{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T17:51:40Z","timestamp":1782409900777,"version":"3.54.5"},"reference-count":51,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T00:00:00Z","timestamp":1782345600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    Accurate identification of bacterial pathogens is essential for effective clinical management; however, bacterial diagnosis remains challenging in routine microbiology laboratories, particularly in emergency settings and outbreak situations. Bacterial meningitis is a life-threatening condition associated with high morbidity and mortality, underscoring the need for sensitive and specific diagnostic approaches. Conventional culture-based methods often fail to identify causative agents, especially in samples with low bacterial load or fastidious organisms. This study aimed to evaluate next-generation sequencing (NGS) as a diagnostic tool compared with classical cultivation methods for bacterial detection in urine and cerebrospinal fluid (CSF) samples. A total of 50 urine samples (30 positive, 15 insignificant, and 5 negative by culture) and 14 CSF samples (4 positive and 10 negative) were collected from the microbiology laboratory at Al-Makassed Hospital in Jerusalem, Palestine. Bacterial identification was performed using both conventional methods and NGS targeting the 16S rRNA gene. Classical culture methods identified common uropathogens, including\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    ,\n                    <jats:italic>Klebsiella<\/jats:italic>\n                    spp.,\n                    <jats:italic>Enterococcus<\/jats:italic>\n                    spp.,\n                    <jats:italic>Lactobacillus<\/jats:italic>\n                    spp., Group B\n                    <jats:italic>Streptococcus<\/jats:italic>\n                    ,\n                    <jats:italic>Acinetobacter<\/jats:italic>\n                    spp., and\n                    <jats:italic>Proteus mirabilis<\/jats:italic>\n                    in urine samples, while CSF cultures detected coagulase-negative\n                    <jats:italic>Staphylococcus<\/jats:italic>\n                    ,\n                    <jats:italic>Enterobacter<\/jats:italic>\n                    spp., and methicillin-resistant\n                    <jats:italic>Staphylococcus aureus<\/jats:italic>\n                    (MRSA). In comparison, NGS provided broader bacterial profiling at genus and species levels. In urine samples with significant growth, NGS identified\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    as the most prevalent species and\n                    <jats:italic>Enterococcus<\/jats:italic>\n                    as the most abundant genus. Importantly, NGS detected multiple bacterial taxa in samples classified as culture-negative or insignificant-growth, including\n                    <jats:italic>Escherichia<\/jats:italic>\n                    ,\n                    <jats:italic>Enterococcus<\/jats:italic>\n                    ,\n                    <jats:italic>Pseudomonas<\/jats:italic>\n                    ,\n                    <jats:italic>Staphylococcus<\/jats:italic>\n                    , and\n                    <jats:italic>Klebsiella<\/jats:italic>\n                    . In CSF samples, NGS additionally identified\n                    <jats:italic>Pseudomonas<\/jats:italic>\n                    ,\n                    <jats:italic>Enterobacter<\/jats:italic>\n                    ,\n                    <jats:italic>Escherichia<\/jats:italic>\n                    ,\n                    <jats:italic>Staphylococcus<\/jats:italic>\n                    , and\n                    <jats:italic>Rickettsia<\/jats:italic>\n                    in culture-negative specimens. Overall, NGS demonstrated substantially higher sensitivity than classical culture methods and provided more comprehensive bacterial identification, highlighting its diagnostic value for detecting slow-growing, fastidious, and low-abundance bacteria missed by conventional techniques.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0350939","type":"journal-article","created":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T17:44:52Z","timestamp":1782409492000},"page":"e0350939","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["A comparison between bacterial cultivation and 16S rRNA next generation sequencing approaches for analysis of bacteria in urine and cerebrospinal fluid 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