- Volume 62, Issue 4, 2013

The success of certain sequence types such as ST131 that produce CTX-M or NDM β-lactamases, and ST405 that produce CTX-M β-lactamases, among extraintestinal Escherichia coli (ExPEC) had previously been linked to a combination of antimicrobial resistance and certain virulence factors. The adherence properties of these sequence types to gastro-intestinal epithelial cells had not been investigated. A study was therefore designed to investigate the phylogenetic groups, virulence factors and adherence properties of E. coli sequence types ST101, ST131 and ST405 that produce CTX-M-15 and NDM-1. Our results show that ST131 was positive for phylogenetic group B2, ST101 for B1 and ST404 for D. ST131 had more virulence factors than ST101 or ST405. Interestingly, ST101 adhered more avidly to HEp-2 and Caco-2 cells than did ST131 and ST405. Our study showed that adherence to gastro-intestinal cells did not seem to play an important role in the worldwide epidemiological success of ST131 and ST405. The exact role of ExPEC-associated virulence genes is unknown and it is unlikely that one set of factors determines the virulence properties and epidemiological success of certain sequence types. Future investigations should be undertaken to study the microbiological and ecological factors that make certain sequence types among ExPEC such successful pathogens.

Dengue fever is re-emerging as a major scourge in south-east Asian countries, affecting about 50–100 million people and causing about 25 000 deaths annually. The Indian population as a whole is at risk of succumbing to this disease. This study genetically characterized viruses causing dengue infection in Kerala, one of the worst affected states of the country, during the disease outbreaks in 2008–2010. All four serotypes of dengue virus (DENV), DENV-1, DENV-2, DENV-3 and DENV-4, were found to be prevalent in the state. The genotypes recognized for these were III, IV, III and I, respectively. Phylogenetic analysis showed that the re-emergence of serotype DENV-4 reported in Maharashtra and Andhra Pradesh recently is spreading to different regions of the country. The circulation of all four DENV serotypes in Kerala may lead to an increase in the prevalence of more severe complications of this emerging disease, such as dengue haemorrhagic fever and dengue shock syndrome.

Microsporidia are obligate intracellular parasites that infect eukaryotic cells and have emerged as major opportunistic human pathogens. Due to the difficulties in definitive laboratory diagnosis and insufficient knowledge, ocular microsporidiosis is infrequently reported in India. To improve diagnostic facilities, we have developed a novel duplex PCR (dPCR) for the simultaneous identification of both genera and species of isolates with microsporidian aetiology that cause keratitis. The material scraped from the corneas of 12 clinically diagnosed microsporidial keratitis patients was subjected to routine microbiological examinations and molecular diagnosis using a novel dPCR that targeted the small-subunit rRNA gene (SSU-rRNA) of microsporidia and Vittaforma corneae using genus- and species-specific primers. Of the 12 corneal scrapes, 6 showed positive results in smears, while dPCR provided positive amplification with both pan-microsporidial and V. corneae species-specific primers for 9 corneal scrapes. The results were validated by sequencing and blast analysis. The sensitivity of this novel dPCR method was higher than that of conventional microscopy in the diagnosis of corneal microsporidial infection. dPCR with specific primers is potentially more sensitive, specific and depends less on more complicated methods for exact identification of the aetiology of microsporidial keratitis.

The major surface glycoprotein (MSG) of Pneumocystis jirovecii is the most abundant surface protein and appears to play a critical role in the pathogenesis of pneumocystosis. The expressed MSG gene is located immediately downstream of a region called the upstream conserved sequence (UCS). The UCS contains a region of tandem repeats that vary in number and sequence. In the present study, we have used capillary electrophoresis and direct sequencing to detect the variability in the repeat units of UCS. By direct sequencing the PCR products from samples of 13 patients, we have identified three types of repeat units which consisted of 10 nt and three different patterns in the UCS region with three and four repeats: 1, 2, 3 (84.6 %); 1, 2, 3, 3 (8.2 %); and a new genotype 2, 2, 3, 3 (8.2 %). The same samples were analysed by capillary electrophoresis. Three samples (23 %) contained a mixture of two or three different patterns of UCS repeats. In conclusion, quantifying the number of repeat units in the UCS by capillary electrophoresis provides a potential new method for the rapid typing of P. jirovecii and the detection of mixed infection.

Newborns are rarely infected by extended-spectrum β-lactamase (ESBL)-producing members of the Enterobacteriaceae. In a neonatal intensive care unit, 14 newborns were infected or colonized by CTX-M-15-producing Enterobacter cloacae. All seven infected patients had underlying medical conditions, and five of them were treated successfully with meropenem, whilst one untreated patient died. Paediatric infections caused by multidrug-resistant ESBL-producing Enterobacter cloacae constitute a critical clinical and epidemiological issue.

