Pub Date : 2025-05-21eCollection Date: 2025-01-01DOI: 10.1099/acmi.0.000895.v3
Mohammed Labrigui, Hamza Layat, Manal Bouikhif, Fatima Ziad, Zimi Khalil, Zineb Jerroundi, Hafid Zahid, Zohra Ouzzif
Loiasis is a parasitic infection transmitted by a vector, specifically through the bites of Chrysops genus tabanid flies. It is often associated with marked and persistent eosinophilia in affected individuals. We report the case of a 28-year-old Cameroonian male patient. His medical history includes an episode of malaria treated on an outpatient basis. As part of a diving internship in Morocco, the young serviceman underwent a medical fitness examination at the Medical Expertise Center for Aircrew Personnel of the Mohamed V Military Hospital, which included a biological assessment. This revealed a mildly elevated bilirubin level, lactate dehydrogenase activity at the upper limit of normal and eosinophilia at 1500 µl-1, without anaemia or thrombocytopaenia. A blood smear was prepared and stained with May-Grünwald Giemsa, revealing the presence of several small worms, with an appearance consistent with Loa loa microfilariae. This case of L. loa, identified in the haematology laboratory, is one of the rare diagnoses in Morocco. Therefore, biologists need to remain vigilant and carry out a thorough analysis of the blood count and blood smear.
{"title":"Fortuitous discovery of a microfilaria of the genus Loa loa during a routine blood smear at the Hematology Laboratory of the Mohamed V Military Instruction Hospital in Rabat: a case report.","authors":"Mohammed Labrigui, Hamza Layat, Manal Bouikhif, Fatima Ziad, Zimi Khalil, Zineb Jerroundi, Hafid Zahid, Zohra Ouzzif","doi":"10.1099/acmi.0.000895.v3","DOIUrl":"10.1099/acmi.0.000895.v3","url":null,"abstract":"<p><p>Loiasis is a parasitic infection transmitted by a vector, specifically through the bites of Chrysops genus tabanid flies. It is often associated with marked and persistent eosinophilia in affected individuals. We report the case of a 28-year-old Cameroonian male patient. His medical history includes an episode of malaria treated on an outpatient basis. As part of a diving internship in Morocco, the young serviceman underwent a medical fitness examination at the Medical Expertise Center for Aircrew Personnel of the Mohamed V Military Hospital, which included a biological assessment. This revealed a mildly elevated bilirubin level, lactate dehydrogenase activity at the upper limit of normal and eosinophilia at 1500 µl<sup>-1</sup>, without anaemia or thrombocytopaenia. A blood smear was prepared and stained with May-Grünwald Giemsa, revealing the presence of several small worms, with an appearance consistent with <i>Loa loa</i> microfilariae. This case of <i>L. loa</i>, identified in the haematology laboratory, is one of the rare diagnoses in Morocco. Therefore, biologists need to remain vigilant and carry out a thorough analysis of the blood count and blood smear.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12095865/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144129951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-05-21eCollection Date: 2025-01-01DOI: 10.1099/acmi.0.000879.v5
Saxon J Mwambene, Adelard B Mtenga, Augustino A Chengula, Abubakar S Hoza
<p><p><b>Introduction.</b> <i>Salmonella</i> is one of the most prevalent foodborne bacteria, posing a significant global health concern and responsible for ~155,000 deaths and 93.8 million human foodborne illnesses annually. The rampant use of antibiotic agents to combat salmonellosis in poultry has contributed to the emergence of resistance against commonly used antibiotics. <b>Methodology.</b> The cross-sectional study was conducted between January and June 2023 across three districts in the Dar es Salaam region, Tanzania. <i>Salmonella</i> isolates were detected and confirmed by using standard microbiological conventional methods and molecular methods such as PCR and genomic sequencing. PCR was used for detecting the presence of the <i>invA</i> gene, and partial DNA sequencing was performed to identify species and their close relatedness. A Kirby-Bauer disc diffusion method was employed to evaluate <i>Salmonella</i> sensitivity to seven different commonly used antibiotics, namely ampicillin, azithromycin, chloramphenicol, ciprofloxacin, gentamycin, trimethoprim/sulfamethoxazole and tetracycline. <i>Salmonella</i> strain with reference number ATCC 8739 was used as a control. <b>Results.