRs were used for the genotypic detection of ESBL and carbapenemase genes, and sequencing was performed to identify CTX-M-15. The medical records of each subject were reviewed on a regular basis in order to assess the risk factors associated with MDR Enterobacteriaceae fecal carriage.

RESULTS

Over the study period, 76.5% of the recruited elderly persons were at least one-time carriers. A total of 178 isolates were obtained. Phenotypic testing revealed that 91.5% of them were ESBL producers, 4% were AmpC producers, 2.8% were co-producers of ESBL and AmpC, and 1.7% were co-producers of OXA-48 and ESBL. Recent antibiotic intake was found to be the only independent risk factor associated with the fecal carriage of MDR Enterobacteriaceae.

CONCLUSIONS

The high prevalence of MDR Enterobacteriaceae detected in this study and the emergence of carbapenem resistance is alarming. Efficient infection control measures and antibiotic stewardship programs are urgently needed in these settings in order to limit the spread of resistant strains.

Molecular epidemiology of carbapenem resistant Enterobacteriaceae in Valle d'Aosta region, Italy, shows the emergence of KPC-2 producing Klebsiella pneumoniae clonal complex 101 (ST101 and ST1789)

BACKGROUND

The spread of carbapenem resistant Enterobacteriaceae (CRE) is an emerging clinical problem, of great relevance in Europe and worldwide. The aim of this study was the molecular epidemiology of CRE isolates in Valle d'Aosta region, Italy, and the mechanism of carbapenem resistance.

RESULTS

Sixty consecutive CRE samples were isolated from 52 hospital inpatients and/or outpatients from November 2013 to August 2014. Genotyping of microbial isolates was done by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST), carbapenemases were identified by PCR and sequencing. Carbapenem resistance gene transfer was performed by filter mating, plasmids from parental and transconjugant strains were assigned to incompatibility groups by PCR-based replicon typing. Molecular characterization of CRE isolates assigned 25 Klebsiella pneumoniae isolates to PFGE types A1-A5 and sequencing type (ST) 101, 17 K. pneumoniae isolates to PFGE type A and ST1789 (a single locus variant of ST101), 7 K. pneumoniae isolates to PFGE types B or C and ST512, 2 K. pneumoniae isolates to PFGE type D and ST405, and 5 Escherichia coli isolates to PFGE type a and ST131. All K. pneumoniae ST101 and ST1789 isolates were extended-spectrum beta-lactamase (ESBL) producers and carried bla CTX-M-1 group gene; 4 K. pneumoniae ST101 isolates were resistant to colistin. Molecular analysis of beta-lactamase genes identified bla KPC-2 and bla CTX-M-group 1 into conjugative plasmid/s assigned to IncFII incompatibility group in ST101 and ST1789 K. pneumoniae isolates, bla KPC-3 into conjugative plasmid/s assigned to IncF incompatibility group in ST512 and ST405 K. pneumoniae isolates, bla VIM-1 into conjugative plasmid/s assigned to IncN incompatibility group in ST131 E. coli isolates.

CONCLUSIONS

The spread of CRE in Valle d'Aosta region was caused by the selection of KPC-2 producing K. pneumoniae ST101 and ST1789 epidemic clones belonging to clonal complex 101, KPC-3 producing K. pneumoniae epidemic clones assigned to ST512 and ST405, and VIM-1 producing E.coli ST131 epidemic clone. Carbapenem resistance, along with bla KPC-2, bla KPC-3 and bla VIM-1 carbapenemase genes, was transferred by conjugative plasmids assigned to IncFII, IncF, and IncN incompatibility groups, respectively, in filter mating experiments. The emergence of colistin resistance was observed in KPC-2 producing K. pneumoniae ST101 isolates.

The pros, cons, and unknowns of search and destroy for carbapenem-resistant enterobacteriaceae

Antibiotic drug discovery has not kept pace with the development of microbial resistance to these agents. There are ever increasing reports where the causative agents of serious infections are multi-drug resistant and in some cases resistant to all known antibiotics. The emergence and spread of carbapenemase-producing Enterobacteriaceae has heightened awareness regarding antibiotic stewardship programs and infection prevention and control measures. There has been much controversy regarding the utility of the "search and destroy" strategy to prevent the spread of carbapenem-resistant Enterobacteriaceae. These controversies center on screening and management of carriers, including decontamination and isolation. It is however clear that a functional infection prevention and control program is fundamental to any strategy that serves to address the spread of microbes within a healthcare facility.