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Common themes in the genome strategies of pathogens.

Genomes of pathogenic bacteria evolve by large-scale changes in gene inventory. The continual acquisition of genomic islands, which refines their metabolic arsenal, is offset by gene loss. Far from this being a passive deletion of genes no longer useful to pathogens, the removal of genes encoding problematic metabolic process and immunogenic surface antigens might be strongly beneficial. Genomes of virulent eukaryotes show the footprint of similar genomic alterations, including acquisition of genes by lateral transfer, and genome degradation in obligate pathogens. These common features suggest that unicellular pathogens share common strategies for adaptation.

Bacteria↗

Rethinking the pathogenicity of intragenic DMD duplications detected by carrier screening: High prevalence of nontandem duplications revealed by long-read sequencing.

PURPOSE: The pathogenicity of intragenic duplications depends on their structural configuration. Tandem duplications often disrupt reading frames and cause gene loss of function, whereas interspersed (nontandem) duplications are largely benign. When the configuration cannot be determined, current guidelines presume a tandem structure, leading to some laboratories automatically classifying such variants as likely pathogenic or pathogenic. This study evaluates the validity of this presumption for DMD, in patients with and without clinical indications of dystrophinopathy. METHODS: We performed high-coverage long-read genome sequencing on 15 patients with intragenic DMD duplications. A total of 4 patients had clinically indicated dystrophinopathy testing, whereas in the remaining 11 patients, the duplications were detected without clear indications of dystrophinopathy (eg, through carrier screening). RESULTS: All 4 patients with clinical indications had tandem duplications. In contrast, 64% (7/11) of the cases without such indications had interspersed duplications, with 4 subsequently reclassified as likely benign, 2 (likely) pathogenic, and 1 uncertain. These duplications were often complex, involving coduplications or codeletions with other regions. CONCLUSION: Our findings challenge the presumption that intragenic DMD duplications are predominantly in tandem. This highlights the need for a cautious variant interpretation approach, particularly in carrier screening and other settings in which variants are identified without indications of dystrophinopathy.

Humans↗

Potentially pathogenic features of heterotrophic plate count bacteria isolated from treated and untreated drinking water.

Heterotrophic plate counts (HPCs) are commonly used to assess the general microbiological quality of drinking water. Drinking water quality specifications worldwide recommend HPC limits from 100 to 500 cfu ml(-1). A number of recent studies revealed evidence that these bacteria may not be as harmless as generally accepted. It appears that immuno-compromised individuals are particularly at risk. This would include the very young and very old patients with diseases such as AIDS and patients on therapy for purposes such as organ transplantation and cancer treatment. In this study, 339 bacterial colonies were isolated at random from selected treated and untreated drinking water in South Africa using routine heterotrophic plate count tests. In a first step to screen for potentially pathogenic properties, 188 (55.5%) of the isolates showed alpha- or beta-haemolysis on human- and horse-blood agar media. Subsequent analysis of the haemolytic isolates for enzymatic properties associated with pathogenicity revealed the presence of chondroitinase in 5.3% of the isolates, coagulase in 16.0%, DNase in 60.6%, elastase in 33.0%, fibrinolysin in 53.7%, gelatinase in 62.2%, hyaluronidase in 21.3%, lecithinase in 47.9%, lipase in 54.8% and proteinase in 64.4%. Fluorescein and pyocyanin were not produced by any of the isolates. Among the haemolytic isolates, 77.7% were resistant to oxacillin 1 microg, 59.6% to penicillin G 2 units, 47.3% to penicillin G 10 units, 54.3% to ampicillin 10 microg and 43.1% to ampicillin 25 microg. Cell culture studies revealed that 96% of haemolytic isolates were cytotoxic to HEp-2 cells, and 98.9% of the 181 cytotoxic isolates adhered to HEp-2 or Caco-2 cells. HEp-2 cells were invaded by 43.6%, and Caco-2 cells by 49.7%, of the 181 cytotoxic isolates. The invasion index on HEp-2 cells ranged from 1.9 x 10(-1) to 8.9 x 10(-6), whereas the invasion index on Caco-2 cells varied between 7.7 x 10(-2) and 8.3 x 10(-6). The most commonly isolated genera with these potentially pathogenic features were Aeromonas, Acinetobacter, Aureobacterium, Bacillus, Chryseobacterium, Corynebacterium, Klebsiella, Moraxella, Pseudomonas, Staphylococcus, Tsukamurella and Vibrio. The results obtained in this study support earlier findings on potentially pathogenic features of bacteria detected by routine HPCs on drinking water. These findings are in agreement with some epidemiological studies, which indicated an association between HPCs in drinking water and the incidence of gastroenteritis in consumers. However, the extent of the health risk concerned needs to be defined in more detail for meaningful revision of quality guidelines for HPCs in drinking water.