This study was designed to investigate the killing activity of levofloxacin, gatifloxacin, moxifloxacin and garenoxacin against 12 Bacteroides fragilis strains by kill kinetics over time. MIC values were determined by Etest and by agar dilution. B. fragilis strains were divided according to their MIC values into two groups: one group with strains with MIC <8.0 µg ml−1 and one group with strains with MIC ≥8.0 µg ml−1. For kill kinetics over time, the strains with MIC <8.0 µg ml−1 were incubated with the antibiotics at 0.5, 1, 2 and 4 times their MIC values. The strains with MIC ≥8.0 µg ml−1 were incubated with 0.5, 1, 2, and 4 times the maximum achievable concentrations of the antibiotics in human plasma (C max). Among the strains with MIC <8.0 µg ml−1 levofloxacin and gatifloxacin showed equal efficacy. The growth of the strains with MIC ≥8.0 µg ml−1 was barely affected by levofloxacin, while gatifloxacin had bactericidal action when concentrations of 4×C max were used. Moxifloxacin was more effective against both groups of strains compared with levofloxacin and gatifloxacin. Garenoxacin was the most active agent against all strains investigated. Due to the varying in vitro activity of the quinolones against obligate anaerobes the treatment with quinolones of patients with intra-abdominal infections needs intensive scrutiny.

Infection with Helicobacter pylori cytotoxin-associated gene A (CagA)-positive strains is associated with the development of gastric cancer (GC). However, some reports have failed to demonstrate an increased frequency of CagA antibodies in GC patients. This study evaluated the response of IgG antibody and subclasses IgG1 and IgG2 against both CagA and H. pylori membrane antigens in patients with pre-cancerous lesions and cases with GC. A total of 137 patients with a positive serum IgG response to H. pylori were selected: 46 with intestinal metaplasia, 41 with gastric adenocarcinoma and 50 with non-atrophic gastritis (NAG) considered as controls. The response of total IgG, IgG1 and IgG2 was investigated by immunoblot and ELISA using an in-house recombinant CagA and membrane antigens from a local strain, and possible associations were estimated using a logistic regression model. Compared with NAG patients, GC patients showed a higher frequency of IgG2 CagA antibodies (55.2 vs 15.4 %, P = 0.001), but a lower frequency (80.5 vs 96.0 %, P = 0.021) and diminished levels of IgG2 H. pylori antibodies [12.5 vs 21.9 ELISA units (EU), P = 0.007]. GC patients also presented lower levels of CagA (32.6 vs 42.4 EU, P = 0.004) and H. pylori total IgG (33.7 vs 38.7 EU, P = 0.029). GC was associated with a positive IgG2 CagA response [odds ratio (OR) = 3.74, 95 % confidence interval (CI) 1.81–5.37; P = 0.002] and with a low titre of total IgG CagA antibodies (OR = 2.18, 95 % CI 1.35–2.69; P = 0.006). These results suggest that the IgG2 response to CagA could be used as a novel serological marker to identify patients with H. pylori-associated GC.

Cholera, caused by Vibrio cholerae, results in significant morbidity and mortality worldwide, including Thailand. Representative V. cholerae strains associated with endemic cholera (n = 32), including strains (n = 3) from surface water sources, in Khon Kaen, Thailand (2003–2011), were subjected to microbiological, molecular and phylogenetic analyses. According to phenotypic and related genetic data, all tested V. cholerae strains belonged to serogroup O1, biotype El Tor (ET), Inaba (IN) or Ogawa (OG). All of the strains were sensitive to gentamicin and ciprofloxacin, while multidrug-resistant (MDR) strains showing resistance to erythromycin, tetracycline, trimethoprim/sulfamethoxazole and ampicillin were predominant in 2007. V. cholerae strains isolated before and after 2007 were non-MDR. All except six diarrhoeal strains possessed ctxA and ctxB genes and were toxigenic altered ET, confirmed by MAMA-PCR and DNA sequencing. Year-wise data revealed that V. cholerae INET strains isolated between 2003 and 2004, plus one strain isolated in 2007, lacked the RS1 sequence (rstC) and toxin-linked cryptic plasmid (TLC)-specific genetic marker, but possessed CTXCL prophage genes ctxB CL and rstR CL. A sharp genetic transition was noted, namely the majority of V. cholerae strains in 2007 and all in 2010 and 2011 were not repressor genotype rstR CL but instead were rstR ET, and all ctx + strains possessed RS1 and TLC-specific genetic markers. DNA sequencing data revealed that strains isolated since 2007 had a mutation in the tcpA gene at amino acid position 64 (N→S). Four clonal types, mostly of environmental origin, including subtypes, reflected genetic diversity, while distinct signatures were observed for clonally related, altered ET from Thailand, Vietnam and Bangladesh, confirmed by distinct subclustering patterns observed in the PFGE (NotI)-based dendrogram, suggesting that endemic cholera is caused by V. cholerae indigenous to Khon Kaen.

