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PubMed2005

Incidence of diarrhea caused by rotavirus infections in rural Zhengding, China: prospective, population-based surveillance.

Rotavirus is the pathogen most commonly associated with severe gastroenteritis in young children in the People's Republic of China, yet there are few population-based data on the incidence of rotavirus infection. The present study investigated the burden of rotavirus diarrhea and rotavirus infections in rural China, according to age. Population-based surveillance was used to study the incidence of rotavirus infection among children <5 years of age in 4 townships of Zhengding County, Hebei Province, China. The total population in the catchment area in 2002 was 75,630 individuals, including 2997 children aged <5 years. Stool samples were obtained and were tested for rotavirus antigen by use of an enzyme-linked immunosorbent assay. During 2002, a total of 2010 cases of diarrhea were detected among children <5 years of age. The incidence of treated cases of diarrhea was 671 cases/1000 children/year for children <5 years of age, and it was highest for children <12 months of age (1467 cases/1000 children/year). The estimated incidence of rotavirus infection was 151 cases/1000 children/year for children <5 years of age. The highest incidence of rotavirus infection was among children aged 1-2 years (340 cases/1000 children/year). Widespread immunization of children against rotavirus before 6 months of age should be considered for the control of rotavirus diarrhea.

Child, Preschool↗
PubMed2001

[Epidemiologic surveillance in intensive care: how to organize it?].

Surveillance of nosocomial infections is the single most effective tool for nosocomial infection prevention. There are two main targets: a) prompt identification of indicators and epidemic events, in order to immediately start adequate interventions; b) comparison of local "own" experience to the nosocomial infections which would be expected in a population with similar clinical features. The microbiological laboratory is a reliable and economical source of information: it allows identification of "dangerous" microorganisms, monitoring of antimicrobial resistances, identification of epidemics due to a single agent. Active surveillance is necessary in every unit, in order to identify those specific indicators of infection, which are able to detect preventable events and which can be useful for "homogeneous" comparisons among ICUs. Accuracy (sensitivity and specificity) of identification methods and of case definition is of uttermost importance. It is equally important to collect patient data and care plan data targeted to document differences in type of treated patient and in type of level of care. A recent national survey among Italian public hospitals revealed a poor diffusion of surveillance: out of 428 responder hospitals, surveillance of epidemics and of antimicrobial resistance was active in less than 10%, surveillance in the unit was active in 15%, surveillance of sentinel pathogens was active in 22%.

Critical Care↗
PubMed2026

Lineage dynamics of invasive Escherichia coli isolates in the Netherlands from 1975 to 2021: a retrospective longitudinal genomic analysis.

BACKGROUND: Escherichia coli is a common cause of invasive infections such as bloodstream and cerebrospinal fluid infections in neonates. Strains positive for the K1 capsule are considered the most common cause of such neonatal invasive infections. This assumption of K1 dominance, and indeed the population genomics of E coli causing invasive infections in general is largely unstudied. We aimed to provide a comprehensive characterisation of this pathogen population using a longitudinal isolate collection. METHODS: In this analysis we report the findings of the SENTINEL study, a longitudinal genomic analysis of 1790 invasive E coli isolates collected mainly from newborns in the Netherlands between 1975 and 2021 by the Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam University Medical Centre, Amsterdam, Netherlands. The dataset included all bacterial strains cultured from cerebrospinal fluid or blood in cases of (clinical) bacterial meningitis (1976 to 1980). In 1981 the criteria were expanded to include neonates (aged &#x2264;4 weeks) with E coli sepsis, and from July, 2016 all infants younger than 1 year with E coli sepsis were included. All isolates were sequenced using either the HiSeq 2500 or HiSeq 4000 platforms (Illumina, San Diego, CA, USA). We confirmed species and identified sequence types (STs), detected antimicrobial resistance genes, virulence genes, and the presence of K1 capsule, and characterised the dynamics of these factors over time. FINDINGS: Our data show a highly dynamic bacterial population that is entirely unaffected by antimicrobial resistance determinants. Key pathogen population fluctuations include the complete disappearance of the dominant lineage ST567 and the swapping of dominant ST95 clones from a single serotype O18:H7 clone to two distinct serotype O1:H7 clones, with changes in virulence factors including major fimbrial adhesins. These findings, combined with only 58&#xb7;8% (1053 of 1790) prevalence in K1-expressing isolates in the entire study population, point to host-pathogen interaction and immune selection pressures as key drivers of bacterial population dynamics in this largely antimicrobial-naive population. INTERPRETATION: Our data show the vital need for ongoing genomic surveillance of microbial pathogen populations to guide appropriate intervention strategies. Additionally, genomic insights of a pathogen population from one specific disease syndrome or patient population cannot always be generalised across other cohorts. FUNDING: Wellcome Antimicrobial and Antimicrobial Resistance Doctoral Training Programme and the National Institute for Health and Care Research Birmingham Biomedical Research Centre.