</b> The overall <i>Salmonella</i> isolates from faecal droppings were 6.04% (<i>n</i>=796). Of the PCR-confirmed isolates, 64.3% (<i>n</i>=28) were resistant to more than two classes of antibiotics and hence considered multidrug resistant. The highest resistance was observed with ampicillin (92.9%, <i>n</i>=26), followed by tetracycline (71.43%, <i>n</i>=20), ciprofloxacin (42.9%, <i>n</i>=12), sulphonamide (42.85%, <i>n</i>=12), gentamicin (35.7%, <i>n</i>=10) and azithromycin (28.9%, <i>n</i>=8). All the isolates were susceptible to chloramphenicol (100%, <i>n</i>=28). Twenty-eight isolates were sent for sequencing, out of which 16 sequences (OR021717-OR021739) met the criteria for phylogenetic analysis. All 16 sequences had a per cent identity to EU348369 strains Senftenberg isolated from China, OL581594 <i>Salmonella</i> Newport isolated from China and EU348368 <i>Salmonella</i> Pullorum isolates from China. Other sequences diverged more distantly; these are <i>Salmonella</i> Abony with accession number CP007541 and <i>Salmonella</i> Kentucky with accession number OL581592. The tree also included an outgroup species, <i>Salmonella bongori</i>, which was downloaded from GenBank with accession numbers NC015761 and NC021870 <i>S. bongori</i>. <b>Conclusion.</b> The high level of antibiotic resistance found in this study could be due to the misuse of antibiotics in poultry management, and/or, probably, there were circulating resistant <i>Salmonella</i> strains in the environment. To reverse the trend observed, immediate interventions such as advocating for the prudent use of antibiotics in poultry production systems by strengthening extension services to poultry farmers and the use of a farmer field school model to improve poultry management through improved fa
介绍。沙门氏菌是最普遍的食源性细菌之一,引起了重大的全球健康问题,每年造成约15.5万人死亡和9380万人食源性疾病。在家禽中广泛使用抗生素来防治沙门氏菌病,导致对常用抗生素产生耐药性。方法。这项横断面研究于2023年1月至6月在坦桑尼亚达累斯萨拉姆地区的三个地区进行。采用标准的微生物学常规方法和PCR、基因组测序等分子方法对分离的沙门氏菌进行检测和鉴定。采用PCR检测invA基因的存在,并进行部分DNA测序,以确定物种及其近亲关系。采用Kirby-Bauer圆盘扩散法评价沙门氏菌对氨苄西林、阿奇霉素、氯霉素、环丙沙星、庆大霉素、甲氧苄啶/磺胺甲恶唑和四环素7种常用抗生素的敏感性。以参考编号为ATCC 8739的沙门氏菌为对照。结果。从粪便中分离的沙门氏菌总数为6.04% (n=796)。在pcr确认的分离株中,64.3% (n=28)对两类以上抗生素耐药,因此被认为具有多重耐药。耐药最高的是氨苄西林(92.9%,n=26),其次是四环素(71.43%,n=20)、环丙沙星(42.9%,n=12)、磺胺(42.85%,n=12)、庆大霉素(35.7%,n=10)和阿奇霉素(28.9%,n=8)。所有菌株均对氯霉素敏感(100%,n=28)。对28株分离株进行测序,其中16个序列(OR021717-OR021739)符合系统发育分析标准。所有16个序列均与中国分离的Senftenberg沙门氏菌EU348369株、Newport沙门氏菌OL581594株和Pullorum沙门氏菌EU348368株具有100%的同源性。其他序列分化得更远;这些是Abony沙门氏菌,编号为CP007541,肯塔基沙门氏菌,编号为OL581592。该树还包括一个外群物种,沙门氏菌bongori,它从GenBank下载,登录号为NC015761和NC021870 S. bongori。结论。本研究中发现的高水平抗生素耐药性可能是由于家禽管理中滥用抗生素,和/或可能是环境中存在耐药沙门氏菌菌株。为扭转已观察到的趋势,需要立即采取干预措施,例如通过加强对家禽养殖户的推广服务,倡导在家禽生产系统中谨慎使用抗生素,并使用农民田间学校模式,通过改善农场生物安全来改善家禽管理。
{"title":"Detection and antibiotic resistance of Salmonella isolates from selected poultry farms in Dar es Salaam, Tanzania.","authors":"Saxon J Mwambene, Adelard B Mtenga, Augustino A Chengula, Abubakar S Hoza","doi":"10.1099/acmi.0.000879.v5","DOIUrl":"10.1099/acmi.0.000879.v5","url":null,"abstract":"<p><p><b>Introduction.</b> <i>Salmonella</i> is one of the most prevalent foodborne bacteria, posing a significant global health concern and responsible for ~155,000 deaths and 93.8 million human foodborne illnesses annually. The rampant use of antibiotic agents to combat salmonellosis in poultry has contributed to the emergence of resistance against commonly used antibiotics. <b>Methodology.</b> The cross-sectional study was conducted between January and June 2023 across three districts in the Dar es Salaam region, Tanzania. <i>Salmonella</i> isolates were detected and confirmed by using standard microbiological conventional methods and molecular methods such as PCR and genomic sequencing. PCR was used for detecting the presence of the <i>invA</i> gene, and partial DNA sequencing was performed to identify species and their close relatedness. A Kirby-Bauer disc diffusion method was employed to evaluate <i>Salmonella</i> sensitivity to seven different commonly used antibiotics, namely ampicillin, azithromycin, chloramphenicol, ciprofloxacin, gentamycin, trimethoprim/sulfamethoxazole and tetracycline. <i>Salmonella</i> strain with reference number ATCC 8739 was used as a control. <b>Results.