Bacteria↗

Antimicrobial resistance profile of five major food-borne pathogens isolated from beef, pork and poultry.

This study was performed to evaluate the resistance rate against antimicrobials of food isolates of the five major food-borne pathogens to compare these and to possibly distinguish a pattern. A total of 922 samples of the major meat species (pork, beef and poultry) were analysed for thermophilic Campylobacter, Salmonella, Yersinia enterocolitica, pathogenic Escherichia coli and Listeria monocytogenes. Isolates were subjected to antimicrobial resistance testing by the disc diffusion method. Roughly the same overall rate of resistance was identified for thermophilic Campylobacter, Salmonella and pathogenic E. coli. Resistance to quinolones and tetracycline was determined most frequently. In contrast, food isolates of Y. enterocolitica and L. monocytogenes were rarely tested resistant. The significance of our findings is that resistance rates in enteric bacteria seem to be much higher than in pathogens found in a variety of environments, closely associated to the host environment.

Animals↗

Antimicrobial properties of lactic acid bacteria and yeast-LAB cultures isolated from traditional fermented milk against pathogenic Escherichia coli and Salmonella enteritidis strains.

The survival and growth of Escherichia coli 3339 and Salmonella enteritidis 949575 isolated from human clinical samples, in milk fermented with lactic acid bacteria (LAB) and yeast strains previously isolated from Zimbabwean naturally fermented milk (NFM) was studied. The LAB starter cultures used were Lactococcus lactis subsp. lactis biovar. diacetylactis C1 alone (C1) or in combination with Candida kefyr 23 (C1/23), L. lactis subsp. lactis Lc261 alone (LC261) or in combination with C. kefyr 23 (Lc261/23). The growth of the same pathogens in milk fermented with a commercial DL culture (CH-N 22) and spontaneously fermented raw milk was also monitored. The C1 and C1/23 cultures significantly (P<0.05) inhibited the growth of both pathogens. When inoculated at the beginning of the fermentation, both E. coli 3339 and S. enteritidis 949575 counts were significantly (P<0.05) reduced by about two log cycles in C1 and C1/23 cultured milk. However, in naturally fermented milk and the DL cultured milk, both E. coli 3339 and S. enteritidis 949575 grew and reached high populations of about 9 and 8.8 log cfu ml(-1), respectively, after 18 h. When E. coli 3339 was inoculated into previously fermented milk, the viable counts were significantly (P<0.05) reduced in the presence of C1 and C1/23 from 7 log cfu ml(-1) to 3 log cfu ml(-1) after 48 h. S. enteritidis 949575 could not be recovered from these cultures after 48 h. The addition of the yeast did not enhance or diminish the inhibitory capacity of the LAB cultures. The pathogens survived in high numbers when inoculated into pre-fermented NFM and the commercial DL- (CH-N 22) cultured milk. The C1 strain, therefore, offered the best protection against the pathogens. Its inhibitory effect was mainly related to fast acid production.

Animals↗

Testing of pathogenic Yersinia enterocolitica in pig herds based on the natural dynamic of infection.

This study was performed to evaluate testing methods of pathogenic Yersinia enterocolitica in pigs at different ages. Relevant tools and procedures are crucial if pig herds should be declared free from pathogenic Y. enterocolitica. Historical data based on serology showed that the two farms investigated in this study (herds A and B) were contaminated with Y. enterocolitica O:3 since at least 1995. Laboratory investigations of 60 pigs were sampled one to four times (herd A) and 20 pigs were sampled one to three times (herd B) at different ages were the basis for this report. The following testing procedures could be used to conclude that a herd is free from pathogenic Y. enterocolitica:--serological testing of pigs could be performed as a basis for categorisation for all ages from about 100 days including at slaughter when the pigs are 150-180 days old, --bacteriological examination of faeces could be used as a basis for categorisation at all ages from 85 days until about 135 days, --bacteriological examination of tonsils could be used as a basis for categorisation at all ages from 85 days including at slaughter when the pigs are 150-180 days old. However, due to animal welfare aspects, one should avoid sampling of tonsils. Accordingly, the serological method or bacteriological examination of faeces at relevant ages should be preferred. One aspect related to slaughter hygiene is that in pigs slaughtered at the age of 135 days or more, the tonsils may be a more significant source of human pathogenic Y. enterocolitica than faeces.

