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PubMed2002

Viral respiratory infections in elderly patients and patients with chronic obstructive pulmonary disease.

Patients with chronic obstructive pulmonary disease (COPD) and elderly individuals are prone to the development of significant lower respiratory tract symptoms from colds caused by viral respiratory pathogens. Longitudinal surveillance studies conducted to assess the impact of viral respiratory tract pathogens on morbidity and mortality in each of these at-risk populations demonstrate that there is a substantial burden of disease from viral respiratory infection (VRI), including rhinovirus infections, with respect to utilization of health-care resources. Despite a similar rate of occurrence of VRI among subjects with COPD and the control group, a cohort with moderate to severe COPD had a 2-fold increase in medical resource utilization, including clinician visits, emergency center visits, and hospitalizations. In surveillance studies of respiratory viruses in the elderly, regular seasonal infections with rhinoviruses cause substantial morbidity, which has been largely underappreciated and underreported.

Age Factors↗
PubMed2005

Antibiotic-resistant bloodstream infections in hospitalized patients: specific risk factors in a high-risk population?

BACKGROUND: The aim of this study was to explore characteristics that are associated with bloodstream infections due to specific multiresistant microorganisms (methicillinresitant Staphylococcus aureus, MRSA; vancomycin-resistant enterococci, VRE; third-generation cephalosporin-resistant Enterobacteriaceae) or Candida spp. in hospitalized patients. PATIENTS AND METHODS: All patients who experienced a bloodstream infection with one of the aforementioned pathogens between September 1999 and October 2001 were included into a statistical analysis of independent risk factors. The possible impact of previous antibiotic and antifungal therapies was evaluated. RESULTS: Of the study population, 22% had two or more episodes with different pathogens. In the 314 patients with a single bloodstream infection MRSA was isolated in 189 patients, VRE in 31, Enterobacteriaceae in 13, and Candida spp. in 80 patients. Crude mortality was high in the study population (overall 40%) and varied between 33% (MRSA bacteremia only) and 58% (VRE bacteremia only). Patients who yielded more than one of the pathogens under surveillance had crude mortalities ranging from 41% to 83% (all four pathogens). In this group of high-risk patients, the following factors were independently associated with the individual pathogen: prior chemotherapy (OR 4.88 CI(95) 1.50-15.87) and bronchoscopy (OR 3.17 CI(95) 1.05-9.52) for VRE patients; burns (OR 4.50 CI(95) 0.90-22.73), presence of a tracheostomy (OR 4.22 CI(95) 1.15-15.38) and acute dialysis (OR 3.62 CI(95) 0.99-13.16) for patients with Enterobacteriaceae; and an underlying malignant disease (OR 1.98 CI95 0.99-3.97), performance of a bowel endoscopy (OR 2.80 CI(95) 1.27-6.13) and presence of a central venous catheter (CVC) (OR 12.34 CI(95) 1.63-90.91) for patients with candidemia. CONCLUSION: Patients with bacteremia due to VRE, Enterobacteriaceae or Candida spp. had more severe risk factors associated with the respective pathogen than patients with MRSA bacteremia.

Adult↗
PubMed1988

Drug-resistant plasmids from fish pathogens.

The epidemiological surveillance of drug-resistant strains of the fish pathogenic bacteria Vibrio anguillarum and Pasteurella piscicida carrying transferable R plasmids in fish farms is described. The DNA structure of R plasmids, and the drug-resistant determinants of R plasmids from the fish pathogens Aeromonas hydrophila,aeromonas salmonicida, Edwardsiella tarda, V. anguillarum, and P. piscicida are discussed.

Animals↗
PubMed2000

Antimicrobial resistance in respiratory tract pathogens: results of an international surveillance study.