</b> The overall <i>Salmonella</i> isolates from faecal droppings were 6.04% (<i>n</i>=796). Of the PCR-confirmed isolates, 64.3% (<i>n</i>=28) were resistant to more than two classes of antibiotics and hence considered multidrug resistant. The highest resistance was observed with ampicillin (92.9%, <i>n</i>=26), followed by tetracycline (71.43%, <i>n</i>=20), ciprofloxacin (42.9%, <i>n</i>=12), sulphonamide (42.85%, <i>n</i>=12), gentamicin (35.7%, <i>n</i>=10) and azithromycin (28.9%, <i>n</i>=8). All the isolates were susceptible to chloramphenicol (100%, <i>n</i>=28). Twenty-eight isolates were sent for sequencing, out of which 16 sequences (OR021717-OR021739) met the criteria for phylogenetic analysis. All 16 sequences had a per cent identity to EU348369 strains Senftenberg isolated from China, OL581594 <i>Salmonella</i> Newport isolated from China and EU348368 <i>Salmonella</i> Pullorum isolates from China. Other sequences diverged more distantly; these are <i>Salmonella</i> Abony with accession number CP007541 and <i>Salmonella</i> Kentucky with accession number OL581592. The tree also included an outgroup species, <i>Salmonella bongori</i>, which was downloaded from GenBank with accession numbers NC015761 and NC021870 <i>S. bongori</i>. <b>Conclusion.</b> The high level of antibiotic resistance found in this study could be due to the misuse of antibiotics in poultry management, and/or, probably, there were circulating resistant <i>Salmonella</i> strains in the environment. To reverse the trend observed, immediate interventions such as advocating for the prudent use of antibiotics in poultry production systems by strengthening extension services to poultry farmers and the use of a farmer field school model to improve poultry management through improved fa","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12095867/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144129947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-05-21eCollection Date: 2025-01-01DOI: 10.1099/acmi.0.000919.v3
Nabil Mohamed Zniber, Hamid Laatiris, Hamza Siyar, Abdelouahab Erraji, Ismail Labrouzi, Mohamed Jnah, Mehdi Talbi, Maryem Iken, Badreddine Lmimouni, Hafida Naoui
Introduction. Malaria remains a significant global health concern, particularly in travellers returning from endemic regions. Haematological abnormalities are often associated with malaria and can serve as diagnostic indicators, especially when clinical symptoms are nonspecific. Objective. This study aims to identify the most relevant haematological parameters for diagnosing malaria in travellers returning from endemic areas, who sought care at the Mohamed V Military Instruction Hospital in Rabat. Methods. We conducted a retrospective comparative study involving 829 patients who returned from malaria-endemic regions between January 2017 and December 2023. Data collected included demographic information, parasitological test results and comprehensive haematological profiles. Statistical analysis was performed to determine the sensitivity and specificity of various haematological parameters in diagnosing malaria. Results. Thrombocytopenia, lymphocytopenia and anaemia were the most significant haematological abnormalities associated with malaria. Thrombocytopenia, defined as a platelet count below 150×10³ µl-1, demonstrated a sensitivity of 75.91% and a specificity of 84.11%. Lymphocytopenia, with a threshold of less than 1.5×10³ µl-1, showed a sensitivity of 69.47% and a specificity of 78.39%. Anaemia, defined by haemoglobin levels below 13 g dl-1 in men and 12 g dl-1 in women, also significantly correlated with malaria diagnosis. Discussion. This study highlights the significance of haematological abnormalities as key diagnostic markers for imported malaria cases. By analysing retrospective data, we observed that these abnormalities, especially thrombocytopenia and anaemia, are common amongst returning travellers with confirmed malaria. These findings suggest that clinicians can use such markers as a valuable tool for early malaria diagnosis, potentially improving patient outcomes. Additionally, the study reinforces the need for heightened awareness amongst healthcare providers in non-endemic regions regarding the presentation of malaria in travellers. Conclusion. Haematological parameters such as thrombocytopenia, lymphocytopenia and anaemia are valuable diagnostic tools for malaria in returning travellers. These findings suggest that these parameters should be integrated into diagnostic protocols to improve the accuracy and timeliness of malaria diagnosis, particularly in clinical settings with limited access to advanced diagnostic tools.