Abattoirs↗

Rapid detection and identification of pathogens in blood cultures by fluorescence in situ hybridization and flow cytometry.

Septicemia is one of the leading causes of death in hospitalized patients. The timely detection and identification of microorganisms from the patient's blood has great diagnostic, prognostic and economic significance. Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has been proven to be a fast method for the identification of human pathogenic bacteria and yeasts. Data presented herein reveal that the combination of FISH and flow cytometry (FC-FISH) is a rapid and reliable technique for identification of pathogens (Gram-negative rods, Candida spp.) directly from blood cultures without further cultivation and biotyping. Moreover, detection of growing pathogens (e.g., Stenotrophomonas maltophilia) in blood cultures is achieved more rapidly by FC-FISH compared to standard detection methods. Therefore, FC-FISH allows rapid detection and identification of pathogens in blood cultures.

Bacteria↗

Threat of infection: microbes of high pathogenic potential--strategies for detection, control and eradication.

Infectious diseases due to microbes of high pathogenic potential remain a constant and variable threat for human and animal health. The emergence of new diseases or the re-emergence of diseases that were previously under control complicates the situation to date. Infectious disease research, which has undergone a dramatic progress in understanding disease mechanisms such as host-pathogen interactions, is now focusing increasingly on new strategies for prevention and therapy. Significant progress has been achieved in the development of delivery systems for protective heterologous protein antigens and in veterinary vaccinology. A landmark of infectious diseases research is the chemical synthesis of genomes, a major new field of research referred to as "synthetic biology", that to date has resulted in the chemical synthesis of the poliovirus and of phage phiX174 genomes and their expression as infectious viruses. On the molecular level the evolution of pathogens and mechanisms of genome flexibility, which account for several pathogenic properties of infectious agents, have received increased attention. Bacterial toxins are an additional threat to human health and their interference with host cells and cellular functions is receiving more attention.

Animals↗

Invasion processes of pathogenic Escherichia coli.

Pathogenic Escherichia coli causes extraintestinal infections such as urinary tract infection and meningitis, which are prevalent and associated with considerable morbidity. Previous investigations have identified common strategies evolved by pathogenic E. coli to exploit host cell function and cause extraintestinal infections, which include the invasion into non-phagocytic eukaryotic cells such as epithelial and endothelial cells and associated host cell actin cytoskeletal rearrangements. However, the mechanisms involved in pathogenic E. coli invasion of eukaryotic cells are shown to differ depending upon types of host tissues and microbial determinants. In this mini-review, invasion processes of pathogenic E. coli are discussed using E. coli K1 invasion of human brain microvascular endothelial cells (HBMEC) as a paradigm. E. coli K1 is the most common Gram-negative organism causing neonatal meningitis, and E. coli invasion of HBMEC is shown to be a prerequisite for E. coli traversal of the blood-brain barrier in vivo. Previous studies have demonstrated that E. coli translocation of the blood-brain barrier is the result of specific E. coli host interactions including specific signal transduction pathways and modulation of endocytic pathways. Recent studies using functional genomics have identified additional microbial determinants contributing to E. coli K1 invasion of HBMEC. Complete understanding of microbial-host interactions that are involved in E. coli K1 invasion of HBMEC should help in the development of new strategies to prevent E. coli meningitis.

Animals↗

Nasopharyngeal pathogens in children with acute otitis media in a low-antibiotic use country.

