Showing papers in "new microbes and new infections in 2015"

The global threat of antimicrobial resistance: science for intervention

Abstract: In the last decade we have witnessed a dramatic increase in the proportion and absolute number of bacterial pathogens resistant to multiple antibacterial agents. Multidrug-resistant bacteria are currently considered as an emergent global disease and a major public health problem. The B-Debate meeting brought together renowned experts representing the main stakeholders (i.e. policy makers, public health authorities, regulatory agencies, pharmaceutical companies and the scientific community at large) to review the global threat of antibiotic resistance and come up with a coordinated set of strategies to fight antimicrobial resistance in a multifaceted approach. We summarize the views of the B-Debate participants regarding the current situation of antimicrobial resistance in animals and the food chain, within the community and the healthcare setting as well as the role of the environment and the development of novel diagnostic and therapeutic strategies, providing expert recommendations to tackle the global threat of antimicrobial resistance.

The bacterial pangenome as a new tool for analysing pathogenic bacteria

Abstract: The bacterial pangenome was introduced in 2005 and, in recent years, has been the subject of many studies. Thanks to progress in next-generation sequencing methods, the pangenome can be divided into two parts, the core (common to the studied strains) and the accessory genome, offering a large panel of uses. In this review, we have presented the analysis methods, the pangenome composition and its application as a study of lifestyle. We have also shown that the pangenome may be used as a new tool for redefining the pathogenic species. We applied this to the Escherichia coli and Shigella species, which have been a subject of controversy regarding their taxonomic and pathogenic position.

Prevalence and pathogenicity of binary toxin–positive Clostridium difficile strains that do not produce toxins A and B

Abstract: Clostridium difficile causes antibiotic-associated diarrhoea and pseudomembranous colitis. The main virulence factors of C. difficile are the toxins A (TcdA) and B (TcdB). A third toxin, called binary toxin (CDT), can be detected in 17% to 23% of strains, but its role in human disease has not been clearly defined. We report six independent cases of patients with diarrhoea suspected of having C. difficile infection due to strains from toxinotype XI/PCR ribotype 033 or 033-like, an unusual toxinotype/PCR ribotype positive for CDT but negative for TcdA and TcdB. Four patients were considered truly infected by clinicians and were specifically treated with oral metronidazole. One of the cases was identified during a prevalence study of A−B−CDT+ strains. In this study, we screened a French collection of 220 nontoxigenic strains and found only one (0.5%) toxinotype XI/PCR ribotype 033 or 033-like strain. The description of such strains raises the question of the role of binary toxin as a virulence factor and could have implications for laboratory diagnostics that currently rarely include testing for binary toxin.

Corrigendum to "The global threat of antimicrobial resistance: science for intervention" [New Microbes New Infect 6 (2015): 22-29].

Abstract: The authors regret that the spelling of author ‘O.E. Heuer’ was initially misspelt as ‘Heure’ in the published article. The authors regret that the spelling of author ‘E. Tacconelli’ was initially misspelt as ‘Taconelli’ in the published article. The authors would like to apologise for any inconvenience caused.

Epidemiology of Staphylococcus aureus in Bangalore, India: emergence of the ST217 clone and high rate of resistance to erythromycin and ciprofloxacin in the community

Abstract: This study aimed to determine the antibiotic susceptibility pattern of Staphylococcus aureus (SA) and the circulating clones in Bangalore, India. Susceptibility testing was performed for all cases of SA infections in a tertiary-care hospital. Panton-Valentine leucocidin (PVL) encoding genes were detected, and sequence type and spa type were determined. Out of the 92 collected strains, 52.2% were methicillin-resistant SA (MRSA), isolated from community-acquired (CA) infections in 60.4% and hospital-acquired (HA) infections in 39.6%. S. aureus isolates were also highly resistant to erythromycin (54.3%) and ciprofloxacin (70.6%) in methicillin-susceptible SA (MSSA) and MRSA, as well as in CA and HA infections. MRSA were found to be significantly more resistant to gentamicin (p <0.001), cotrimoxazole (p <0.001) and ciprofloxacin (p 0.001) than MSSA, but no significant difference was observed between CA- and HA-SA. ST217 appeared as a new emerging and prevalent clone, but ST772 remained the predominant clone, all being PVL-positive isolates. Our study points out the high prevalence of MRSA, even in the community, and the worrying increase of resistance to ciprofloxacin and erythromycin among CA-MSSA. Emergence of clone ST217 is reported for the first time in India.