Detailed genetic analysis was carried out of the VP4/VP2 coding region in human rhinovirus species C (HRV-C) strains detected in patients with acute respiratory infection in Japan. Phylogenetic trees were constructed by the neighbour-joining (NJ) and maximum-likelihood (ML) methods. The NJ phylogenetic tree assigned 11 genotypes to the present strains, whilst the ML tree showed that the strains diversified sometime in the early 1870s. Moreover, the pairwise distance among the present strains was relatively long, and the rate of molecular evolution of the coding region was rapid (3.07×10−3 substitutions per site per year). The results suggest that the present HRV-C strains have a wide genetic divergence and a unique evolutionary timescale.

The hands of healthcare workers (HCWs) are the most common vehicle for the transmission of micro-organisms from patient to patient and within the healthcare environment. The aim of this study was to evaluate the impact of a multimodal campaign on the type and amount of resident and transient flora and the presence of potential risk factors for hand contamination during routine care. A before–after (PRE and POST periods) interventional study was carried out in medical wards of a tertiary care hospital. Eighty-nine samples were analysed. Samples were cultured immediately before patient contact using a glove-juice method. Data collected included socio-demographic and risk factors for hand contamination. Flora was measured as log10 c.f.u. ml−1 and evaluated by comparing median values in the PRE and POST periods. Transient flora was isolated from the hands of 67.4 and 46.1 % of HCWs in the PRE and POST periods, respectively (P<0.001). Enterobacteriaceae, Pseudomonas spp. and meticillin-sensitive Staphylococcus aureus were the predominant contaminants. Resident flora was isolated from 92.1 % of HCWs in the PRE period and from 70.8 % in the POST period (P<0.001). The meticillin-resistant coagulase-negative staphylococci log10 c.f.u. count ml−1 decreased from 1.96±1.2 to 0.89±1.2 (mean±sd; P<0.001), and the global flora count decreased from 2.77±1.1 to 1.56±1.4 (P<0.001). In the POST period, the wearing of fewer rings (P<0.001), shorter fingernail length (P = 0.008), a shorter time since recent hand hygiene (HH) (P = 0.007) and an increased use of alcohol-based hand rub instead of soap (P<0.001) were documented. The HH multimodal strategy reduced the number of risk factors and the level of HCW hand contamination.

Bacterial aggregation and/or adhesion are key factors for colonization of the digestive ecosystem and the ability of probiotic strains to exclude pathogens. In the present study, two probiotic strains, Lactobacillus rhamnosus CNCM-I-3698 and Lactobacillus farciminis CNCM-I-3699, were evaluated as viable or heat-killed forms and compared with probiotic reference Lactobacillus strains (Lb. rhamnosus GG and Lb. farciminis CIP 103136). The autoaggregation potential of both forms was higher than that of reference strains and twice that of pathogenic strains. The coaggregation potential of these two beneficial micro-organisms was evaluated against several pathogenic agents that threaten the global safety of the feed/food chain: Escherichia coli, Salmonella spp., Campylobacter spp. and Listeria monocytogenes. The strongest coaggregative interactions were demonstrated with Campylobacter spp. by a coaggregation test, confirmed by electron microscopic examination for the two forms. Viable forms were investigated for the nature of the bacterial cell-surface molecules involved, by sugar reversal tests and chemical and enzymic pretreatments. The results suggest that the coaggregation between both probiotic strains and C. jejuni CIP 70.2T is mediated by a carbohydrate–lectin interaction. The autoaggregation potential of the two probiotics decreased upon exposure to proteinase, SDS or LiCl, showing that proteinaceous components on the surface of the two lactobacilli play an important role in this interaction. Adhesion abilities of both Lactobacillus strains were also demonstrated at significant levels on Caco-2 cells, mucin and extracellular matrix material. Both viable and heat-killed forms of the two probiotic lactobacilli inhibited the attachment of C. jejuni CIP 70.2T to mucin. In conclusion, in vitro assays showed that Lb. rhamnosus CNCM-I-3698 and Lb. farciminis CNCM-I-3699, as viable or heat-killed forms, are adherent to different intestinal matrix models and are highly aggregative in vitro with pathogens, especially Campylobacter spp., the most commonly reported zoonotic agent in the European Union. This study supports the need for further in vivo investigations to demonstrate the potential food safety benefits of Lb. rhamnosus CNCM-I-3698 and Lb. farciminis CNCM-I-3699, live or heat-killed, in the global feed/food chain.