OBJECTIVE: Acute otitis media (AOM) is one of the most common diseases of childhood. Knowledge, of which bacteria are the most common pathogens in AOM and their susceptibilities towards antibiotics, is essential for the reasonable empiric treatment. With rapidly increasing frequencies of antibiotic resistance surveillance of the common etiologic pathogens has become pertinent. The purpose of this paper is to present the bacteriological findings and antibiotic susceptibilities, in cultures from nasopharyngeal swabs, in Danish children with AOM. METHODS: Children aged up to 10 years who had AOM diagnosed in general practice in Denmark were swabbed in nasopharynx, cultures were incubated and susceptibility testing was performed as tablet diffusion and minimal inhibitory concentrations (MICs) were determined by E-test. RESULTS: We included 331 patients, in 257 bacteria were found, which could be classified as commonly ear pathogenic. The most frequent bacteria found was Streptococcus pneumoniae followed by Haemophilus influenzae and Moraxella catarrhalis. Ninety-six percent of the tested S. pneumoniae were susceptible towards penicillin and 99% towards erythromycin. Eighty-nine percent of the H. influenzae were susceptible to ampicillin and all tested M. catarrhalis were susceptible towards erythromycin. In more than 30% of H. influenzae MIC of phenoxymethylpenicillin were above the level that could be achieved in middle ear fluid. CONCLUSION: Antimicrobial resistance is still infrequent in pathogens that might cause AOM in children in Denmark; this is probably due to minimal use of antibiotics as well as the use of phenoxymethylpenicillin as primary drug for treatment of AOM. Phenoxymethylpenicillin and azithromycin are not efficient for treating the majority of infections due to H. influenzae.

Acute Disease↗

In vitro investigation of the indirect pathogenicity of beta-lactamase-producing microorganisms in the nasopharyngeal microflora.

OBJECTIVE: Nasopharyngeal microflora contains some beta-lactamase-producing microorganisms. In this study, we investigated in vitro on the indirect pathogenicities of Haemophilus parainfluenzae (H. parainfluenzae) and Moraxella catarrhalis (M. catarrhalis) against the antipneumococcul activities of some beta-lactams. METHODS: We compared the antimicrobial and bactericidal activities of beta-lactams against penicillin-susceptible Streptococcus pneumoniae (PSSP) with or without presence of the enzymes of two species of beta-lactamase-producing microorganisms, H. parainfluenzae and M. catarrhalis. RESULTS: When adding the enzymes extracted from these two beta-lactamase-producing microorganisms in equivalent amounts of 10(7) CFU/spot, the minimum inhibitory concentrations of amoxicillin (AMPC) and cefaclor (CCL) increased to >64 microg/mL. Even third-generation cephalosporins, such as cefditren (CDTR) and ceftriaxone (CTRX) showed marked increases with the enzyme of M. catarrhalis. In time-kill kinetics, same phenomenon was observed in mixed culture indicating the indirect pathogenicities of distinct bacteria, not extracted enzymes, on the cidal activities of beta-lactams against PSSP. Clavulanic acid (CVA)/AMPC, faropenem (FRPM), and imipenem (IPM) were not affected by these beta-lactamase-producing strains with respect to their activities against PSSP. However, these two beta-lactamase-producing strains and their enzymes did not show any significant influence on the antipneumococcul activities of beta-lactams, until the number of bacterial cells reached >10(8) CFU/mL. CONCLUSION: Our results suggest that these two species of beta-lactamase-producing microorganisms in the nasopharyngeal microflora may act as indirect pathogens on the antipneumococcul activities of beta-lactams with reflecting their substrate profiles, but this is dependent on sufficient amounts of enzyme for their influence as indirect pathogens.

Amoxicillin↗

The role of pathogenic B-cell clones in antibody mediated autoimmune disorders.

Our understanding of the role of B-cells in the immunopathogenesis of certain antibody mediated diseases has developed remarkably in the past few years. In this review, autoantibody mediated immune disorders associated with pathogenic B-cell clones are discussed. We have focused on the roles and pathogenic mechanisms of B-cell clones in autoantibodyimmune diseases. The roles of pathogenic B-cells in Castleman's disease in PNP patients is used as one example. The developments in the treatment of B-cell mediated autoimmune diseases, such as intravenous immunoglobulin (IVIg), targets the regulatory pathway of B-cells, using anti-CD20, CD19, CD22 and, CD95 monoclonal antibody therapy, etc. are also discussed. Immunotherapy, targeting specific pathogenic B-cells, is believed to be one approach in the management of autoimmune diseases.