Rapid identification of carbapenemase-producing Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii using a modified Carba NP test.

Abstract: Biochemical tests have been previously developed to identify carbapenemase-producing Enterobacteriaceae, Pseudomonas spp. (Carba NP test) and Acinetobacter spp. (CarbAcineto NP test). We evaluated a modified Carba NP test to detect carbapenemase production in Enterobacteriaceae, Pseudomonas and Acinetobacter species using a single protocol with rapid results and found good reliability and speed.

International Mycoplasma pneumoniae typing study: interpretation of M. pneumoniae multilocus variable-number tandem-repeat analysis

Abstract: Typing of Mycoplasma pneumoniae by multiple-locus variable-number tandem repeat analysis (MLVA) is increasingly in use. However, no specific internationally agreed guidance is available. Thirty M. pneumoniae DNA samples including serial dilutions of a type strain were sent to six international laboratories to perform MLVA and results were compared. Good correlation was observed, indicating that this methodology can be robustly performed in multiple sites. However, differences due to interpretation of fragment size, repeat sequence identification and repeat numbering led to inconsistency in the final profiles assigned by laboratories. We propose guidelines for interpreting M. pneumoniae MLVA typing and assigning the number of repeats.

Serologic and molecular survey for hepatitis E virus in wild boar (Sus scrofa) in Central Italy.

Abstract: The aim of this study was to further investigate the role of wild boar (Sus scrofa) as a reservoir for hepatitis E virus (HEV). Sixty-four blood and faecal samples collected from wild boar hunted in Central Italy in 2011–2012 were examined by indirect enzyme-linked immunosorbent assay and RT-PCR analysis. Positive RT-PCR samples were further examined by nucleotide sequence determination and subsequent phylogenetic analysis. Thirty-six sera (56.2%) were positive for HEV-specific antibodies, and six (9.4%) faecal samples scored RT-PCR-positive results. Four animals were positive by both enzyme-linked immunosorbent assay and RT-PCR. Phylogenetic analysis showed that the detected wild boar–derived HEV sequences clustered within genotype 3, with similarity to sequences of human origin collected in a nearby area in 2012. Our data confirm that HEV is endemic in the wild boar population in the research area and that these wild animals could play an important role in the epidemiology of HEV infection.

Candidatus 'Rickettsia senegalensis' in cat fleas in Senegal.

Abstract: Epidemiological studies of Rickettsia felis and related bacteria are very important, because the natural cycle of this important infection has not yet been established. The recent emergence of R. felis-associated febrile diseases in West and East Africa demands insightful epidemiological studies of the vectors and reservoirs of this bacterium in Africa. Twenty-nine cat fleas, Ctenocephalides felis, were tested for the presence of rickettsiae, including R. felis, bartonellae, and borreliae, with specific quantitative real-time PCR assays. Supporting our previous studies, R. felis was not detected in the fleas collected. In addition, neither Bartonella nor Borrelia was found. In five (17%) examined fleas, we found another species of rickettsia. We isolated three rickettsial strains, and genetic analysis demonstrated that these strains represent a probable new species, provisionally called Candidatus Rickettsia senegalensis here.

Changing trends in the epidemiology of vertebral osteomyelitis in Marseille, France