介绍。疟疾仍然是一个重大的全球健康问题,特别是在从流行地区返回的旅行者中。血液学异常通常与疟疾有关,可作为诊断指标,特别是在临床症状无特异性的情况下。目标。本研究旨在确定从流行地区返回并在拉巴特穆罕默德五世军事指导医院寻求治疗的旅行者中诊断疟疾的最相关血液学参数。方法。我们对2017年1月至2023年12月期间从疟疾流行地区返回的829例患者进行了回顾性比较研究。收集的数据包括人口统计信息、寄生虫学测试结果和综合血液学概况。统计分析各种血液学参数诊断疟疾的敏感性和特异性。结果。血小板减少症、淋巴细胞减少症和贫血是与疟疾相关的最显著的血液学异常。血小板减少症,定义为血小板计数低于150×10³µl-1,灵敏度为75.91%,特异性为84.11%。淋巴细胞减少症的阈值小于1.5×10³µl-1,敏感性为69.47%,特异性为78.39%。贫血,即男性血红蛋白水平低于13 g dl-1,女性血红蛋白水平低于12 g dl-1,也与疟疾诊断显著相关。讨论。本研究强调了血液学异常作为输入性疟疾病例关键诊断指标的重要性。通过分析回顾性数据,我们观察到这些异常,特别是血小板减少症和贫血,在确认患有疟疾的返回旅行者中很常见。这些发现表明,临床医生可以将这些标记物作为早期疟疾诊断的一种有价值的工具,从而有可能改善患者的预后。此外,该研究还强调,有必要提高非流行地区医疗保健提供者对旅行者中出现疟疾的认识。结论。血液学参数,如血小板减少症、淋巴细胞减少症和贫血症,是回国旅行者疟疾的宝贵诊断工具。这些发现表明,应将这些参数纳入诊断方案,以提高疟疾诊断的准确性和及时性,特别是在无法获得先进诊断工具的临床环境中。
{"title":"Haematological abnormalities as diagnostic indicators of malaria in returning travellers: a retrospective study at Mohamed V Military Instruction Hospital.","authors":"Nabil Mohamed Zniber, Hamid Laatiris, Hamza Siyar, Abdelouahab Erraji, Ismail Labrouzi, Mohamed Jnah, Mehdi Talbi, Maryem Iken, Badreddine Lmimouni, Hafida Naoui","doi":"10.1099/acmi.0.000919.v3","DOIUrl":"10.1099/acmi.0.000919.v3","url":null,"abstract":"<p><p><b>Introduction.</b> Malaria remains a significant global health concern, particularly in travellers returning from endemic regions. Haematological abnormalities are often associated with malaria and can serve as diagnostic indicators, especially when clinical symptoms are nonspecific. <b>Objective.</b> This study aims to identify the most relevant haematological parameters for diagnosing malaria in travellers returning from endemic areas, who sought care at the Mohamed V Military Instruction Hospital in Rabat. <b>Methods.</b> We conducted a retrospective comparative study involving 829 patients who returned from malaria-endemic regions between January 2017 and December 2023. Data collected included demographic information, parasitological test results and comprehensive haematological profiles. Statistical analysis was performed to determine the sensitivity and specificity of various haematological parameters in diagnosing malaria. <b>Results.</b> Thrombocytopenia, lymphocytopenia and anaemia were the most significant haematological abnormalities associated with malaria. Thrombocytopenia, defined as a platelet count below 150×10³ µl<sup>-1</sup>, demonstrated a sensitivity of 75.91% and a specificity of 84.11%. Lymphocytopenia, with a threshold of less than 1.5×10³ µl<sup>-1</sup>, showed a sensitivity of 69.47% and a specificity of 78.39%. Anaemia, defined by haemoglobin levels below 13 g dl<sup>-1</sup> in men and 12 g dl<sup>-1</sup> in women, also significantly correlated with malaria diagnosis. <b>Discussion.</b> This study highlights the significance of haematological abnormalities as key diagnostic markers for imported malaria cases. By analysing retrospective data, we observed that these abnormalities, especially thrombocytopenia and anaemia, are common amongst returning travellers with confirmed malaria. These findings suggest that clinicians can use such markers as a valuable tool for early malaria diagnosis, potentially improving patient outcomes. Additionally, the study reinforces the need for heightened awareness amongst healthcare providers in non-endemic regions regarding the presentation of malaria in travellers. <b>Conclusion.</b> Haematological parameters such as thrombocytopenia, lymphocytopenia and anaemia are valuable diagnostic tools for malaria in returning travellers. These findings suggest that these parameters should be integrated into diagnostic protocols to improve the accuracy and timeliness of malaria diagnosis, particularly in clinical settings with limited access to advanced diagnostic tools.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12095866/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144129952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-05-16eCollection Date: 2025-01-01DOI: 10.1099/acmi.0.000933.v3
Zakaria Malihy, Ikram El Abdallaoui, Tilila Abassor, Salah Sghir, Yassine Ben Lahlou, Rachid Abilkassem, Elmostafa Benaissa, Mariama Chadli
Serratia marcescens (S. marcescens) is a Gram-negative rod-shaped bacterium belonging to the Enterobacteriaceae family, commonly found in various environments. This opportunistic pathogen can cause urinary tract infections, respiratory infections and septicaemia, but endocarditis is particularly rare and concerning due to its rapid and devastating progression. We report the first documented case worldwide of infective endocarditis (IE) caused by S. marcescens producing NDM-type carbapenemase, and the second reported case of S. marcescens endocarditis in a preterm infant. The patient was a preterm male infant born at 34 weeks of gestation, from a triplet pregnancy, admitted to the neonatal intensive care unit on day 2 of life for respiratory distress. The mother, aged 39, had undiagnosed gestational diabetes. Premature rupture of membranes had occurred 10 days before delivery, necessitating prophylactic treatment with amoxicillin. On day 4 of life, the newborn developed a fever with elevated C-reactive protein (CRP) levels and leucocytosis, leading to antibiotic therapy with colistin, imipenem and amikacin. Blood cultures revealed the presence of carbapenemase-producing S. marcescens sensitive to fluoroquinolones. A cardiac ultrasound showed a vegetation on the mitral valve, confirming the diagnosis of IE. Despite intensive treatment, the newborn died on day 16 of life due to septic shock. This rare case of endocarditis caused by S. marcescens highlights the severity of this infection in preterm infants. Treatment relies on appropriate antibiotic therapy. Prevention requires strict hygiene measures. Further research is needed to establish optimal therapeutic recommendations.