Netherlands↗
PubMed1997

Vibrio furnissii isolated from humans in Peru: a possible human pathogen?

During a cholera surveillance programme, Vibrio furnissii was isolated in late January and early February 1994 from stool samples collected from 14 persons of whom six had diarrhoea. The remaining eight persons were healthy family members or neighbours to cholera cases. No common source of infection was found. Strains isolated from stool samples each showed typical biochemical reactions of V. furnissii including gas production. Each isolate, except one, agglutinated O-antisera yielding a total of eight different serotypes. Most isolates were sensitive to 10 antibiotics tested, except to ampicillin and the vibriostatic agent O/129 (10 micrograms). Eight of 14 (57%) strains carried plasmids in the size range 2.6-88 kb, however, no correlation was found between antibiotic susceptibility patterns and plasmid content. Altogether, seven closely related HindIII ribotypes were observed among the 14 V. furnissii isolates studied. V. furnissii strains isolated from family members and other persons living close together often showed different ribotypes suggesting that the isolation was not associated with neighbourhood. Serotyping, plasmid profiling and ribotyping revealed a high strain diversity within V. furnissii, however, the importance of V. furnissii as an enteric pathogen remains to be elucidated.

Adolescent↗
PubMed2026

Genomic Insights Into Multidrug-Resistant Foodborne Serratia liquefaciens Strains Carrying mcr-9 and Comparative Genomic Analysis of Novel Biosynthetic Gene Clusters.

Serratia liquefaciens is an opportunistic nosocomial pathogen with a wide range of antibiotic resistance patterns. This study reports the characterization of the first mcr-9-positive S. liquefaciens strains, 35E-19E1 and CST-066, isolated from meat products in Japan. The strains were screened for the presence of &#x3b2;-lactamases, plasmid-mediated mobile colistin resistance (mcr) genes, and carbapenemase-encoding genes using PCR. Antimicrobial susceptibility was tested using the broth microdilution method. The strains exhibited multidrug resistance (MDR) phenotypes to third-generation cephalosporins, cephamycin, fosfomycin, and other clinically important antimicrobials. Genomic DNA sequencing showed that the genome sizes of CST-066 and 35E-19E1 are 5,529,704 and 5,261,506&#x2009;bps, respectively. mcr-9 was identified on a chromosome within a genetic environment that included the two-component system qseBC, which plays a key role in the signaling network that triggers colistin resistance in Enterobacterales. Downstream genome analysis revealed a 1695-bp eptB-like kdo2-lipid phosphoethanolamine transferase, which is involved in intrinsic polymyxin resistance mechanisms in Serratia spp. The strain 35E-19E1 carries five CRISPR-Cas enzymes that are essential for adaptive immunity in bacteria, allowing defense against invading elements. Functional analysis using subsystem technology revealed that both strains possess subsystem features responsible for invasion and adhesion within the host biomes. Genome mining using antiSMASH and BAGL4 revealed various biosynthetic gene clusters, responsible for secondary metabolite synthesis. Notably, we identified novel gene clusters, mainly nonribosomal peptide synthetases, in both the strains, indicating their potential to produce bioactive compounds. Although the presence of mcr-9 in Serratia may not be of clinical significance because of natural resistance of the strain to polymyxins, we shed light on the genomic characteristics of this MDR pathogen and the potential spread of mcr-9 among other bacterial species. The emergence of mcr-9 in drug-resistant S. liquefaciens provides significant insights, underscoring the need for increased surveillance of this pathogen.