Abstract: The incidence and significant morbidity of vertebral osteomyelitis are increasing despite the progress of diagnosis competences. Among the 50 cases of vertebral osteomyelitis managed in our centers over the past 5 years, 84% of the cases were in men. The mean age was 55 years. Sixty-two percent of patients had comorbidities and risk factors: diabetes mellitus (24%), malignancy (16%), intravenous drug use (10%) and alcoholism (4%). A source of infection was identified in 66% of cases, including postvertebral surgery infection (18%) and hematogenous infection (48%). The mean time to diagnosis was 36 days. Back pain were occurred in 90% of cases, fever (70%), neurologic deficits (40%), epidural abscesses (32%), completed vertebral bone destruction (26%) and psoas abscess (12%). A single organism was isolated in 92% of cases. Gram-positive bacteria were identified in 76% of cases, while Gram-negative bacilli (GNB) were found in 18% of cases. The presence of GNB was significantly associated with malignancy (p 0.041). The mean duration of antibiotic therapy was 123 days. Surgical treatment was performed in 41 cases: spinal stabilization (26%), drainage of abscesses (32%) and relief of compression (40%). Residual pain was found in 24% of cases, and neurologic sequelae in 22%. Cervical or thoracic localization was a risk factor for neurologic compromise (p 0.042). The epidemiology of vertebral osteomyelitis has changed; an increase in malignancy that was significantly associated with vertebral osteomyelitis due to GNB has been observed. Our study shows that the rate of neurologic complications remains high despite improved diagnostic capabilities and optimal treatment.

First report of NDM-5-producing Escherichia coli ST1284 isolated from dog in Bejaia, Algeria

Abstract: Carbapenemase-producing isolates have been isolated from humans, environmental samples and, more recently, companion animals [1]. Among the newly emerged carbapenemases, New Delhi metallo-β-lactamase (NDM) represents the latest threat for public health [2]. Sixteen variants of NDM-type carbapenemase (NDM-1 to NDM-16) have been reported (http://www.lahey.org/Studies). Here we report what is to our knowledge the first case of Escherichia coli carrying the blaNDM-5 gene isolated from a dog in Algeria. In March 2015 a rectal swab was collected from a 3-year-old German Shepherd dog with a tumor at its third finger. The sample was cultured in 10 mL nutrient broth containing half a disc of ertapenem. After incubation at 37°C for 24 hours, 200 μL was streaked on MacConkey agar plates containing imipenem at a concentration of 0.5 μg/mL. An Escherichia coli isolate was identified by MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; Microflex, Bruker Daltonics, Bremen, Germany). Antibiotic susceptibility testing was performed by the disk diffusion method and interpreted according to the European Committee on Antimicrobial Susceptibility Testing guidelines (http://www.eucast.org/). The minimum inhibitory concentration (MIC) values of β-lactams were determined using Etest strips according to the manufacturer's recommendations (AB bioMerieux, Solna, Sweden). The E. coli isolate was found resistant to β-lactams, including carbapenems (MICs >32 μg/mL) and extended-spectrum cephalosporins (MICs >256 μg/mL). The isolate was also resistant to tetracycline and fluoroquinolones but was susceptible to amikacin, cotrimoxazole, colistin and tigecycline. The isolate was screened for carbapenemase production using the modified Carba NP test [3], and the production of metallo-β-lactamases was detected by the inhibition of the metallo-β-lactamase activity by ethylenediaminetetraacetic acid (EDTA) as previously described [4]. The E. coli isolate was positive for production of carbapenemase, which is inhibited by EDTA. PCR was used to screen for the presence of genes encoding for class A carbapenemases (blaKPC and blaGES), class D carbapenemases (blaOXA-48) and metallo-β-lactamases (blaNDM-1 and blaVIM) as previously described [5], followed by sequencing, which led to the identification of blaNDM-5. A review the literature at PubMed found 12 reports on NDM-5, which were all recovered from clinical specimens; no reports were from veterinary isolates, however. Among these 12 reports, one was from Algeria [6]. The authors of this study reported three isolates of E. coli sequence type (ST) 2659 recovered from urine and blood specimen isolated between January 2012 and February 2013 in the university hospital of Annaba (east Algeria). Thus, this is the first report of NDM-5-producing E. coli isolated from companion animals. Furthermore, other types of carbapenemases have been reported from domesticated animals, including NDM-1 in multidrug-resistant E. coli strains recovered from companion animals in the United States [7], and OXA-48 carbapenemase-producing Klebsiella pneumoniae and E. coli isolates obtained from a dog in Germany [8]. The E. coli isolate also carried the blaTEM-33 gene. The transferability of the resistance phenotype was studied by a conjugation experiment using sodium azide–resistant E. coli strain J53 as a recipient. The transconjugants were selected on Luria agar plates containing ceftazidime (8 μg/mL) and sodium azide (200 μg/mL) [2]. Only transconjugants carrying the blaTEM-33 gene were obtained. To determine the localization of the blaNDM-5 gene the isolate was subjected to plasmid extraction using the High Purity Plasmid Miniprep Kit (Neobiotech, Los Angeles, CA, USA) and the QIAquick Gel extraction kit (Qiagen, Germantown, MD, USA), followed by PCR amplification targeting blaNDM-5 performed on the extracted plasmid. The result showed that the isolate harboured only one plasmid which did not contain the blaNDM-5 gene, indicating that this gene is probably integrated into the chromosome. Genotyping of the isolate was performed by multilocus sequence typing (MLST) using seven housekeeping genes (adk, fumC, gyrB, icd, mdh, purA and recA), as described at the E. coli MLST Database (http://mlst.warwick.ac.uk/mlst/dbs/Ecoli). According to MLST analysis, the E. coli isolate was attributed to ST1284. This ST has been identified previously in E. coli isolates producing extended-spectrum β-lactamase recovered from animals [9]. In summary, this report documents the emergence of NDM-5 among E. coli ST1284 isolated for the first time from a companion animal in the North African countries.