Autoantibodies↗

Microplastics as vectors for microbial pollutants: Biofilm-associated transfer of pathogens and antibiotic resistance genes in zebrafish intestine.

As composite carriers of microorganisms and pollutants, biofilm-attached microplastics (MPs) serve as potential vectors for the environmental migration and biotransmission of antibiotic resistance genes (ARGs) and pathogens. In this study, traditional polypropylene (PP) and biodegradable polylactic acid (PLA) MPs were used to investigate the interference effects of biofilms-attached MPs on gut microbiota and ARGs transmission, through a combination of laboratory biofilm cultivation, zebrafish (Danio rerio) exposure simulations, metagenomic sequencing, and metabolomic profiling. Results showed that MP biofilms likely induced gut dysbiosis and were associated with altered diversity and abundance of pathogens and ARGs. At the phylum level, Nitrospira was transferred from PP biofilms to the gut. At the genus level, 23 genera were transferred from MP biofilms, with PLA (23 genera) showing higher transfer capacity than PP (4 genera). Notably, two human pathogens, one opportunistic pathogen, and two ARGs (adeF and oqxB) were specifically transferred from PLA biofilms, highlighting the unique dissemination risk of biodegradable MPs. Mechanistically, MPs may activate mobile genetic elements (e.g., Tn916 transposon) through metabolic remodeling and quorum sensing, thereby promoting horizontal gene transfer and ARGs dissemination within the gut. Our findings highlight the potential role of MPs as carriers of microorganisms and ARGs, underscoring the biotransmission risks of antibiotic resistance caused by composite pollution.

Animals↗

Cross-transmission of nosocomial pathogens in an adult intensive care unit: incidence and risk factors.

The incidence and determinants of cross-transmission in an adult intensive care unit (ICU) were examined under normal conditions. Four hundred and thirty patients were followed for 3947 patient-days. Cross-transmitted pathogens were identified by genetic typing. A cross-transmission episode was defined as when two or more patients had indistinguishable isolates and had been treated in the ICU during intervals up to seven days apart. The direction of cross-transmission was confirmed if the incriminated pathogen was isolated from the donor before admission of the recipient; otherwise, both patients could potentially be a donor or a recipient. These patients were excluded from the risk factor analysis. Recipients of pathogens were compared with those who were not involved in cross-transmission. Out of 22 056 examined specimens, 275 isolates were typed and 40 episodes of cross-transmission were detected. The overall incidence of cross-transmission was 10.7 [95% confidence intervals (CI) 7.6-14.5] per 1000 patient-days. In multivariate analysis, those who were nursed in an understaffed environment [odds ratio (OR) = 3.3, 95% CI 1.4-7.8], had a nasogastric tube (OR = 2.9, 95% CI 1.1-7.8) and were ventilated (OR = 2.5, 95% CI 1.1-6.0) for all of their stay, compared with none or part of their stay, showed an increase in the risk of cross-transmission. Repeated bronchoscopy (OR = 5.1, 95% CI 1.04-25) compared with no bronchoscopy and immunosuppresion (OR = 3.9, 95% CI 1.2-12.5) also increased the risk. This study showed that cross-transmission of nosocomial pathogens in the ICU is associated with understaffing, immunosuppression and factors that result in multiple staff/patient contacts, thus emphasizing the importance of hand hygiene.

Adult↗

Hand rub consumption and hand hygiene compliance are not indicators of pathogen transmission in intensive care units.

The objective of this study was to investigate whether nosocomial infection (NI) rates, hand hygiene compliance rates and the amount of alcohol-based hand rub used for hand disinfection are useful indicators of pathogen transmission in intensive care units (ICUs), and whether they could be helpful in identifying infection control problems. All isolates of 10 of the most frequent pathogens from patients who were hospitalized in an ICU for >48 h were genotyped to identify transmission episodes in five ICUs. The incidence of transmission was correlated with hand hygiene compliance, hand rub consumption and NI rates. The incidence of transmission episodes varied between 2.8 and 6.8 in the five ICUs. The NI rate was 8.6-22.5 per 1000 patient-days, hand hygiene compliance was 30-47% and hand rub consumption was 57-102 L per 1000 patient-days. There was no correlation between the incidence of transmission episodes and hand rub consumption or hand hygiene compliance. The correlation between transmission rates and NI rates was 0.4 (P = 0.5), and with the exclusion of one ICU, it was 1 (P < 0.01). The incidence of NI is a relatively good indicator for the identification of pathogen transmissions, but hand rub consumption and hand hygiene compliance, at least with the relatively low level of compliance found in this study, are not indicators of pathogen transmission.