An international surveillance study was performed to assess the resistance patterns among respiratory tract pathogens during the winter of 1997-1998. The pathogens studied included Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis. The antibiotics tested included five beta-lactams (penicillin, ampicillin, amoxicillin, amoxicillin-clavulanic acid, cefuroxime axetil and ceftriaxone), two macrolides (azithromycin and clarithromycin), one sulfonamide (trimethoprim-sulfamethoxazole), one glycopeptide (vancomycin) and one fluoroquinolone (levofloxacin). A total of 11,502 isolates were tested from nine countries, using microdilution susceptibility tests as recommended by National Committee for Clinical Laboratory Standards (NCCLS) guidelines. The susceptibility rates varied greatly around the world. Ninety percent of M. catarrhalis isolates produced beta-lactamase, making them resistant to ampicillin. beta-Lactamase production by H. influenzae ranged from 5% in Germany to 34% in the USA (mean 17.5%). Of the S. pneumoniae isolates, 32.8% had some resistance to penicillin, but this ranged greatly from 7.8% in Germany to 66.5% in France. Penicillin resistance in S. pneumoniae was associated with resistance to other beta-lactams, macrolides and sulfonamides, but not to levofloxacin or vancomycin. All isolates of H. influenzae and M. catarrhalis were susceptible to levofloxacin. Results of this study support the conclusion that these three respiratory tract pathogens are becoming more resistant to selected antimicrobials, and that the level of resistance in these isolates to the antimicrobials varies greatly from one country to another.

Drug Resistance, Microbial↗
PubMed2003

Surveillance for antibiotic resistance in veterinary pathogens from the perspective of a regional diagnostic laboratory.

The Toowoomba Veterinary Laboratory tests for antibiotic resistance through passive surveillance of bacterial pathogens from diseased, frequently intensively managed, animals. Testing is carried out on the basis of the number of animals involved, the nature and severity of the disease and the identity and significance of the bacterium, the results guiding the submitting veterinarian in implementing appropriate treatment. The antibiotics chosen for testing are those that are currently registered for veterinary use and are considered effective in the given situation. Testing is carried out according to the current National Committee for Clinical Laboratory Standards Approved Standard for Disc Susceptibility Tests. This paper presents some results of testing bacterial pathogens from cattle and pigs.

Animal Diseases↗
PubMed2003

Australia's notifiable diseases status, 2001: annual report of the National Notifiable Diseases Surveillance System.

In 2001 there were 104,187 notifications of communicable diseases in Australia reported to the National Notifiable Diseases Surveillance System (NNDSS). The number of notifications in 2001 was an increase of 16 per cent of those reported in 2000 (89,740) and the largest annual total since the NNDSS commenced in 1991. In 2001, nine new diseases were added to the list of diseases reported to NNDSS and four diseases were removed. The new diseases were cryptosporidiosis, laboratory-confirmed influenza, invasive pneumococcal disease, Japanese encephalitis, Kunjin virus infection, Murray Valley encephalitis virus infection, anthrax, Australian bat lyssavirus, and other lyssaviruses (not elsewhere classified). Bloodborne virus infections remained the most frequently notified disease (29,057 reports, 27.9% of total), followed by sexually transmitted infections (27,647, 26.5%), gastrointestinal diseases (26,086, 25%), vaccine preventable diseases (13,030 (12.5%), vectorborne diseases (5,294, 5.1%), other bacterial infections (1,978, 1.9%), zoonotic infections (1,091, 1%) and four cases of quarantinable diseases. In 2001 there were increases in the number of notifications of incident hepatitis C, chlamydial infections, pertussis, Barmah Forest virus infection and ornithosis. There were decreases in the number of notifications of hepatitis A, Haemophilus influenzae type b infections, measles, rubella, Ross River virus infections and brucellosis. This report also summarises data on communicable diseases from other surveillance systems including the Laboratory Virology and Serology Reporting Scheme and sentinel general practitioner schemes. In addition, this report comments on other important developments in communicable disease control in Australia in 2001.

Australia↗
PubMed2006

Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays.