First detection of Aspergillus fumigatus azole-resistant strain due to Cyp51A TR46/Y121F/T289A in an azole-naive patient in Spain

Abstract: We report the first isolation of a voriconazole-resistant Aspergillus fumigatus strain harbouring the azole resistance mechanism TR46/Y121F/T289A, recovered from an azole-naive patient in Spain with chronic obstructive pulmonary disease. This new finding in Spain suggests the spread of this resistance mechanism and reinforces the need for antifungal susceptibility surveillance.

Enterococcus hirae, an unusual pathogen in humans causing urinary tract infection in a patient with benign prostatic hyperplasia: first case report in Algeria.

Abstract: Enterococcus hirae is a zoonotic pathogen rarely isolated from human infections. This case is the first description of E. hirae causing urinary tract infection in a diabetic man with benign prostatic hyperplasia from Algeria. The clinical isolate was identified by MALDI-TOF MS and displayed a multisensitivity antibiotic profile.

First report of mecC MRSA in human samples from Austria: molecular characteristics and clinical data.

Abstract: Reports of mecC methicillin-resistant Staphylococcus aureus (MRSA) strains have been published from several European countries. We describe the first six mecC MRSA isolates of human origin from Austria and report the application of a rapid PCR test. Candidate isolates (n = 295) received between 2009 and 2013 were investigated phenotypically by cefoxitin screening and streaking on ChromID MRSA plates. The presence of mecC was confirmed in six isolates from blood cultures, wound swabs and screening samples of four female and two male patients (age range 7–89 years) by an in-house PCR method and the new Genspeed MRSA test (Greiner Bio-One, Kremsmunster, Austria). The mecC MRSA were further characterized by whole genome sequencing, multilocus sequence and spa typing. Antimicrobial susceptibility testing was performed by Eucast disk-diffusion method and Vitek 2. The six mecC MRSA isolates were from two clonal lineages (CC130, including a new single-locus variant, and CC599) and four different spa types (t843, t1535, t3256, t5930). Analysis for virulence factor genes yielded lukED, eta, etd2 and edin-B (CC130 isolates) and tst, lukED, eta and sel (ST599 isolates). The Genspeed MRSA test identified mecC in all isolates whereas Vitek 2 failed to detect methicillin resistance in one isolate. The strains were susceptible to a wide range of non-β-lactam antibiotics. All patients were successfully treated or decolonized. mecC MRSA are present in Austria as colonizers but may also cause infections. Thus, laboratories must choose appropriate test methods such as cefoxitin screening and confirmation using molecular assays specifically targeting mecC.

New Microbes New Infections promotes modern prokaryotic taxonomy: a new section "TaxonoGenomics: new genomes of microorganisms in humans".