biosynthetic gene cluster↗
PubMed1999

Streptococcus pyogenes isolated in Portugal: macrolide resistance phenotypes and correlation with T types. Portuguese Surveillance Group for the Study of Respiratory Pathogens.

From January 1998 to June 1999, 302 clinical isolates of Streptococcus pyogenes were collected from 10 microbiology laboratories in Portugal. All strains were highly sensitive to penicillin (MIC90 = 0.012 mg/liter). The prevalence of erythromycin resistance was 35.8% and of tetracycline resistance 41.4%. The majority (79.6 %) of erythromycin-resistant strains were of the MLSB constitutive resistance (CR) phenotype with high-level resistance to erythromycin (MIC90 >256 mg/liter) and to clindamycin (MIC90 >256 mg/liter), 16.7% showed the M phenotype with low-level erythromycin-resistance (MIC90 = 24 mg/liter) and susceptibility to clindamycin, and four isolates showed a phenotype characterized by low-level erythromycin resistance (MIC90 = 8 mg/liter) and high-level clindamycin resistance (MIC90 >256 mg/liter), not previously described. Erythromycin resistance was not associated with invasive strains. Only minor discrepancies between disk diffusion and E-test methods were observed. T serotyping was very useful for the epidemiological characterization of the strains. The most prevalent T types were T1, T4, T9, T12, T13, and T28. A statistically significant association with resistance patterns was found: T12 with erythromycin resistance MLS(B) CR phenotype (p< 0.001), T4 with erythromycin resistance M phenotype (p<0.001), and T13 with tetracycline resistance (p<0.01). Because of the high prevalence of resistance, careful surveillance of S. pyogenes isolates in Portugal is essential, routine antimicrobial susceptibility testing in clinical microbiology laboratories should be strongly encouraged, antibiotic prescription should be reviewed, and macrolides should no longer be used in the empirical therapy of acute pharyngitis.

Anti-Bacterial Agents↗
PubMedDate not supplied

Molecular epidemiologic typing systems of bacterial pathogens: current issues and perspectives.

The epidemiologic typing of bacterial pathogens can be applied to answer a number of different questions: in case of outbreak, what is the extent and mode of transmission of epidemic clone(s)? In case of long-term surveillance, what is the prevalence over time and the geographic spread of epidemic and endemic clones in the population? A number of molecular typing methods can be used to classify bacteria based on genomic diversity into groups of closely-related isolates (presumed to arise from a common ancestor in the same chain of transmission) and divergent, epidemiologically-unrelated isolates (arising from independent sources of infection). Ribotyping, IS-RFLP fingerprinting, macrorestriction analysis of chromosomal DNA and PCR-fingerprinting using arbitrary sequence or repeat element primers are useful methods for outbreak investigations and regional surveillance. Library typing systems based on multilocus sequence-based analysis and strain-specific probe hybridization schemes are in development for the international surveillance of major pathogens like Mycobacterium tuberculosis. Accurate epidemiological interpretation of data obtained with molecular typing systems still requires additional research on the evolution rate of polymorphic loci in bacterial pathogens.

Bacterial Typing Techniques↗
PubMed2026

Genomic characterization of blaIMP-harboring plasmids in Klebsiella spp.