{"title":"First case of infective endocarditis due to NDM-type carbapenemase-producing Serratia marcescens in a preterm infant: a case report.","authors":"Zakaria Malihy, Ikram El Abdallaoui, Tilila Abassor, Salah Sghir, Yassine Ben Lahlou, Rachid Abilkassem, Elmostafa Benaissa, Mariama Chadli","doi":"10.1099/acmi.0.000933.v3","DOIUrl":"10.1099/acmi.0.000933.v3","url":null,"abstract":"<p><p><i>Serratia marcescens (S. marcescens)</i> is a Gram-negative rod-shaped bacterium belonging to the <i>Enterobacteriaceae</i> family, commonly found in various environments. This opportunistic pathogen can cause urinary tract infections, respiratory infections and septicaemia, but endocarditis is particularly rare and concerning due to its rapid and devastating progression. We report the first documented case worldwide of infective endocarditis (IE) caused by <i>S. marcescens</i> producing NDM-type carbapenemase, and the second reported case of <i>S. marcescens</i> endocarditis in a preterm infant. The patient was a preterm male infant born at 34 weeks of gestation, from a triplet pregnancy, admitted to the neonatal intensive care unit on day 2 of life for respiratory distress. The mother, aged 39, had undiagnosed gestational diabetes. Premature rupture of membranes had occurred 10 days before delivery, necessitating prophylactic treatment with amoxicillin. On day 4 of life, the newborn developed a fever with elevated C-reactive protein (CRP) levels and leucocytosis, leading to antibiotic therapy with colistin, imipenem and amikacin. Blood cultures revealed the presence of carbapenemase-producing <i>S. marcescens</i> sensitive to fluoroquinolones. A cardiac ultrasound showed a vegetation on the mitral valve, confirming the diagnosis of IE. Despite intensive treatment, the newborn died on day 16 of life due to septic shock. This rare case of endocarditis caused by <i>S. marcescens</i> highlights the severity of this infection in preterm infants. Treatment relies on appropriate antibiotic therapy. Prevention requires strict hygiene measures. Further research is needed to establish optimal therapeutic recommendations.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12084542/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144096141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-05-16eCollection Date: 2025-01-01DOI: 10.1099/acmi.0.000990.v3
Rachelle Fernández-Vargas, Sara Jiménez-Alpízar, Valeria Leandro-Arce, Bradd Mendoza-Guido, Keilor Rojas-Jimenez
Here, we report the draft genome sequences of four Bradyrhizobium spp. isolates obtained from root nodules of the native legumes Pentaclethra macroloba, Chamaecrista nictitans, Erythrina fusca and Zygia engelsingii in tropical forests of Costa Rica. Genomes ranged from 8.6 to 9.8 Mb with GC contents between 62.8% and 63.8%. Phylogenomic analysis, along with average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) comparisons, confirmed that these isolates represent potential new species. ANI values ranged from 88.3% to 90.3%, and dDDH values from 28.8% to 41.8%, compared with their closest Bradyrhizobium species. Functional annotation revealed some genes related to nitrogen fixation (nifA, nifB, nifH) and nodulation capacity (nodB, nodC, nodJ). These results provide insights into the diversity and symbiotic capabilities of Bradyrhizobium in tropical ecosystems.
{"title":"Draft genome sequences of four potential new species of the genus Bradyrhizobium isolated from root nodules of native legumes in Costa Rican forests.","authors":"Rachelle Fernández-Vargas, Sara Jiménez-Alpízar, Valeria Leandro-Arce, Bradd Mendoza-Guido, Keilor Rojas-Jimenez","doi":"10.1099/acmi.0.000990.v3","DOIUrl":"10.1099/acmi.0.000990.v3","url":null,"abstract":"<p><p>Here, we report the draft genome sequences of four <i>Bradyrhizobium</i> spp. isolates obtained from root nodules of the native legumes <i>Pentaclethra macroloba</i>, <i>Chamaecrista nictitans</i>, <i>Erythrina fusca</i> and <i>Zygia engelsingii</i> in tropical forests of Costa Rica. Genomes ranged from 8.6 to 9.8 Mb with GC contents between 62.8% and 63.8%. Phylogenomic analysis, along with average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) comparisons, confirmed that these isolates represent potential new species. ANI values ranged from 88.3% to 90.3%, and dDDH values from 28.8% to 41.8%, compared with their closest <i>Bradyrhizobium</i> species. Functional annotation revealed some genes related to nitrogen fixation (<i>nifA</i>, <i>nifB</i>, <i>nifH</i>) and nodulation capacity (<i>nodB</i>, <i>nodC</i>, <i>nodJ</i>). These results provide insights into the diversity and symbiotic capabilities of <i>Bradyrhizobium</i> in tropical ecosystems.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12084545/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144096137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-05-14eCollection Date: 2025-01-01DOI: 10.1099/acmi.0.000857.v4
Pradeep Kumar N, Ajithlal P M, Prasanta Saini, Aiswarya R S, Abidha Suresh, Philip Samuel, Balasubramaniam R, Jessu Mathew, Sonia T, Amju K P, Raju K H K, Veerapathiran A, Selvam A, Balaji T, Ashwani Kumar