Abstract: “New Microbes and New Infections” being devoted to new facts in infections and clinical microbiology comprises a “New Genomes of Microorganisms and Viruses in Humans” section featuring its own format. This section will evolve towards a “TaxonoGenomics: new genomes of microorganisms in humans” section to better take into consideration recent developments in prokaryote genome sequencing and incorporate the recent proposal that genome sequence and proteome must be part of the description of microbes of medical interest. Indeed, there is an impressive rise in bacterial genome sequencing, with 35,000 genomes currently available from virtually all major bacterial phyla. These sequences are an unprecedented source of information to develop molecular assays for detection or genotyping, to detect antibiotic resistance and virulence markers, to develop new culture media or to identify candidate antigens for vaccines [1]. A second breakthrough was the use of MALDI-TOF-mass spectrometry (MALDI-TOF-MS) for the routine identification of clinical isolates of bacteria and fungi [2,3]. Finally, the renewal of culture, through the culturomics strategy based on a diversification of culture conditions, enabled identifying more than 120 new human-associated bacterial species in a limited time [4]. These three tools have in common the advantage of producing data that can easily be shared and compared, either in international databases or culture collections. Surprisingly, although it has undergone many changes over time according to the introduction of new diagnostic methods, microbial systematics has not been adapted to incorporate genomic sequence and MALDI-TOF-MS, despite the fact that these methods are now widely used worldwide. Currently, although there is no universal agreement on the rules and criteria used for microorganism identification, several taxonomic criteria, based on phenotypic and genotypic characteristics [5–7], are used to determine whether a new bacterium fulfils the requirements to be classified as a new taxon. These include: i) routinely obtainable phenotypic properties (morphology, staining and antigenic properties, growth preferences, enzyme production, sugar metabolism, susceptibility to antibiotics, pathogenesis and habitat) [8]; ii) chemotaxonomic parameters such as the characterization of polar lipids, whole cell fatty acid content, respiratory quinones and peptidoglycan structure [9–11]; and iii) the determination of DNA-DNA hybridization (DDH) [12]. However, the latter two taxonomic criteria lack inter- and intra-laboratory reproducibility, require the use of methods restricted to few laboratories, are of no practical value for the routine identification of bacterial isolates. Recently, several genomic tools have been proposed as alternatives of DDH for the taxonomic classification of prokaryotes, including average genomic identity of orthologous gene sequence (AGIOS), average nucleotide identity (ANI), digital DDH, maximum unique matches index (MUMi), multilocus sequence analysis, multilocus sequence typing, and tetranucleotide regression [13], the former three of which have permitted the valid publication of several new species names [14–24]. In addition, a new polyphasic taxonomic strategy named taxono-genomics including both MALDI-TOF-MS instead of chemotaxonomic analysis and genome sequence analysis, in addition to common phenotypic criteria, was proposed to describe eight new bacterial species [17–24]. Therefore, there is now clear evidence that genomic and MALDI-TOF-MS data may be integrated as alternatives to chemotaxonomy and DDH, respectively, for the taxonomic description of bacteria, provided that the new isolates are compared to the phylogenetically closest species with standing in nomenclature. Accordingly, “New Microbes and New Infections” will now accommodate two formats in the new “TaxonoGenomics” section, including a short 500-words format and one item to report on new genome of already described organism and a 1,500-word format and three items to report on new genome as part as the description of a novel organisms. This new section will accommodate only microbes of medical interest and not environmental ones without known connection with populations and patients.

Persistence of anti-chikungunya virus-specific antibodies in a cohort of patients followed from the acute phase of infection after the 2007 outbreak in Italy

Abstract: Chikungunya is a mosquito-borne infection of humans, and its diffusion has increased worldwide. In 2007 an outbreak occurred in Italy. In this study, the antibody response of 133 patients followed up starting from the acute phase of infection was investigated. Antibody titres were periodically scored up to 1 year since the infection: 82.7% of the IgM antibody disappeared within 12 months, and the IgG response lasted longer than 12 months. Nevertheless, the IgG mean titre was lower in 95.5% of patients at the end of follow-up, thus suggesting a decrease within a relatively short period.