UNLABELLED: The spread of carbapenem-resistant Klebsiella spp. poses a significant public health threat, partly due to the acquisition of the blaIMP genes, which encode IMP-type metallo-&#x3b2;-lactamases. These enzymes confer resistance to a broad spectrum of &#x3b2;-lactam antibiotics, including carbapenems, thereby complicating treatment options. This study aims to provide a comprehensive genomic characterization of blaIMP-harboring plasmids across different species within the genus Klebsiella, based on the genomic characteristics of the plasmid pT117-2 of Klebsiella variicola strain T117 isolated from clinical settings in China, along with all available blaIMP-harboring plasmids of Klebsiella spp. fromthe GenBank database until 26 April 2025. Among the 123 blaIMP-harboring plasmids of Klebsiella spp., nine variants were identified, with blaIMP-4 (carried by 69 plasmids) and blaIMP-1 (carried by 37 plasmids) being the most prevalent. The blaIMP-4 gene was associated with IncN type (~50 kb, conjugative) and untypeable (~300 kb, non-mobilizable) plasmids in China, whereas in Australia, it was linked to IncC (~200 kb) and IncM2 (~80 kb) type conjugative plasmids. Meanwhile, blaIMP-1 was found to be associated with IncN (~50 kb), IncM (~80 kb), and IncFII (80 ~200 kb) type conjugative plasmids mainly in Japan. Notably, our results highlight the prevalence of IncN-type conjugative plasmids, including the plasmid pT117-2 identified in this study, as key vehicles for the dissemination of blaIMP genes. This study provides critical insights into the genetic mechanisms of blaIMP-harboring plasmids persistence and spread in Klebsiella spp., advancing our understanding of their dissemination. IMPORTANCE: Carbapenem-resistant Enterobacterales (CRE) mediated by metallo-&#x3b2;-lactamases (MBLs) pose a major global public health threat that challenges clinical antimicrobial therapy; based on our study, blaIMP-4 in China is predominantly associated with IncN plasmids (forming the "IncN-blaIMP-4-qnrS1" axis), while blaIMP-1 in Japan links to IncN/IncM/IncFII plasmids, with these regional differences highlighting the need for geographically targeted surveillance, and notably, the high-risk ST146 Klebsiella variicola carrying blaIMP-4 on a conjugative IncN plasmid serves as an underrecognized reservoir for resistance genes, extending surveillance beyond common pathogenic Enterobacterales; limitations of this study include restricted sample size and geographic scope, and future research should validate these patterns via multi-center studies, explore plasmid evolution mechanisms, and integrate findings into routine surveillance to optimize antibiotic stewardship and infection control, thereby mitigating the global spread of MBL-mediated CRE.

Plasmids↗
PubMed2003

National surveillance programme on susceptibility patterns of respiratory pathogens in South Africa: moxifloxacin compared with eight other antimicrobial agents.

AIMS: The susceptibility patterns of Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Klebsiella pneumoniae, and Streptococcus pyogenes isolated from specimens submitted to 12 private laboratories in South Africa were determined. METHODS: Minimum inhibitory concentration (MIC) determinations were performed on the isolates in the microbiology laboratory at Tygerberg Hospital according to the recommendations of the National Committee for Clinical Laboratory Standards (NCCLS). RESULTS: According to the NCCLS breakpoints, 24% of 729 S pneumoniae isolates were sensitive, 30% intermediate, and 46% resistant to penicillin. Rates of macrolide resistance were high, with 61% of the pneumococci being resistant to clarithromycin and azithromycin. Co-trimoxazole resistance was also high, with 28% of pneumococcal strains being sensitive, 21% intermediate, and 51% resistant. beta Lactamase was produced by 7% of 736 H influenzae isolates and 91% of 256 M catarrhalis isolates. The quinolones, moxifloxacin and levofloxacin, were universally active against all isolates tested, which included S pneumoniae, H influenzae, M catarrhalis, K pneumoniae, and S pyogenes. CONCLUSIONS: Haemophilus influenzae and S pneumoniae were the most commonly isolated organisms. Resistance to penicillin was one of the highest reported in the world (76%) in S pneumoniae, as was macrolide resistance in pneumonocci, although surprisingly, only 14% of S pyogenes were resistant. The quinolones, moxifloxacin and levofloxacin, were active against all organisms tested, including the penicillin and macrolide resistant strains and moxifloxacin was more active than levofloxacin against pneumococci.