The exponential growth of pathogen nucleic acid sequences available in public domain databases has invited their direct use in pathogen detection, identification, and surveillance strategies. DNA microarray technology has offered the potential for the direct DNA sequence analysis of a broad spectrum of pathogens of interest. However, to achieve the practical attainment of this potential, numerous technical issues, especially nucleic acid amplification, probe specificity, and interpretation strategies of sequence detection, need to be addressed. In this report, we demonstrate an approach that combines the use of a custom-designed Affymetrix resequencing Respiratory Pathogen Microarray (RPM v.1) with methods for microbial nucleic acid enrichment, random nucleic acid amplification, and automated sequence similarity searching for broad-spectrum respiratory pathogen surveillance. Successful proof-of-concept experiments, utilizing clinical samples obtained from patients presenting adenovirus or influenza virus-induced febrile respiratory illness (FRI), demonstrate the ability of this approach for correct species- and strain-level identification with unambiguous statistical interpretation at clinically relevant sensitivity levels. Our results underscore the feasibility of using this approach to expedite the early surveillance of diseases, and provide new information on the incidence of multiple pathogens.

Bacterial Typing Techniques↗
PubMed1988

The bacterial flora of neonates in intensive care-monitoring and manipulation.

Unlike healthy babies, newborns hospitalized in the neonatal intensive care unit (NICU) are colonized with bacterial flora that reflects their exposure to pathogens in the NICU, not bacterial acquired from mother in the perinatal period. For example, nosocomial Gram-negative bacilli, such as klebsiella, enterobacter, and citrobacter but not Escherichia coli tend to colonize the gastrointestinal tract. Colonization with Gram-negative bacilli generally is a prerequisite for nosocomial infection with these pathogens, but surveillance cultures may not be a cost effective approach to predicting which babies will ultimately become ill. However, screening cultures to detect the emergence of antibiotic-resistant Gram-negative bacilli facilitate containment and guide empiric antibiotic therapy, and surveillance cultures are necessary to detect colonized babies when nosocomial Gram-negative bacilli become epidemic in the NICU. Such cultures are inexpensive and easy to perform if appropriate selective media are used. Surveillance cultures to detect coagulase-negative staphylococci, which numerous investigators claim are increasingly important NICU pathogens, are of little value since colonization is virtually universal in the first week of life. Documentation of colonization with group B streptococci or Staphylococcus aureus also cannot be justified on a routine basis. Screening for methicillin-resistant S. aureus, however, may be indicated since early detection of these strains can limit dissemination in the NICU. Research aimed at restoring colonization resistance with elements of normal bacterial flora or preventing colonization by nosocomial pathogens is in its infancy.

Bacteriological Techniques↗
PubMed2001

[Surveillance of gastroenteritic infections in lower Saxony: results and experiences from a regional public-health project over six years].

In Lower Saxony, a regional public health project on a pathogen-specific surveillance of Enteritis infectiosa was carried out from 1994 to 2000. In a separate reporting procedure thirteen health departments transmitted data on the specific pathogen collected from laboratory reports for a joint analysis. The results were distributed among the participants, providing them with information on the situation and trends in their districts and in addition giving them the possibility to compare their data with those of other districts. The incidence of Enteritis infectiosa was 199 reported cases per 100,000 person years. Salmonella was reported most frequently (51 %; S. enteritidis: 33 %, S. TYPHIMURIUM: 14 %, 111 other serotypes: 4 %), followed by Campylobacter (18 %), Rotavirus (17 %), Yersinia enterocolitica (6 %) and Adenovirus (5 %). The incidences of Salmonella and Yersinia enterocolitica were found to be nearly constant over the project period while the incidences of Campylobacter, Rotavirus and Adenovirus increased. This, however, may be due to intensified diagnostics and better reporting behaviour rather than to a real increase. The incidence rates and their trends differed from other German states. This observation emphasizes the need for a regional analysis of infectious disease surveillance data.

Bacteriological Techniques↗
PubMed1978

A study of acute respiratory disease in the community of Port Chalmers. I. Illnesses within a group of selected families and the relative incidence of respiratory pathogens in the whole community.