Outcome of mucormycosis after treatment: report of five cases

Abstract: Mucormycoses are serious infections caused by filamentous fungi of the order Mucorales. They occur most often in immunocompromised patients. We report five cases of mucormycosis in patients hospitalized in the Infectious Diseases Department in Sousse – Tunisia between 2000 and 2013. They were 4 males and one female, mean age 60 years. Three patients were diabetic and one patient had acute leukemia. The locations of mucormycosis were rhinocerebral, rhino-orbital, auricular, pulmonary and cutaneous. The Mucorales isolated were Rhizopus arrhizus in 3 cases and Lichteimia in 2 cases. All patients were treated with amphotericin B and 2 patients had, in addition, surgical debridement. Two patients died and 2 kept peripheral facial paralysis.

Associations of the major international high-risk resistant clones and virulent clones with specific ompK36 allele groups in Klebsiella pneumoniae in Taiwan.

Abstract: This study was conducted to investigate the association between ompK36 variants and international high-risk clones in Klebsiella pneumoniae. Fifty-nine sequence types (STs) divided into four ompK36 allele groups (groups A to D) were identified among 185 K. pneumoniae isolates. The major high-risk clones (29 ST11, 13 ST15, 7 ST37 and 1 ST147 isolates) were assigned to group A, while 6 STs (15 ST23, 2 ST65, 3 ST86, 1 ST163, 1 ST373 and 2 ST375 isolates) associated with pyogenic liver abscess were assigned to group C. The genotyping assay developed in this study may be useful for screening of epidemic STs.

Sphingobacterium multivorum: case report and literature review

Abstract: We describe the case of a 67-year-old African American woman with multiple medical problems who presented with septic shock resulting from Sphingobacterium multivorum bacteraemia. S. multivorum, a Gram-negative bacillus, is ubiquitous in nature and is rarely involved in human infections. However, it is intrinsically resistant to many commonly administered antibiotics and can be a life-threatening microorganism.

First bacteraemic human infection with Escherichia albertii.

Abstract: The facultative anaerobic Gram-negative species Escherichia albertii has been isolated from human faeces in gastrointestinal infection and from a range of wild bird species. Here we report the first case of a febrile infection associated with E. albertii bacteraemia in a 76-year-old woman with gastric dysplasia.

Butyricimonas virosa: the first clinical case of bacteraemia.

Abstract: The strictly anaerobic Gram-negative bacteria Butyricimonas species have recently been described in human faeces and have to our knowledge not been isolated in infectious clinical materials. We report the first case of Butyricimonas virosa bacteraemia in a 72-year-old man with colon adenocarcinoma, who underwent aortic aneurysm replacement surgery.

Roles of bovine Waddlia chondrophila and Chlamydia trachomatis in human preterm birth

Abstract: Waddlia chondrophila and Chlamydia trachomatis are intracellular bacteria associated with human miscarriage. We investigated their role in human preterm birth. Whereas presence of Chlamydia trachomatis DNA in genital tract was associated with human preterm birth, Waddlia was not, despite being present in women's genital tracts.

Faecal Escherichia coli isolates show potential to cause endogenous infection in patients admitted to the ICU in a tertiary care hospital

Abstract: Nosocomial infections are acquired during hospital treatment or in a hospital environment. One such infecting agent, Escherichia coli, harbours many virulence genes that enable it to become pathogenic, causing damage to the host. The mechanism of the E. coli virulence factors provenance to cause infection in host environments is not clearly elucidated. We investigated the virulence and pathogenicity of E. coli affected by the host environment. For this, blood (n = 78) and faecal (n = 83) E. coli isolates were collected from patients with and without sepsis, respectively, who had been admitted to the intensive care unit. The E. coli genomic DNA was isolated; the phylogenetic grouping was conducted by triplex PCR. The occurrence of nine virulence genes among the all the isolates was confirmed by gene-specific PCR. The prevalence of E. coli in blood isolates was more in phylogenetic groups B2 and D compared to groups A and B1. However, in faecal isolates, there was no significant difference. The prevalence of adhesin and toxin (papG, sfa, afa, cnf1, hlyA) genes was higher in blood compared to faecal E. coli isolates. However, the prevalence of aer, traT and PAI was similar as well as higher among both of these groups. These observations indicate a role of external environment (hospital setting) on host susceptibility (development of infection) in the faecal E. coli isolates, thereby making the patient prone to a sepsis condition.