Anti-Bacterial Agents↗
PubMed2005

The relationship between hospital infection surveillance and control activities and antibiotic-resistant pathogen rates.

BACKGROUND: Antibiotic-resistant pathogen rates are rising in Canada and the United States with significant health and economic costs. The examination of the relationship of surveillance and control activities in hospitals with rates of nosocomial methicillin-resistant Staphylococcus aureus (MRSA), Clostridium difficile -associated diarrhea (CDAD), and vancomycin-resistant Enterococcus (VRE) may identify strategies for controlling this growing problem. METHODS: Surveys were sent to infection control programs in hospitals that participated in an earlier survey of infection control practices in Canadian acute care hospitals. RESULTS: One hundred twenty of 145 (82.8%) hospitals responded to the survey. The mean MRSA rate was 2.0 (SD 2.9) per 1000 admissions, the mean CDAD rate was 3.8 (SD 4.3), and the mean VRE rate was 0.4 (SD 1.5). Multiple stepwise regression analysis found that hospitals that reported infection rates by specific risk groups ( r = -0.27, P < .01) and that kept attendance records of infection control teaching activities ( r = -0.23, P < .01) were associated with lower MRSA rates. Multiple stepwise regression analysis found that larger hospitals ( r = 0.25, P < .01) and hospitals at which infection control committees or staff had the direct authority to close a ward or unit to further admissions because of outbreaks ( r = 0.22, P < .05) were associated with higher CDAD rates. Multiple logistic regression analysis found that larger hospitals (OR, 1.6; 95% CI, 1.2-2.0; P = .003) and teaching hospitals (OR, 3.7 95% CI, 1.2-11.8; P = .02) were associated with the presence of VRE. Hospitals were less likely to have VRE when infection control staff frequently contacted physicians and nurses for reports of new infections (OR, 0.5; 95% CI, 0.3-0.7; P = .02) and there were in-service programs for updating nursing and ancillary staff on current infection control practices (OR, 0.2; 95% CI, 0.1-0.7; P = .01). CONCLUSION: Surveillance and control activities were associated with MRSA and CDAD rates and the presence of VRE. Surveillance and control activities might be especially beneficial in large and teaching hospitals.

Canada↗
PubMed1998

National surveillance for antibiotic resistance in zoonotic enteric pathogens.

Treatment of food-producing animals with antimicrobial agents that are important in human therapy may present a public health risk by the transfer of resistant zoonotic pathogens from animals to humans. Resistant bacteria can diminish the effectiveness of antibiotics and demand the use of more expensive or less safe alternatives. In 1996, the Centers for Disease Control (CDC), United States Department of Agriculture (USDA), and Food and Drug Administration (FDA) established the National Antimicrobial Monitoring System to prospectively monitor changes in antimicrobial susceptibilities of zoonotic pathogens from human and animal clinical specimens, healthy farm animals, and carcasses of food-producing animals at slaughter plants. This article describes the development, implementation, and objectives of the monitoring system and presents initial data generated by the system.

Animals↗
PubMed1999

Antimicrobial activity evaluations of gatifloxacin, a new fluoroquinolone: contemporary pathogen results from a global antimicrobial resistance surveillance program (SENTRY, 1997).