A study of respiratory diseases in the semi-isolated community of Port Chamlers, New Zealand, began in April 1973. The intensive surveillance of a selected group fo 26 families involved the weekly reporting of illness, the collection of specimens for virus, Group A streptococci and Mycoplasma pneumoniae isolation and the collection of sera at 6-month intervals. A total of 956 illnesses were reported during 32 months. The median number of illnesses per year were: infants 4.4, children 2.5, female adults 2.4 and male adults 2.0. Of all these illnesses, 57% were upper respiratory, 31% were lower respiratory and 9% were enteric. The severity of these illnesses was not greater than would be expected in open communities. Surveillance by pathogen isolation only of the whole community through the patients in the general practice was carried out concurrently. A total of 640 nasopharyngeal swab specimens were collected from which 161 viruses, 47 Group A streptococci and 2 M. pneumoniae were isolated. The overall isolation rate was 33%. The similarities between the epidemiological patterns of respiratory disease in the open community and the isolated community are discussed.

Adolescent↗
PubMed2000

The Naval Health Research Center Respiratory Disease Laboratory.

Concern about emerging and reemerging respiratory pathogens prompted the development of a respiratory disease reference laboratory at the Naval Health Research Center. Professionals working in this laboratory have instituted population-based surveillance for pathogens that affect military trainees and responded to threats of increased respiratory disease among high-risk military groups. Capabilities of this laboratory that are unique within the Department of Defense include adenovirus testing by viral shell culture and microneutralization serotyping, influenza culture and hemagglutination inhibition serotyping, and other special testing for Streptococcus pneumoniae, Streptococcus pyogenes, Mycoplasma pneumonia, and Chlamydia pneumoniae. Projected capabilities of this laboratory include more advanced testing for these pathogens and testing for other emerging pathogens, including Bordetella pertussis, Legionella pneumoniae, and Haemophilus influenzae type B. Such capabilities make the laboratory a valuable resource for military public health.

Clinical Laboratory Techniques↗
PubMed2006

The cell biology of acute childhood respiratory disease: therapeutic implications.

Respiratory syncytial virus (RSV), the recently identified human metapneumovirus (HMPV), and the human parainfluenza viruses (HPIVs), cause most cases of childhood croup, bronchiolitis, and pneumonia. Influenza virus also causes a significant burden of disease in young children, although its significance in children was not fully recognized until recently. This article discusses pathogens that have been studied for several decades, including RSV and HPIVs, and also explores the newly identified viral pathogens HMPV and human coronavirus NL63. The escalating rate of emergence of new infectious agents, fortunately meeting with equally rapid advancements in molecular methods of surveillance and pathogen discovery, means that new organisms will soon be added to the list. A section on therapies for bronchiolitis addresses the final common pathways that can result from infection with diverse pathogens, highlighting the mechanisms that may be amenable to therapeutic approaches. The article concludes with a discussion of the overarching impact of new diagnostic strategies.

Acute Disease↗
PubMed2003

Global screening for human viral pathogens.

We propose a system for continuing surveillance of viral pathogens circulating in large human populations. We base this system on the physical isolation of viruses from large pooled samples of human serum and plasma (e.g., discarded specimens from diagnostic laboratories), followed by shotgun sequencing of the resulting genomes. The technology for concentrating virions from 100-L volumes was developed previously at Oak Ridge National Laboratory, and the means for purifying and concentrating virions from volumes in microliters have been developed recently. At the same time, marine virologists have developed efficient methods for concentrating, amplifying, and sequencing complex viral mixtures obtained from the ocean. Given this existing technology base, we believe an integrated, automated, and contained system for surveillance of the human "virome" can be implemented within 1 to 2 years. Such a system could monitor the levels of known viruses in human populations, rapidly detect outbreaks, and systematically discover novel or variant human viruses.

Automation↗
PubMed2001

Multicenter surveillance of antimicrobial resistance of major bacterial pathogens in intensive care units in 2000 in Taiwan.