High prevalence of blaOXA-23 in Acinetobacter spp. and detection of blaNDM-1 in A. soli in Cuba: report from National Surveillance Program (2010–2012)

Abstract: As a first national surveillance of Acinetobacter in Cuba, a total of 500 Acinetobacter spp. isolates recovered from 30 hospitals between 2010 and 2012 were studied. Acinetobacter baumannii–calcoaceticus complex accounted for 96.4% of all the Acinetobacter isolates, while other species were detected at low frequency (A. junii 1.6%, A. lwoffii 1%, A. haemolyticus 0.8%, A. soli 0.2%). Resistance rates of isolates were 34–61% to third-generation cephalosporins, 49–50% to β-lactams/inhibitor combinations, 42–47% to aminoglycosides, 42–44% to carbapenems and 55% to ciprofloxacin. However, resistance rates to colistin, doxycycline, tetracycline and rifampin were less than 5%. Among carbapenem-resistant isolates, 75% harboured different blaOXA genes (OXA-23, 73%; OXA-24, 18%; OXA-58, 3%). The blaNDM-1 gene was identified in an A. soli strain, of which the species was confirmed by sequence analysis of 16S rRNA gene, rpoB, rpoB–rpoC and rpoL–rpoB intergenic spacer regions and gyrB. The sequences of blaNDM-1 and its surrounding genes were identical to those reported for plasmids of A. baumannii and A. lwoffi strains. This is the first report of blaNDM-1 in A. soli, together with a high prevalence of OXA-23 carbapenemase for carbapenem resistance in Acinetobacter spp. in Cuba.

Enterococcus cecorum human infection, France

Abstract: Enterococcus cecorum is a bacterium of the intestinal tract of many domestic animals that is rarely reported as human pathogen. Here we report the first case of incisional hernia plate infection and the first case of urinary tract colonization due to E. cecorum from patients in Marseille, France.

Resistance and integron characterization of Acinetobacter baumannii in a teaching hospital in Chongqing, China

Abstract: A total of 189 Acinetobacter baumannii isolates were collected in 2011 from a teaching hospital in Chongqing, China. Susceptibility data showed strains carrying integrons were significantly more resistant to all tested antibiotics that strains lacking integrons. Five types of gene cassettes belonging to class I integrons were identified in this study, and for the first time two types of gene cassettes belonging to class II integrons are reported. Most of the cassettes belong to a class I integron (136/144) encoding arr3, aacA4, dfrA17, aadA5, aadB, cat, blaOXA10, aadA1, aadA2, dfrA and aacC1. Isolates contained a class I gene cassette; AadA2-HP-dfrA was the prevalent strain in this hospital. A class II integron was detected in eight strains, which contained the type IV fimbriae expression regulatory gene pilR and sulfate adenylyltransferase, suggesting a possible role in multidrug resistance. The major epidemic strains from intensive care unit patients belong to international clone 2. In conclusion, the presence of integrons was significantly associated with multiple drug resistance of A. baumannii in this hospital, and class I integron isolates bearing AadA2-HP-dfrA were the prevalent strain in this hospital.

Vitamin D receptor expression levels determine the severity and complexity of disease progression among leprosy reaction patients.

Abstract: We studied the roles of vitamin D and its receptor, VDR, in the progression of leprosy. The majority of individuals with leprosy from Kolkata, India, with a type 1 or type 2 reaction have low levels of vitamin D3 in serum samples. Interestingly, individuals with a type 2 reaction associated with neuritis/erythema nodosum leprosum had very low VDR mRNA expression levels, ranging from 5% to 10%, compared to that of healthy control subjects; these patients also had a high bacilli index, ranging from 3+ to 5+. This is the first report to indicate that VDR expression levels may determine the complexity and severity of the progression of leprosy.

Clostridium difficile infections among adults and children in Mwanza/Tanzania: is it an underappreciated pathogen among immunocompromised patients in sub-Saharan Africa?