An outbreak of Zika fever occurred in Thiruvananthapuram City, Kerala, India, during 2021. At the request of the Kerala state health administration, we investigated the same, towards proposing requisite containment strategies for the disease outbreak. Epidemiological investigations indicated a clustering pattern of Zika fever cases with the presumed index case from a multi-speciality hospital in the city. Preliminary reports on the same had been already reported elsewhere during 2021. Further, entomological surveys carried out evinced the predominant mosquito species in the city, viz. Aedes albopictus (65.55%), Aedes aegypti (22.0%) and Aedes vittatus (12.0%) were naturally infected with Zika virus (ZIKV), the minimum infection rates being 17.9, 7.8 and 3.6, respectively. Also, trans-ovarian transmission was recorded in both Ae. aegypti and Ae. albopictus. This is the first report on the detection of ZIKV from Ae. albopictus in India. Analysis of phylogenetically informative genes of the ZIKV genome indicated the emergence of a distinct lineage of the Asian strain of virus, with five unique non-synonymous mutations, viz. 'A22T' and 'I160M' (pre-membrane) and 'D348N', 'T470A' and 'V473L' (envelope), that were involved in the outbreak. The altered gene expression pattern and evolutionary implications of these unique mutations remain to be investigated. Genetic analysis of the virus isolates from this and other investigations carried out on sporadic outbreaks of ZIKV in the country subsequently indicated that ZIKV is re-emerging as a distinct genetic lineage in India. These findings and other recent reports on ZIKV outbreaks warrant an urgent need for a systematic countrywide surveillance strategy, towards the prevention/preparedness/containment of a massive outbreak of this emerging neurovirulent arboviral disease.
{"title":"Is the Zika virus re-emerging as a distinct genetic lineage in India?","authors":"Pradeep Kumar N, Ajithlal P M, Prasanta Saini, Aiswarya R S, Abidha Suresh, Philip Samuel, Balasubramaniam R, Jessu Mathew, Sonia T, Amju K P, Raju K H K, Veerapathiran A, Selvam A, Balaji T, Ashwani Kumar","doi":"10.1099/acmi.0.000857.v4","DOIUrl":"https://doi.org/10.1099/acmi.0.000857.v4","url":null,"abstract":"<p><p>An outbreak of Zika fever occurred in Thiruvananthapuram City, Kerala, India, during 2021. At the request of the Kerala state health administration, we investigated the same, towards proposing requisite containment strategies for the disease outbreak. Epidemiological investigations indicated a clustering pattern of Zika fever cases with the presumed index case from a multi-speciality hospital in the city. Preliminary reports on the same had been already reported elsewhere during 2021. Further, entomological surveys carried out evinced the predominant mosquito species in the city, viz. <i>Aedes albopictus</i> (65.55%), <i>Aedes aegypti</i> (22.0%) and <i>Aedes vittatus</i> (12.0%) were naturally infected with Zika virus (ZIKV), the minimum infection rates being 17.9, 7.8 and 3.6, respectively. Also, trans-ovarian transmission was recorded in both <i>Ae. aegypti</i> and <i>Ae. albopictus</i>. This is the first report on the detection of ZIKV from <i>Ae. albopictus</i> in India. Analysis of phylogenetically informative genes of the ZIKV genome indicated the emergence of a distinct lineage of the Asian strain of virus, with five unique non-synonymous mutations, viz. 'A22T' and 'I160M' (pre-membrane) and 'D348N', 'T470A' and 'V473L' (envelope), that were involved in the outbreak. The altered gene expression pattern and evolutionary implications of these unique mutations remain to be investigated. Genetic analysis of the virus isolates from this and other investigations carried out on sporadic outbreaks of ZIKV in the country subsequently indicated that ZIKV is re-emerging as a distinct genetic lineage in India. These findings and other recent reports on ZIKV outbreaks warrant an urgent need for a systematic countrywide surveillance strategy, towards the prevention/preparedness/containment of a massive outbreak of this emerging neurovirulent arboviral disease.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12078788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144083133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-05-12eCollection Date: 2025-01-01DOI: 10.1099/acmi.0.000964.v3
Isabel Rancu, Benjamin Sobkowiak, Joshua L Warren, Nelly Ciobanu, Alexandru Codreanu, Valeriu Crudu, Caroline Colijn, Ted Cohen, Melanie H Chitwood
Over the past three decades, molecular epidemiological studies have provided new opportunities to investigate the transmission dynamics of Mycobacterium tuberculosis. In most studies, a sizable fraction of individuals with notified tuberculosis cannot be included, either because they do not have culture-positive disease (and thus do not have specimens available for molecular typing) or because resources for conducting sequencing are limited. A recent study introduced a regression-based approach for inferring the membership of unsequenced tuberculosis cases in transmission clusters based on host demographic and epidemiological data. This method was able to identify the most likely cluster to which an unsequenced strain belonged with an accuracy of 35%, although this was in a low-burden setting where a large fraction of cases occurred among foreign-born migrants. Here, we apply a similar model to M. tuberculosis whole-genome sequencing data from the Republic of Moldova, a setting of relatively high local transmission. Using a maximum cluster span of ~40 single nucleotide polymorphisms (SNPs) and a cluster size cutoff of n≥10, we could best predict the specific cluster to which each clustered case was most likely to be a member with an accuracy of 17.2 %. In sensitivity analyses, we found that a more restrictive (~20 SNPs threshold) or permissive (~80 SNPs) threshold did not improve performance. We found that increasing the minimum cluster size improved prediction accuracy. These findings highlight the challenges of transmission inference in high-burden settings like Moldova.