Anti-Infective Agents, Local↗

Surveillance of the susceptibility of ocular bacterial pathogens to the fluoroquinolone gatifloxacin and other antimicrobials in Europe during 2001/2002.

OBJECTIVES: To determine the identity of European ocular bacterial pathogens and their susceptibility to topical antimicrobial agents. METHODS: Bacterial isolates derived from clinically significant ocular infections were collected from 10 European centres. Bacteria were re-identified and susceptibility to gatifloxacin, ciprofloxacin, ofloxacin, fusidic acid, gentamicin and chloramphenicol was determined using the NCCLS agar incorporation method at a central testing laboratory. RESULTS: Five hundred and thirty-two isolates were submitted for analysis. The most common pathogen was methicillin-susceptible Staphylococcus aureus, followed by Haemophilus influenzae and Streptococcus pneumoniae. Gatifloxacin was the most potent antimicrobial agent tested for isolates from each European country as measured by pure MIC or percentage resistance (using 95% confidence intervals). Only methicillin-resistant S. aureus was in any way refractory to the action of gatifloxacin and other fluoroquinolones. CONCLUSIONS: Fluoroquinolones offer broad-spectrum coverage for the treatment of ocular pathogens. Gatifloxacin ophthalmic solution should be a significant improvement on currently available fluoroquinolones mainly due to enhanced activity against streptococci and coagulase-negative staphylococci (which accounted for almost one-third of ocular pathogens).

Administration, Topical↗

Pathogenicity and virulence.

Invertebrate pathologists have multiple definitions for the terms pathogenicity and virulence, and these definitions vary across disciplines that focus on host-pathogen interactions. We surveyed various literatures, including plant pathology, invertebrate pathology, evolutionary biology, and medicine, and found most define pathogenicity as the broader term, which incorporates virulence. Virulence is seen as the severity of disease manifestation that can only be measured in infected individuals. These definitions readily apply to both lethal and non-lethal diseases. Invertebrate pathologists commonly use dose-response bioassays to estimate LD(50) or LC(50) (dose or concentration needed to kill 50% of hosts exposed). These bioassays measure pathogenicity if the bioassay includes a transmission component, and measure virulence if the bioassay is measured in infected individuals only. Another common bioassay estimate is LT(50) (median time to death of infected hosts), which is a measure of virulence as long as survivors are not included in its calculation.

Animals↗

The role of food plant and pathogen-induced behaviour in the persistence of a nucleopolyhedrovirus.

Insect baculoviruses can survive between epidemics as infectious particles external to the host. Many pathogens persist in reservoirs, i.e., microhabitats where survival is enhanced, for example due to protection from the degrading effects of UV irradiation. However, the probability of infecting new susceptible hosts is usually reduced. Persistence of pathogens and their movement in and out of reservoirs is an important, albeit little understood, aspect of insect pathogen ecology. This study investigated interactions between the behaviour of infected insect hosts, virus distribution and plant species on the persistence of the winter moth (Operophtera brumata) nucleopolyhedrovirus. Habitat influenced the persistence of infectious baculovirus in the field: virus on Sitka spruce (Picea sitchensis) and oak (Quercus robur) in forested areas retained more infectivity than virus on heather (Calluna vulgaris) in an unshaded habitat. Plant species per se did not directly affect the persistence of virus on the foliage of potted seedlings. Virally infected insects had altered behaviour and moved down plants relative to control insects, whereas in other systems larvae show height-seeking behaviour. Consequently, the majority of virus particles were distributed on plant stems. In two experiments (one using winter moth NPV and one Mamestra brassicae NPV) virus persisted better on plant stems relative to foliage. Neonate larvae were shown to be able to acquire infections from tree stems contaminated with a low level of virus. These data suggest that plant stems may be important reservoirs for between-year persistence of this pathogen. The observed virus-induced changes in host behaviour in winter moth could enhance the viral persistence by increasing the deposition of occlusion bodies in these reservoirs.

Animals↗