Abstract: Little is known regarding the epidemiology Clostridium difficile in developing countries. Fresh stool samples from patients with diarrhoea were cultured anaerobically. C. difficile was detected in nine (6.4%) of 141 (95% confidence interval 4.2-13.1), of which seven (77.8%) were from children. HIV infection, prolonged hospitalization and antibiotic use were independent factors associated with the occurrence of C. difficile in the gastrointestinal tract. Two of the toxigenic isolates were typed as ribotype 045, and the other two had unknown ribotype. All C. difficile isolates were susceptible to metronidazole, moxifloxacin and clarithromycin, while three isolates were resistant to clarithromycin. C. difficile may be an important pathogen causing diarrhoea in sub-Saharan Africa among immunocompromised patients.

Prevalence of Smqnr and plasmid-mediated quinolone resistance determinants in clinical isolates of Stenotrophomonas maltophilia from Japan: novel variants of Smqnr.

Abstract: Stenotrophomonas maltophilia is an important pathogen in healthcare-associated infections. S. maltophilia may contain Smqnr, a quinolone resistance gene encoding the pentapeptide repeat protein, which confers low-level quinolone resistance upon expression in a heterologous host. We investigated the prevalence of Smqnr and plasmid-mediated quinolone resistance (PMQR) determinants in S. maltophilia isolates from Japan. A total of 181 consecutive and nonduplicate clinical isolates of S. maltophilia were collected from four areas of Japan. The antimicrobial susceptibility profiles for these strains were determined. PCR was conducted for Smqnr and PMQR genes, including qnrA, qnrB, qnrC, qnrS,aac(6′)-Ib and qepA. PCR products for Smqnr and aac(6′)-Ib were sequenced. For the S. maltophilia isolates containing Smqnr, pulsed-field gel electrophoresis (PFGE) was performed using XbaI. Resistance rates to ceftazidime, levofloxacin, trimethoprim–sulfamethoxazole, chloramphenicol and minocycline were 67.4%, 6.1%, 17.7%, 8.8% and 0%, respectively. The minimum inhibitory concentration required to inhibit the growth of 50% and 90% of organisms were 0.5 and 2 mg/L for moxifloxacin but 1 and 4 mg/L for levofloxacin, respectively. Smqnr was detected in 104 of the 181 S. maltophilia isolates (57.5%), and the most frequent was Smqnr6, followed by Smqnr8 and Smqnr11. Eleven novel variants from Smqnr48 to Smqnr58 were detected. The 24 Smqnr-containing S. maltophilia isolates were typed by PFGE and divided into 21 unique types. Nine S. maltophilia isolates (5.0%) carried aac(6′)-Ib-cr. No qnr or qepA genes were detected. This study describes a high prevalence of Smqnr and novel variants of Smqnr among S. maltophilia from Japan. Continuous antimicrobial surveillance and further molecular epidemiological studies on quinolone resistance in S. maltophilia are needed.

Burden of extensively drug-resistant and pandrug-resistant Gram-negative bacteria at a tertiary-care centre

Abstract: The emergence of resistance to multiple antimicrobial agents in Gram-negative bacteria is a significant threat to public health, as it restricts the armamentarium of the clinician against these infections. The aim of this study was to determine the burden of extensively drug-resistant (XDR) and pandrug-resistant (PDR) Gram-negative bacteria at a tertiary-care centre. Antimicrobial susceptibility testing of 1240 clinical isolates of Gram-negative bacteria obtained from various clinical samples during the study period was carried out by the Kirby-Bauer disc diffusion method. Minimum inhibitory concentration of all antibiotics including tigecycline and colistin was determined by Vitek-2 automated susceptibility testing system. Out of 1240 isolates of Gram-negative bacteria, 112 isolates (9%) were resistant to all the antibiotics tested by Kirby-Bauer disc diffusion method. This finding was corroborated by Vitek-2. In addition, Vitek-2 found that 67 isolates were resistant to all antibiotics except tigecycline and colistin. A total of 30 isolates were susceptible to only colistin, and four isolates were susceptible to only tigecycline. It was also found that six isolates (excluding five isolates of Proteus spp.) were resistant to both colistin and tigecycline. Thus, 101 (8.1%) out of 1240 isolates were XDR and 11 isolates (0.9%) were PDR. The findings of this study reveal increased burden of XDR and PDR Gram-negative bacteria in our centre. It also highlights the widespread dissemination of these bacteria in the community. This situation warrants the regular surveillance of antimicrobial resistance of Gram-negative bacteria and implementation of an efficient infection control program.