{"title":"Classification of unsequenced Mycobacterium tuberculosis strains in a high-burden setting using a pairwise logistic regression approach.","authors":"Isabel Rancu, Benjamin Sobkowiak, Joshua L Warren, Nelly Ciobanu, Alexandru Codreanu, Valeriu Crudu, Caroline Colijn, Ted Cohen, Melanie H Chitwood","doi":"10.1099/acmi.0.000964.v3","DOIUrl":"10.1099/acmi.0.000964.v3","url":null,"abstract":"<p><p>Over the past three decades, molecular epidemiological studies have provided new opportunities to investigate the transmission dynamics of <i>Mycobacterium tuberculosis</i>. In most studies, a sizable fraction of individuals with notified tuberculosis cannot be included, either because they do not have culture-positive disease (and thus do not have specimens available for molecular typing) or because resources for conducting sequencing are limited. A recent study introduced a regression-based approach for inferring the membership of unsequenced tuberculosis cases in transmission clusters based on host demographic and epidemiological data. This method was able to identify the most likely cluster to which an unsequenced strain belonged with an accuracy of 35%, although this was in a low-burden setting where a large fraction of cases occurred among foreign-born migrants. Here, we apply a similar model to <i>M. tuberculosis</i> whole-genome sequencing data from the Republic of Moldova, a setting of relatively high local transmission. Using a maximum cluster span of ~40 single nucleotide polymorphisms (SNPs) and a cluster size cutoff of <i>n</i>≥10, we could best predict the specific cluster to which each clustered case was most likely to be a member with an accuracy of 17.2 %. In sensitivity analyses, we found that a more restrictive (~20 SNPs threshold) or permissive (~80 SNPs) threshold did not improve performance. We found that increasing the minimum cluster size improved prediction accuracy. These findings highlight the challenges of transmission inference in high-burden settings like Moldova.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12163731/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144304265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-05-08eCollection Date: 2025-01-01DOI: 10.1099/acmi.0.001048
Melissa M Lacey, Michael J Dillon, Sean Goodman, Victoria Easton, Alison I Graham
[This corrects the article DOI: 10.1099/acmi.0.000995.v3.].
[这更正了文章DOI: 10.1099/acmi.0.000995.v3.]。
{"title":"Erratum: Towards an inclusive conference experience: evaluation of the Education and Outreach Symposium at the Microbiology Society Annual Conference 2024.","authors":"Melissa M Lacey, Michael J Dillon, Sean Goodman, Victoria Easton, Alison I Graham","doi":"10.1099/acmi.0.001048","DOIUrl":"https://doi.org/10.1099/acmi.0.001048","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1099/acmi.0.000995.v3.].</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":"001048"},"PeriodicalIF":0.0,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12281734/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144692972","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-05-08eCollection Date: 2025-01-01DOI: 10.1099/acmi.0.000817.v3
Nisha George, Daniel Pan, Shirley Sze, Caroline Williams, Zein El-Dean, Victor Zlocha, Elizabeth Webb, Manish Pareek
A 50-year-old Romanian gentleman presented with fever, myalgia and 30 kg weight loss. He was treated for syphilis after acquiring it 16 years ago. On examination, there was a pansystolic murmur in the axilla, and the patient had an ataxic gait. Blood tests showed raised inflammatory markers. However, standard investigations for infective endocarditis, including multiple blood cultures, serological titres for fastidious organisms and antibody tests were negative. A computed tomography (CT) of the chest, abdomen and pelvis demonstrated hepatosplenomegaly with multiple splenic infarcts. A magnetic resonance imaging (MRI) of the head with contrast showed multiple punctate enhancement in the bilateral hemispheres with leptomeningeal enhancement. Transthoracic echocardiogram demonstrated a large vegetation leading to severe mitral regurgitation. Serum treponemal antibodies were positive; Treponema pallidum particle agglutination (TPPA) was positive at 1 : 1280, and rapid plasma reagin (RPR) 1 : 4 treponemal IgM was negative; lumbar puncture syphilis serology was negative. The patient was treated with an extensive period of intravenous antibiotics, in addition to a prosthetic metallic valve replacement, where unusual ragged calcified valvular tissue was observed. Tertiary syphilis is a difficult diagnosis to confirm, since it can often be indolent and occur in areas of the body where it may go unnoticed. In our case, a diagnosis of probable syphilitic endocarditis was made from a combination of the history, an initial increase in the size of the lesion following antibiotic therapy and observation of likely gumma on the mitral valve during surgery. In such cases, surgery in addition to optimal antimicrobial therapy is necessary for effective treatment. This case adds to the current literature that treatment with penicillin is likely inadequate to prevent late complications.