A susceptibility surveillance study of 1,274 bacterial isolates recovered from various clinical specimens from patients in intensive care units (ICUs) of five major teaching hospitals was carried out from March, 2000, to June, 2000, in Taiwan. This study demonstrated a high rate (66%) of oxacillin resistance in Staphylococcus aureus (ORSA), a high rate of nonsusceptibility to penicillin (intermediate, 50% and highly resistant, 8%), and high rates of cefotaxime nonsusceptibility for S. pneumoniae (intermediate, 29% and resistant, 4%), Enterobacter cloacae (57%), Serratia marcescens (34%), and Citrobacter freundii (60%). High rate of ceftazidime nonsusceptibility for Pseudomonas aeruginosa (22%), and high rates of imipenem nonsusceptibility for P. aeruginosa (15%) and Acinetobacter baumannii (22%) were also found. The percentage (11.9%) of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli was greater than that (11.3%) for Klebsiella pneumoniae. Rates of quinupristin-dalfopristin nonsusceptibility for S. pneumoniae (42%), Enterococcus faecium (71%), and ORSA (39%) were high, but no vancomycin-resistant enterococci were found in this study. The resistance rates of some pathogen varied by institution or type of ICUs. Surveillance for antimicrobial resistance among bacterial pathogens in hospitals, particularly in ICU settings with a preexisting higher resistance burden, is mandatory in establishing and/or modifying guidelines for empirical treatment of severe infections in ICU patients caused by these antimicrobial-resistant pathogens.

Bacteria↗
PubMed2001

Empiric antibiotic therapy and mortality among medicare pneumonia inpatients in 10 western states : 1993, 1995, and 1997.

STUDY OBJECTIVES: To examine the association of empiric inpatient antibiotic treatment of community-acquired pneumonia (CAP) with mortality, and whether this association varies from year to year. DESIGN: Population-based, retrospective study adjusting for demographics, comorbidities, and clinical characteristics. SETTING: Acute-care hospitals in 10 western states. PATIENTS: A group of 10,069 Medicare beneficiaries aged > or = 65 years who were hospitalized with CAP during fiscal years 1993, 1995, and 1997. MEASUREMENTS AND RESULTS: We examined the risk for mortality during the 30 days after admission to the hospital. The impact of specific antibiotic regimens varied greatly from year to year. In 1993, therapy with a macrolide plus a beta-lactam was associated with significantly lower mortality than therapy with either a beta-lactam alone (adjusted odds ratio [AOR], 0.42; 95% confidence interval [CI], 0.25 to 0.69) or other regimens that did not include a macrolide, beta-lactam, or fluoroquinolone (AOR, 0.35; 95% CI, 0.20 to 0.62). Those associations were not observed in 1995 or 1997. Lower mortality was associated with fluoroquinolone monotherapy compared with beta-lactam monotherapy in 1997 (AOR, 0.27; 95% CI, 0.07 to 0.96) and with macrolide monotherapy compared with other regimens in 1995 (AOR, 0.24; 95% CI, 0.06 to 0.93), but the number of patients who received these regimens was small. CONCLUSIONS: The inclusion of a macrolide or a fluoroquinolone in initial empiric CAP treatment was associated with improved survival, but this association varied from year to year, perhaps as a result of a temporal variation in the incidence of atypical pathogen pneumonia. Improved testing and surveillance for atypical pathogen pneumonia are needed to guide empiric therapy.

Aged↗
PubMed2003

Serious bacterial infections in febrile infants younger than 90 days of age: the importance of ampicillin-resistant pathogens.