OBJECTIVE: To investigate the in vitro potency and spectrum of activity of gatifloxacin and five comparator fluoroquinolones tested against over 23 000 clinical isolates from diverse geographic and clinical sources in the Americas. METHODS: Gram-negative, Gram-positive and fastidious bacterial isolates were tested against gatifloxacin, ciprofloxacin, levofloxacin, ofloxacin, sparfloxacin and trovafloxacin using broth microdilution methods recommended by the National Committee for Clinical Laboratory Standards (NCCLS). RESULTS: Gatifloxacin demonstrated a potency and spectrum very similar to those of other new fluoroquinolones such as levofloxacin, sparfloxacin, and trovafloxacin. Gatifloxacin was particularly active against the Enterobacteriaceae (94.8% susceptible at </=2 mg/L), Acinetobacter spp. (77.2%), Stenotrophomonas maltophilia (75.1%), Streptococcus pneumoniae (99.8%), other Streptococcus spp. (>/=98.9%), and various Staphylococcus spp. (79.2-100.0%). Trovafloxacin was the most similar comparison drug overall. CONCLUSIONS: These results indicate a potential therapeutic role for gatifloxacin that would widen the potency or spectrum of fluoroquinolones, particularly against Gram-positive species, when considering its favorable bioavailability.

Journal Article↗
PubMedDate not supplied

Evolving patterns of resistance to respiratory pathogens in Canada.

Active surveillance of changing resistance patterns is difficult but important for rational therapeutic choices. In Canada, penicillin resistance in Streptococcus pneumoniae has evolved more slowly than in other countries (in Europe and Israel rates exceed 50%). Currently, penicillin resistance is found in roughly 21% of Canadian isolates, and cross-resistance is becoming common. Beta-lactamase production is now found in approximately 28% of Haemophilus influenzae isolates, although more recently, rates over 30% have been found in some areas of Canada. In Moraxella catarrhalis, beta-lactamases are produced by 80% to 90% of bacteria, with resistance to trimethoprim/sulphamethoxazole also found. To date, there have been only a few reports of resistance to the fluoroquinolones. The apparent increase in the rate of development of resistance and cross-resistance will lead to new therapeutic challenges.

Anti-Bacterial Agents↗
PubMed2002

Age-related trends in pathogen frequency and antimicrobial susceptibility of bloodstream isolates in North America: SENTRY Antimicrobial Surveillance Program, 1997-2000.

We report age-related trends in pathogen frequency and antimicrobial susceptibility from 25,745 bloodstream infections (BSI) due to bacterial pathogens reported from medical centres participating in the North American SENTRY Antimicrobial Surveillance Program between January 1997 and September 2000. Staphylococcus aureus, Escherichia coli and coagulase-negative staphylococci (CoNS) were the most common pathogens, together accounting for 55% of all BSI pathogens during this time period. Among nosocomial BSI, CoNS were the most frequently isolated pathogens in infants less than 1 year of age, but S. aureus increased in frequency with increasing age. Among community-onset BSI pathogens, Streptococcus pneumoniae was the most frequently reported pathogen causing BSI in patients aged 1-5, S. aureus among those aged 6-64, and E. coli predominated at the extremes of age (less than 1 year and > or = 65 years of age). Among key organism: antimicrobial agent combinations evaluated, oxacillin resistance in S. aureus increased with increasing age; conversely, oxacillin resistance among CoNS was highest among children 5 years of age or younger. Penicillin resistance among S. pneumoniae BSI was highest in children younger than 5 years, while vancomycin resistance among Enterococcus spp. predominated among nosocomial BSI in patients over 50 years of age. Important age-related differences exist in species distribution and antimicrobial susceptibility of pathogens causing BSI. This information should be helpful for clinicians as they consider empirical antimicrobial therapy for patients with suspected BSI across the age continuum.

Adolescent↗
PubMed1996

Heterogeneity in the haemagglutinin gene and emergence of the highly pathogenic phenotype among recent H5N2 avian influenza viruses from Mexico.