{"title":"Gummatous mitral valve endocarditis from tertiary syphilis.","authors":"Nisha George, Daniel Pan, Shirley Sze, Caroline Williams, Zein El-Dean, Victor Zlocha, Elizabeth Webb, Manish Pareek","doi":"10.1099/acmi.0.000817.v3","DOIUrl":"10.1099/acmi.0.000817.v3","url":null,"abstract":"<p><p>A 50-year-old Romanian gentleman presented with fever, myalgia and 30 kg weight loss. He was treated for syphilis after acquiring it 16 years ago. On examination, there was a pansystolic murmur in the axilla, and the patient had an ataxic gait. Blood tests showed raised inflammatory markers. However, standard investigations for infective endocarditis, including multiple blood cultures, serological titres for fastidious organisms and antibody tests were negative. A computed tomography (CT) of the chest, abdomen and pelvis demonstrated hepatosplenomegaly with multiple splenic infarcts. A magnetic resonance imaging (MRI) of the head with contrast showed multiple punctate enhancement in the bilateral hemispheres with leptomeningeal enhancement. Transthoracic echocardiogram demonstrated a large vegetation leading to severe mitral regurgitation. Serum treponemal antibodies were positive; <i>Treponema pallidum</i> particle agglutination (TPPA) was positive at 1 : 1280, and rapid plasma reagin (RPR) 1 : 4 treponemal IgM was negative; lumbar puncture syphilis serology was negative. The patient was treated with an extensive period of intravenous antibiotics, in addition to a prosthetic metallic valve replacement, where unusual ragged calcified valvular tissue was observed. Tertiary syphilis is a difficult diagnosis to confirm, since it can often be indolent and occur in areas of the body where it may go unnoticed. In our case, a diagnosis of probable syphilitic endocarditis was made from a combination of the history, an initial increase in the size of the lesion following antibiotic therapy and observation of likely gumma on the mitral valve during surgery. In such cases, surgery in addition to optimal antimicrobial therapy is necessary for effective treatment. This case adds to the current literature that treatment with penicillin is likely inadequate to prevent late complications.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12281932/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144692973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-05-07eCollection Date: 2025-01-01DOI: 10.1099/acmi.0.000844.v3
Hajar Dahou, Fataou Saley Younoussa, Imane Aragon, Salma El Aouadi, Yahya El Harras, Elmostafa Benaissa, Yassine Ben Lahlou, Abdelaali Bahadi, Jamal El Fenni, Adil Maleb, Mariama Chadli, Mostafa Elouennass
Tuberculosis (TB) remains one of the world's leading causes of morbidity and mortality. It occurs in both pulmonary and extra-pulmonary forms. Primary iliac bone TB remains a rare clinical entity, even in endemic areas. The diagnosis of the disease can be challenging due to its similarity to other bone diseases. We report a rare case of primary iliac bone TB in a 63-year-old patient who was on peritoneal dialysis and had a medical history of hypertension and type II diabetes, which was complicated by diabetic retinopathy and diabetic kidney disease. Magnetic resonance imaging revealed osteomyelitis in the iliac bone, while real-time polymerase chain reaction using the GeneXpert® system on a gluteal collection sample confirmed the diagnosis of TB. The integration of advanced molecular tools, such as GeneXpert®, represents significant progress, enabling rapid and accurate diagnosis of TB and facilitating early initiation of treatment.
{"title":"Primary iliac bone tuberculosis: a case report.","authors":"Hajar Dahou, Fataou Saley Younoussa, Imane Aragon, Salma El Aouadi, Yahya El Harras, Elmostafa Benaissa, Yassine Ben Lahlou, Abdelaali Bahadi, Jamal El Fenni, Adil Maleb, Mariama Chadli, Mostafa Elouennass","doi":"10.1099/acmi.0.000844.v3","DOIUrl":"10.1099/acmi.0.000844.v3","url":null,"abstract":"<p><p>Tuberculosis (TB) remains one of the world's leading causes of morbidity and mortality. It occurs in both pulmonary and extra-pulmonary forms. Primary iliac bone TB remains a rare clinical entity, even in endemic areas. The diagnosis of the disease can be challenging due to its similarity to other bone diseases. We report a rare case of primary iliac bone TB in a 63-year-old patient who was on peritoneal dialysis and had a medical history of hypertension and type II diabetes, which was complicated by diabetic retinopathy and diabetic kidney disease. Magnetic resonance imaging revealed osteomyelitis in the iliac bone, while real-time polymerase chain reaction using the GeneXpert<sup>®</sup> system on a gluteal collection sample confirmed the diagnosis of TB. The integration of advanced molecular tools, such as GeneXpert<sup>®</sup>, represents significant progress, enabling rapid and accurate diagnosis of TB and facilitating early initiation of treatment.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12281756/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144692974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}