BACKGROUND: Intrapartum antibiotic prophylaxis against group B Streptococcus (GBS) has reduced the occurrence of serious bacterial infections (SBI) in young infants caused by GBS. Recommendations for initial antibiotic therapy for the febrile infant 1 to 90 days old were developed when infections with GBS were common and antibiotic resistance was rare. OBJECTIVE: To document the pathogens responsible for SBI in recent years in febrile infants 1 to 90 days old and the antibiotic susceptibility of these organisms. METHODS: The results of bacterial cultures from infants 1 to 90 days old evaluated for fever at Primary Children's Medical Center in Salt Lake City, Utah, between July 1999 and April 2002 were analyzed. Antibiotic susceptibility profiles were collected and patient records were reviewed to determine if initial antibiotic therapy was changed following the identification of the organism. RESULTS: Of 1298 febrile infants enrolled from the Primary Children's Medical Center emergency department, 105 (8%) had SBI. The mean age of the infants with SBI was 39 days (range 2-82 days) and 2 (2%) were <7 days. SBI included urinary tract infection (UTI; 67%), bacteremia (16%), bacteremia and UTI (6%), bacteremia and meningitis (5%), meningitis (2%), abscess (2%), meningitis and UTI (1%), and meningitis and gastroenteritis (1%). Eighty-three (79%) of 105 episodes of SBI were caused by Gram-negative bacteria, including 92% of UTI, 54% of bacteremia, and 44% of meningitis cases. The most common pathogen was Escherichia coli (61%). Other Gram-negative pathogens were responsible for 19% of SBI. Staphylococcus aureus was the most common Gram-positive pathogen, causing 8% of SBI. GBS accounted for 6% of SBI. Of the 105 pathogens, 56 (53%) were resistant to ampicillin. Of the pathogens causing meningitis, UTI, and bacteremia, 78%, 53%, and 50%, respectively, were resistant to ampicillin. Antibiotic therapy was changed in 54% of cases of SBI following identification of the organism. CONCLUSIONS: In Utah, ampicillin-resistant Gram-negative bacteria are the most common cause of SBI in febrile infants <90 days old. This finding impacts antibiotic selection, especially in cases of meningitis. Local surveillance of pathogens and antibiotic susceptibility patterns is critical to determine appropriate antibiotic therapy.

Ampicillin Resistance↗
PubMed2026

Evaluation of one-step amplicon-based targeted enrichment for SARS-CoV-2 whole-genome sequencing using the Midnight amplicon scheme.

Genomic surveillance proved invaluable during the COVID-19 pandemic for tracking SARS-CoV-2 variants and guiding outbreak responses, underscoring the ongoing need to reduce whole-genome sequencing (WGS) costs and improve workflow efficiency to ensure accessibility in resource limited settings. Here, we evaluated a one-step reverse transcription polymerase chain reaction (RT-PCR) approach using the Midnight V2 primer scheme for targeted amplification of the SARS-CoV-2 genome, assessed its compatibility with Illumina sequencing, and compared its performance to a well-established two-step method. Initially, we determined optimal RT-PCR reaction conditions using the Midnight V2 primer panel for the one-step RT-PCR kit and scaled reaction volumes for both RT-PCR and library preparation. Clinical specimens (n&#x202f;=&#x202f;53) that had undergone routine WGS for surveillance purposes using the established two-step RT-PCR method were compared using the one-step RT-PCR assay. For samples with genome completeness greater than 70%, both methods gave comparable results with similar sequence coverage and 100% concordance for lineage assignment. Further investigation revealed a higher percentage of reads aligning to the SARS-CoV-2 genome with a greater depth of coverage using the one-step method compared to the two-step method. Finally, analysis of scaled one-step and library reaction volumes revealed significant cost savings for samples undergoing WGS. Overall, the results presented here verify the accuracy and reproducibility of one-step targeted amplification and offer an efficient and cost-effective workflow for routine SARS-CoV-2 genomic surveillance.

Humans↗
PubMed2002

[Evaluation of trends in ue of antibiotics and resistance in selected bacterial pathogens].

BACKGROUND: Evaluation of antibiotic consumption and the surveillance of bacterial pathogens resistance appears to be an indispensable part of antibiotic policy. The aim of this study was to evaluate dynamics of antibiotics consumption and resistance development in selected bacterial strains (Pseudomonas aueruginosa, Staphylococcus aureus and Staphylococcus epidermidis) in the environment of Faculty Hospital. METHODS AND RESULTS: The analysis was focused on the development of antibiotic consumption and monitoring of the development of bacterial resistance. Samples were taken in internal and surgical departments of General Faculty Hospital in Prague in 1992, 1995, and 1999. The evaluation of antibiotic consumption was based on Anatomical Therapeutic and Chemical classification system and the Defined Daily Doses (DDD). The consumption in the follow up period almost doubled in surgical department while in internal medicine department was decreased by almost one third. In both department, namely in the surgical one significant increase of bacterial resistance of tested antibiotics was noted. CONCLUSION: The important part of the local antibiotic policy is the monitoring of development of bacterial resistance and consumption of antibiotics.

Anti-Bacterial Agents↗