Molecular changes in the haemagglutinin (HA)-coding regions and proteolytic cleavage sites from multiple H5N2 subtype viruses isolated during a recent outbreak of avian influenza (AI) in central Mexico have been characterized. Eighteen isolates, collected during a 15 month period (October 1993 to January 1995) from six central states, were sequenced. None of the 18 predicted HA1 amino acid sequences were identical and changes were not restricted to a specific region of the sequence. Phylogenetic analyses of the HA1 sequences demonstrated two virus lineages, designated Puebla and Jalisco, with sequence variation as high as 10.5 percent for amino acid and 6.2 percent for nucleotide sequences. During the latter months of the surveillance period, highly pathogenic (HP) strains of AI emerged causing lethal disease in commercial poultry flocks. In each of the HP strains isolated, the HA protein was cleaved in chicken embryo fibroblast cells in the absence of trypsin, and two alterations not found in earlier non-HP isolates were detected. In the HA protein, HP strains all had a glutamic acid --> lysine substitution at amino acid position 324 and an insertion of arginine and lysine as new residues 325 and 326. The insertion appears to be due to a duplication of the nucleotide sequence AAAGAA at nucleotide positions 965-970 of the HA1-coding region. Computer-assisted secondary structure analyses place the target for the insertion in a predicted RNA stem-loop structure. A mechanism is suggested by which the polymerase duplicates the sequence.

Amino Acid Sequence↗
PubMed2026

Portable metagenomics for preventive surveillance and outbreak control in livestock and poultry: Pathogen detection, resistome profiling, and antimicrobial stewardship.

Conventional diagnostics for livestock and poultry outbreaks commonly rely on culture or targeted PCR panels, which may be too slow or too narrow to guide early control decisions. Portable metagenomics, particularly real-time nanopore sequencing, offers a route to broad pathogen detection, antimicrobial-resistance gene profiling, and outbreak investigation within an integrated workflow. This implementation-focused review evaluates how near-point-of-care metagenomics may support preventive veterinary medicine through earlier detection, surveillance, cohorting, biosecurity decisions, and antimicrobial stewardship. We synthesize sample-to-answer workflows for enteric and respiratory disease in food-producing animals, including sampling, nucleic-acid extraction, host depletion or target enrichment, library preparation, sequencing, bioinformatics, quality control, and interpretation. Applications in calf diarrhea, bovine respiratory disease, poultry outbreaks, mastitis, and resistome monitoring are considered alongside the central limitation that detection alone does not establish causation. Pathogen and resistance-gene signals must therefore be interpreted with clinical signs, lesions, epidemiology, controls, and confirmatory testing. We also propose a minimum reporting checklist, intended as a practical framework rather than a validated consensus standard. Portable metagenomics is not a replacement for conventional diagnostics, but appropriately validated workflows can reduce uncertainty during time-sensitive outbreaks and support more judicious antimicrobial use.

Animals↗
PubMed2005

[The National Reference Centres and Reference Laboratories. Importance and tasks].

Since 1995, the German Federal Ministry for Health and Social Security funds National Reference Centres (NRC) for the laboratory surveillance of important pathogens and syndromes. Which pathogens or syndromes are selected to be covered by a NRC depends on their epidemiological relevance, the special diagnostic tools, problems with antimicrobial resistance and necessary infection control measures. Currently, there are 15 NRC, which are appointed for a period of 3 years (currently from January 2005 through December 2007). Towards the end of their appointment all NRC are evaluated by a group of specialists. The assessment of their achievements is guided by a catalogue of tasks for the NRC. In addition to the NRC, a total of 50 laboratories are appointed which provide specialist expertise for additional pathogens in order to have a broad range of pathogens for which specialist laboratories are available. Their predominant task is to give advice and support for special diagnostic problems. Both NRC and the specialist laboratories are important parts of the network for infectious disease epidemiology.

Academies and Institutes↗