A survey of extended-spectrum beta-lactamase-producing <i>Enterobacteriaceae</i> in urban wetlands in southwestern Nigeria as a step towards generating prevalence maps of antimicrobial resistance

In many countries, emission of insufficiently treated wastewater into water bodies appears to be an important factor in spreading clinically relevant antimicrobial resistant bacteria. In this study, we looked for the presence of Enterobacteriaceae strains with resistance to 3rd generation cephalosporin antibiotics in four urban wetlands in southwestern Nigeria by isolation, whole genome sequencing and qPCR enumeration of marker genes. Genome analysis of multi-drug resistant and potentially pathogenic Escherichia coli isolates (members of the widely distributed ST10 complex) revealed the presence of the extended spectrum beta-lactamase gene blaCTX-M-15 on self-transmissible IncF plasmids. The gene was also present together with a blaTEM-1B gene on self-transmissible IncH plasmids in multi-drug resistant Enterobacter cloacae isolates. A Citrobacter freundii isolate carried blaTEM-1B on an IncR-type plasmid without discernable conjugation apparatus. All strains were isolated from a wetland for which previous qPCR enumeration of marker genes, in particular the ratio of intI1 to 16S rRNA gene copy numbers, had indicated a strong anthropogenic impact. Consistent with the isolation origin, qPCR analysis in this study showed that the blaCTX-M gene was present at an abundance of 1x10-4 relative to bacterial 16S rRNA gene copy numbers. The results indicate that contamination of these urban aquatic ecosystems with clinically relevant antibiotic resistant bacteria is substantial in some areas. Measures should therefore be put in place to mitigate the propagation of clinically relevant antimicrobial resistance within the Nigerian aquatic ecosystems.在诸多国家，未经充分处理的废水排放至水体，似乎是传播具有临床相关性的抗菌耐药细菌的关键诱因。本研究通过分离培养、全基因组测序（whole genome sequencing）以及定量聚合酶链反应（qPCR）计数标记基因的方法，在尼日利亚西南部的四座城市湿地中，筛查了对第三代头孢菌素（3rd generation cephalosporin）耐药的肠杆菌科（Enterobacteriaceae）菌株的存在情况。对多重耐药且具有潜在致病性的大肠杆菌分离株（属于广泛分布的ST10复合体）进行基因组分析后发现，其可自主转移的IncF质粒上携带超广谱β-内酰胺酶基因blaCTX-M-15。在多重耐药的阴沟肠杆菌分离株中，该基因与blaTEM-1B基因共同存在于可自主转移的IncH质粒上。一株弗氏柠檬酸杆菌分离株的IncR型质粒上携带blaTEM-1B基因，但该质粒未携带可识别的接合装置。所有菌株均分离自某一湿地，此前针对该湿地开展的标记基因qPCR计数分析（尤其是intI1与16S rRNA基因拷贝数的比值）已表明其受到强烈的人为活动影响。与菌株的分离来源一致，本研究的qPCR分析显示，相较于细菌16S rRNA基因拷贝数，blaCTX-M基因的丰度为1×10^-4。研究结果表明，部分区域内这些城市水生生态系统受到的具有临床相关性的抗菌耐药细菌污染程度相当严重。因此，应采取相应措施以减缓具有临床相关性的抗菌耐药性在尼日利亚水生生态系统中的传播。